[med-svn] [gmap] 01/08: Imported Upstream version 2016-04-04
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri May 13 17:05:50 UTC 2016
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit a34949ea8d6a70864bdcfb0cd7a787396c6e892d
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Sat Apr 23 10:34:37 2016 +0200
Imported Upstream version 2016-04-04
---
ChangeLog | 929 +-
Makefile.am | 3 +-
Makefile.in | 15 +-
TODO | 3 +
VERSION | 2 +-
acinclude.m4 | 3 +-
config/ax_compiler_vendor.m4 | 87 +
config/ax_ext.m4 | 508 +-
config/builtin-popcount.m4 | 58 -
configure | 6005 +++----
configure.ac | 450 +-
mpi/Makefile.am | 111 -
mpi/Makefile.in | 2042 ---
src/ChangeLog | 0
src/Makefile.am | 362 +-
src/Makefile.in | 37412 ++++++++++++++++++++++++++++++++++++-----
src/access.c | 472 +-
src/access.h | 23 +-
src/atoi.c | 43 +-
src/atoi.h | 12 +-
src/atoiindex.c | 1039 +-
src/bitpack64-access.c | 1368 +-
src/bitpack64-access.h | 15 +-
src/bitpack64-incr.c | 10115 +++++++++++
src/bitpack64-incr.h | 29 +
src/bitpack64-read.c | 119 +-
src/bitpack64-read.h | 12 +-
src/bitpack64-readtwo.c | 90 +-
src/bitpack64-readtwo.h | 4 +-
src/bitpack64-write.c | 401 +-
src/bitpack64-write.h | 17 +-
src/block.c | 28 +-
src/block.h | 8 +-
src/bytecoding.c | 179 +-
src/bytecoding.h | 10 +-
src/chimera.c | 4 +-
src/chimera.h | 2 +-
src/chrom.c | 24 +-
src/chrom.h | 7 +-
src/cmet.c | 43 +-
src/cmet.h | 12 +-
src/cmetindex.c | 1088 +-
src/compile | 165 +
src/compress-write.c | 73 +-
src/compress.c | 29 +-
src/config.h.in | 44 +-
src/cpuid.c | 107 +
src/cpuid.h | 10 +
src/datadir.c | 10 +-
src/dynprog.c | 259 +-
src/dynprog.h | 61 +-
src/dynprog_cdna.c | 66 +-
src/dynprog_cdna.h | 4 +-
src/dynprog_end.c | 421 +-
src/dynprog_end.h | 18 +-
src/dynprog_genome.c | 71 +-
src/dynprog_simd.c | 8216 +++++++--
src/dynprog_simd.h | 31 +-
src/dynprog_single.c | 75 +-
src/dynprog_single.h | 4 +-
src/genome-write.c | 26 +-
src/genome-write.h | 4 +-
src/genome.c | 41 +-
src/genome.h | 4 +-
src/genome128_hr.c | 215 +-
src/genome128_hr.h | 28 +-
src/genome_sites.c | 97 +-
src/genome_sites.h | 12 +-
src/get-genome.c | 51 +-
src/gmap.c | 377 +-
src/gmap_select.c | 195 +
src/gmapindex.c | 374 +-
src/gmapl_select.c | 195 +
src/gregion.c | 13 +-
src/gregion.h | 5 +-
src/gsnap.c | 344 +-
src/gsnap_select.c | 195 +
src/gsnapl_select.c | 195 +
src/iit-read-univ.c | 179 +-
src/iit-read-univ.h | 4 +-
src/iit-read.c | 961 +-
src/iit-read.h | 19 +-
src/iit-write.c | 228 +-
src/iit_dump.c | 6 +-
src/iit_get.c | 39 +-
src/iit_store.c | 5 +-
src/inbuffer.c | 6 +-
src/indel.c | 60 +-
src/indel.h | 12 +-
src/indexdb-write.c | 1752 +-
src/indexdb-write.h | 48 +-
src/indexdb.c | 757 +-
src/indexdb.h | 30 +-
src/indexdb_hr.c | 91 +-
src/indexdb_hr.h | 28 +-
src/indexdbdef.h | 14 +-
src/junction.c | 4 +-
src/mapq.c | 15 +-
src/mapq.h | 6 +-
src/oligo.c | 587 +-
src/oligo.h | 16 +-
src/oligoindex_hr.c | 35238 +++++++++++++++++++++++++++++++-------
src/oligoindex_hr.h | 50 +-
src/outbuffer.c | 6 +-
src/output.c | 124 +-
src/pair.c | 405 +-
src/pair.h | 30 +-
src/pairpool.c | 66 +-
src/pairpool.h | 8 +-
src/parserange.c | 21 +-
src/pbinom.c | 6 +-
src/popcount.c | 8 +-
src/popcount.h | 8 +-
src/result.c | 54 +-
src/result.h | 13 +-
src/resulthr.c | 73 +-
src/resulthr.h | 18 +-
src/sam_sort.c | 60 +-
src/samprint.c | 545 +-
src/samprint.h | 8 +-
src/samread.c | 2 +-
src/sarray-read.c | 1616 +-
src/sarray-read.h | 13 +-
src/sarray-write.c | 746 +-
src/sarray-write.h | 14 +-
src/semaphore.c | 104 +
src/semaphore.h | 45 +
src/sequence.c | 4 +-
src/shortread.c | 9 +-
src/smooth.c | 36 +-
src/snpindex.c | 594 +-
src/spanningelt.c | 8 +-
src/spanningelt.h | 4 +-
src/splice.c | 203 +-
src/splice.h | 30 +-
src/splicetrie.c | 32 +-
src/splicetrie_build.c | 45 +-
src/stage1.c | 243 +-
src/stage1.h | 9 +-
src/stage1hr.c | 1930 +--
src/stage1hr.h | 16 +-
src/stage2.c | 584 +-
src/stage2.h | 36 +-
src/stage3.c | 908 +-
src/stage3.h | 18 +-
src/stage3hr.c | 2721 ++-
src/stage3hr.h | 103 +-
src/substring.c | 1401 +-
src/substring.h | 45 +-
src/table.c | 4 +-
src/tableint.c | 3 +-
src/tableuint.c | 3 +-
src/tableuint8.c | 3 +-
src/translation.c | 73 +-
src/translation.h | 8 +-
src/types.h | 51 +-
src/uint8list.c | 10 +-
src/uniqscan.c | 106 +-
tests/Makefile.in | 9 +-
tests/coords1.test.ok | 3 +-
util/Makefile.in | 9 +-
util/fa_coords.pl.in | 34 +-
util/gmap_build.pl.in | 37 +-
util/gmap_process.pl.in | 11 +-
164 files changed, 100734 insertions(+), 27946 deletions(-)
diff --git a/ChangeLog b/ChangeLog
index af65f81..dbe0a12 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,202 +1,913 @@
+2016-04-04 twu
+
+ * archive.html, index.html: Revised for latest version
+
+ * splice.c: Checking for more than 10% mismatches in either end. Using
+ value of min_shortend in Splice_resolve_sense and
+ Splice_resolve_antisense.
+
+ * sarray-read.c: Modified debugging statements
+
+2016-03-31 twu
+
+ * gmapindex.c: Not creating altscaffold IIT file if no alt scaffolds are
+ observed
+
+2016-03-30 twu
+
+ * gmap.c: Using new interface to Univ_IIT_altlocp
+
+ * VERSION: Updated version number
+
+ * uniqscan.c: Using new interface to Univ_IIT_altlocp
+
+ * index.html: Updated for latest version
+
+ * stage3hr.c: Removed low_alias and high_alias fields. Using altlocp,
+ alias_starts, and alias_ends.
+
+ * resulthr.c: Using npaths_primary and npaths_altloc
+
+ * gsnap.c, iit-read-univ.c, iit-read-univ.h: Reading altloc IIT file
+
+2016-03-29 twu
+
+ * sam_sort.c: Added option --restore-orig-order
+
+ * samprint.c: Removed print statement
+
+ * iit-read.c: Trying adding .iit suffix first
+
+ * stage3hr.c: Turning off DISTANT_SPLICE_SPECIAL, so we can find distant
+ splices. For substrings, updating found_score only when the new one is
+ better. Using nmismatches_whole for score field.
+
+ * sarray-read.c: Fixed debugging statements
+
2016-03-17 twu
- * gff3_genes.pl.in, gff3_introns.pl.in, gff3_splicesites.pl.in: Merged
- revision 186095 from trunk to handle parsing of latest NCBI gff3 files
+ * gff3_genes.pl.in, gff3_introns.pl.in, gff3_splicesites.pl.in: Handling
+ Parent and ID fields in exon and CDS types of recent NCBI gff3 files.
+ Handling new transcript types.
- * pair.c, stage2.c: Changed occurrences of abs() to explicit conditional
- statements, since abs() can give large integers with -m64 compiler flag
+ * pair.c: Changed occurrences of abs() to explicit conditional statements,
+ since abs() can give large integers with -m64 compiler flag
+
+ * stage2.c: Added parentheses
* gsnap.c, stage1hr.c, stage1hr.h, uniqscan.c: Added option --max-anchors
- * samread.c: Made version consistent with trunk, adding breaks after cases
- and handling EOF. Added debugging statements.
+ * samread.c: Added debugging statements
+
+2016-02-19 twu
- * sam_sort.c: Added todo comment
+ * VERSION: Updated for latest version
+
+ * index.html: Updated version latest version
+
+ * stage3hr.c: Turned off debugging
+
+ * stage1hr.c, stage3hr.c, substring.c: Fixed query coordinates for salvage
+ terminal procedure on minus strand
2016-02-18 twu
- * stage3hr.c: Applied revision 184528 from trunk to check for stage2pairs
- being NULL
+ * stage3hr.c: Checking for stage2pairs being NULL when running GMAP on
+ substrings or previous GMAP
- * gmap_build.pl.in: Applied revision 184521 from trunk to add quotes around
- bindir programs
+ * gmap_build.pl.in: Restored removal of fasta_sources and coordsfile
+ temporary files
- * stage3hr.c: Applied revision 184518 from trunk to fix creating stage 2
- pairs for circular chromosomes
+ * gmap_build.pl.in: Added quotes around bindir programs
- * substring.c: Fixed overflow bug from using this->genomiclength instead of
- querylength
+ * stage3hr.c: Fixed creating stage 2 pairs for circular chromosomes
+
+ * stage3.c: Fixed debugging statements
+
+ * indel.c: Require more matches on both ends than the length of the
+ insertion
+
+ * indel.c, oligoindex_hr.c, sarray-read.c, stage1hr.c, stage3hr.c,
+ stage3hr.h, substring.c, substring.h: Removed genomiclength as a field
+ from Substring_T objects. Fixed overflow bug for large insertion
+ substrings.
+
+ * sarray-read.c: Fixed code for SSE2 compilation
+
+ * stage3hr.c: Removed assertion, which is not valid
+
+ * indexdb.c: Handling stderr message for single sequence, where number of
+ seconds is not defined
+
+ * stage3hr.c: Changed assertion to handle large genomes
+
+ * stage1hr.c: Removed unused variables and parameters
+
+ * splicetrie_build.c: Removed unused variables
+
+ * splicetrie.c: Using new interface to dynprog procedures
+
+ * smooth.c: Removed unused variables and parameters
+
+ * sarray-write.c: Removed unused variables
+
+ * pbinom.c: Hiding unused procedures
+
+ * pair.c: Removed unused parameters
+
+ * output.c, stage3.h: Removed unused parameters in Stage3_print_sam
+
+ * stage3.c, translation.c, translation.h: Removed unused variables and
+ parameters
+
+ * outbuffer.c: Hiding unused procedures
+
+ * oligoindex_hr.c: Fixed comparison between unsigned and signed values
+
+ * indexdb.c: Removed unused variables
+
+ * indexdb-write.c: Removed unused variables
+
+ * indel.c, indel.h, sarray-read.c, sarray-read.h: Removed unused parameters
+
+ * iit-write.c: Hiding unused procedures
+
+ * gmapindex.c: Removed unused variables
+
+ * gmap.c, gregion.c, gregion.h, stage1.c, stage1.h: Removed unused variables
+ and parameters
+
+ * get-genome.c: Hiding unused procedures
+
+ * genome128_hr.c: Hiding procedures specific to GSNAP
+
+ * dynprog_cdna.c, dynprog_end.c, dynprog_end.h, dynprog_genome.c,
+ dynprog_single.c, dynprog_single.h: Changed check for HAVE_SSE4_1 or
+ HAVE_SSE2 to just HAVE_SSE2
+
+ * compress.c: Put macros around a variable
+
+ * bitpack64-readtwo.c: Put macros around a variable
+
+2016-02-17 twu
+
+ * stage1hr.c, stage3.c: Removed unused parameters
+
+ * sarray-read.c, splice.c, splice.h: Removed unused variables and parameters
+
+ * dynprog_single.c: Removed unused variables
+
+ * stage3hr.c: Using new interfaces to stage 2 procedures
+
+ * splicetrie.c: Using new interfaces to dynprog procedures
+
+ * gmap.c, stage1hr.c, stage2.c, stage2.h, stage3.c: Removed stage2_source
+ and stage2_indexsize as return values from procedures
+
+ * dynprog_single.c: Removed unused parameters
+
+ * dynprog.c, dynprog_cdna.c, dynprog_cdna.h, dynprog_end.c, dynprog_end.h,
+ dynprog_genome.c, dynprog_simd.c, dynprog_simd.h: Removed unused
+ parameters
+
+ * stage3hr.c: Fixed comparisons of signed and unsigned integers
+
+ * gmap.c, stage3.c, stage3.h: Removed stage2 and stage3 benchmarking fields
+ from Stage3_T object
+
+ * output.c, samprint.c, samprint.h: Removed unused variables and parameters
+ from pair procedures
+
+ * chimera.c, pair.c, pair.h: Removed unused variables and parameters from
+ pair procedures
+
+ * dynprog_single.c: Reduced parameters for Pairpool_add_genomeskip and
+ Dynprog_traceback_std
+
+ * dynprog.c, dynprog.h, dynprog_cdna.c, dynprog_end.c, dynprog_genome.c,
+ dynprog_simd.c, pairpool.c, pairpool.h: Reduced parameters for
+ Pairpool_add_genomeskip and Dynprog_traceback_std
+
+ * gsnap.c, stage1hr.c, stage3hr.c, stage3hr.h, uniqscan.c: Putting
+ subopt_levels into Stage3hr_setup. Removing cutoff_level as parameter
+ from optimal score procedures
+
+ * stage1hr.c, stage3hr.c, stage3hr.h: Removed unused parameters from display
+ and eval procedures
+
+ * sarray-read.c, stage1hr.c, stage3hr.c, stage3hr.h: Removed unused
+ parameters for stage3hr procedures
+
+ * sarray-read.c, splice.c, stage1hr.c, stage3hr.c, stage3hr.h: Removed
+ unused parameters and variables
+
+2016-02-16 twu
+
+ * stage1hr.c, stage3hr.c, stage3hr.h: Using new interfaces to functions
+ without first_read_p
+
+ * mapq.c, mapq.h: Hiding unused functions
+
+ * bitpack64-readtwo.c: Hiding unused functions
+
+ * bitpack64-read.c: Put correct macros around variable
+
+ * indel.c, splice.c: Using new interfaces to procedures without first_read_p
+
+ * sarray-read.c: Removed unused field first_read_p
+
+ * substring.c, substring.h: Removed unused field first_read_p
+
+ * samprint.c: Removed unused parameter concordant_chrpos
+
+2016-02-13 twu
+
+ * gsnap.c, stage1hr.c, stage1hr.h, uniqscan.c: Removed unused variables and
+ parameters in stage1hr.c
+
+ * gmap.c, gsnap.c, indexdb_hr.c, oligo.c, sarray-read.c, sarray-read.h,
+ stage1hr.c, stage2.c, stage2.h, stage3.c, stage3hr.c: Removed unused
+ variables and parameters from sarray procedures
+
+2016-02-12 twu
+
+ * genome-write.c, genome-write.h, gmapindex.c: Removed altstrain_iit as a
+ parameter to Genome_write_comp32
+
+ * genome_sites.c: Hiding unused function
+
+ * genome_sites.c, genome_sites.h: Hiding unused functions
+
+ * genome128_hr.c, genome128_hr.h, indel.c, mapq.c, sarray-read.c, splice.c,
+ splicetrie.c, stage1hr.c, stage3hr.c, substring.c: Removed first_read_p as
+ a parameter from all genome128 procedures
+
+ * sequence.c: Hiding unused function
+
+ * compress.c: Removed unused variables
+
+ * iit_get.c: Removed unused variables and parameters
+
+ * parserange.c: Removed unused variable
+
+ * iit-read.c, iit-read.h, stage3.c: Removed map_bothstrands_p as a parameter
+ to IIT_print_header
+
+ * iit-read-univ.c, iit-read.c, iit-read.h, iit_get.c: Removed sortp as a
+ parameter from IIT_get_values routines
+
+ * get-genome.c, gmap.c, gsnap.c, iit-read.c, iit-read.h, iit_dump.c,
+ iit_fetch.c, iit_get.c, parserange.c, snpindex.c, uniqscan.c: Removed
+ labels_read_p as a parameter from IIT_read
+
+ * access.c: Restored check for number of attached processes when
+ deallocating
+
+ * iit-read-univ.c: Removed unused variable
+
+ * iit-read.c, iit-read.h, splicing-scan.c: Removed parameter annotationonlyp
+ from IIT_dump
+
+ * access.c: Hiding unused functions
+
+ * genome128.c, gmapindex.c, sarray-read.c, snpindex.c: Removed eltsize as an
+ argument to Access_mmap routines
+
+ * access.c, access.h, atoiindex.c, cmetindex.c, genome.c, iit-read-univ.c,
+ iit-read.c, indexdb-write.c, indexdb.c, sarray-write.c: Removed eltsize as
+ an argument to Access_mmap routines
+
+ * gsnap.c, stage3hr.c, stage3hr.h, uniqscan.c: Added --end-detail flag
+
+ * access.c: No longer printing long string of periods and commas during
+ pre-load
+
+2016-02-10 twu
+
+ * gmap.c, gsnap.c: Added message to remove shared memory manually
+
+ * access.c: Removed warning message
+
+ * spanningelt.c: Removed debugging code
+
+ * spanningelt.c: For debugging purposes
+
+2016-02-09 twu
+
+ * atoiindex.c, cmetindex.c, gmapindex.c, indexdb.c, indexdb_hr.c,
+ sarray-write.c, src: Using new interface to Access_allocate_private
+
+ * sarray-read.c: Using new interface to Access_allocate_shared and
+ Access_allocate_private. Removed code for USE_CSA.
+
+ * genome.c, indexdb.c, indexdb.h, indexdbdef.h: Using new interface to
+ Access_allocate_shared and Access_allocate_private
+
+ * access.c, access.h: If shared allocation fails, now using memory mapping
+ if possible. Setting access variable.
+
+ * gsnap.c: Using new interface to Access_setup
+
+ * gmap.c: Using new interface to Access_setup
+
+ * dynprog_cdna.c: Changed variable initialization
+
+ * uniqscan.c: Using new interface to Access_setup
+
+ * semaphore.c: Changed variable names
+
+ * access.c: Storing all semaphore IDs, and looking at their
+ resident/freeable status. Handling emergency stops better.
+
+ * Makefile.gsnaptoo.am, access.c, semaphore.c, semaphore.h: Put semaphore
+ commands in a separate file. Fixed small bugs with deleting semaphores
+ and shared memory.
+
+2016-02-05 twu
+
+ * stage2.c: Removed unnecessary calls to abs(). Replaced with a comparison
+ between gendistance and querydistance.
+
+ * shortread.c: Using size_t instead of unsigned long long
+
+ * bitpack64-write.c, indexdb_hr.c, junction.c, pair.c, parserange.c,
+ sarray-write.c, splicetrie_build.c, substring.c, uint8list.c: Using %llu
+ for formatting instead of %u
+
+ * access.c, access.h, genuncompress.c, iit-read-univ.c, iit-read.c,
+ indexdb-write.c, indexdb.c, sam_sort.c: Changed off_t to size_t for
+ filesize
+
+ * gsnap.c: Removed testing code
+
+ * gsnap.c: For testing purposes
2016-02-04 twu
- * stage2.c: Fixed termination condition for while loop
+ * pairpool.c: Fixed assertion on genomepos
+
+ * stage3hr.c: Fixed computation of minus chromosome coordinates for circular
+ chromosomes
+
+2016-02-03 twu
+
+ * gmap.c: Creating altlocp, alias_starts, and alias_ends for user-provided
+ genomic segment
+
+ * coords1.test.ok: Revised for alternate genomic contigs
+
+ * gsnap.c: Allowing for npaths_primary and npaths_alternate. Letting
+ insertion length be arbitrarily long when user does not specify
+ --max-middle-insertions.
+
+ * gmap.c: Allowing for npaths_primary and npaths_alternate
+
+ * uniqscan.c: Using new interfaces to functions
+
+ * substring.h: Trimming novel spliceends for substrings
+
+ * substring.c: Trimming novel spliceends for substrings
+
+ * stage3hr.h: Allowing for npaths_primary and npaths_alternate
+
+ * stage3hr.c: Allowing for npaths_primary and npaths_alternate. Changed
+ logic for extending substrings using GMAP. Implemented extension of GMAP
+ alignments.
+
+ * stage3.h: Allowing for npaths_primary and npaths_alternate
- * output.c, samprint.c, samprint.h: Added check for artificial mate in
- --add-paired-nomappers mode, to set SAM flag correctly
+ * stage3.c: In find_novel_spliceends, using trim lengths at ends to define
+ two regions, one with a stronger and one with a weaker criterion for
+ splice site probability.
-2016-01-21 twu
+ * stage2.c, stage2.h: Implemented Stage2_compute_starts and
+ Stage2_compute_ends for extending ends of alignments. Fixed a condition
+ for termination of while loop.
- * dynprog_genome.c: Fixed bug in checking bestrL before it is computed,
- resulting in no splicing solutions
+ * stage1hr.h: Allowing for npaths_primary and npaths_alternate. Allowing
+ for arbitrarily long insertions when --max-middle-insertions is not set by
+ user.
+
+ * stage1hr.c: Allowing for npaths_primary and npaths_alternate. Making call
+ to extend gmap alignments. Allowing for arbitrarily long insertions when
+ --max-middle-insertions is not set by user
+
+ * sarray-read.h: Allowing for arbitrarily long insertions when
+ --max-middle-insertions is not set by user
+
+ * sarray-read.c: Allowing for arbitrarily long insertions when
+ --max-middle-insertions is not set by user
+
+ * samprint.c, samprint.h: Allowing for npaths_primary and npaths_alternate.
+ Added parameter for artificial mate in --add-paired-nomappers.
+
+ * pairpool.c: Added assertion for genomepos
+
+ * pair.c, pair.h: Allowing for npaths_primary and npaths_alternate. Added
+ function Pair_trim_distances, used by new find_novel_spliceends function
+ for pairs.
+
+ * output.c: Allowing for npaths_primary and npaths_alternate. Using new
+ interface using artificial_mate_p.
+
+ * gmapindex.c: Allowing for alternate scaffolds
+
+ * dynprog_simd.c: Calling correct printing procedures for debugging
+
+ * dynprog_genome.c: Requiring finalscore to be >= 0
+
+ * Makefile.gsnaptoo.am: Added parserange.c and parserange.h for sam_sort
2016-01-15 twu
- * stage1hr.c: Fixed array overflow involving MAX_ANCHORS algorithm
+ * result.c, result.h, resulthr.c, resulthr.h, src: Merging revision 182439
+ from branches/2014-09-04-secondary-chr to handle npaths_primary and
+ npaths_altloc
+
+ * iit-read.c, iit_store.c, src: Merging revision 182435 to use new interface
+ to Chrom_from_string
+
+ * parserange.c, src: Merging revision 182431 from
+ branches/2014-09-04-secondary-chr to check if contig_iit is NULL
+
+ * Makefile.gsnaptoo.am: Merging revisions 162111 and 182429 from
+ branches/2014-09-04-secondary-chr to add tableint.c, tableint.h,
+ parserange.c, and parserange.h where needed
+
+ * chrom.c, chrom.h: Merged revisions 162112 and 182427 from
+ branches/2014-09-04-secondary-chr to add fields for alt_scaffold_start and
+ alt_scaffold_end
+
+ * table.c, tableint.c, tableuint.c, tableuint8.c: Merged revision 162110
+ from branches/2014-09-04-secondary-chr to fix memory leak
+
+ * iit-read-univ.c, iit-read-univ.h: Merged revision 182424 from
+ branches/2014-09-04-secondary-chr to add function Univ_IIT_altlocp
+
+ * fa_coords.pl.in, gmap_build.pl.in, gmap_process.pl.in, util: Merged
+ revisions 146896 through 182422 from branches/2014-09-04-secondary-chr
+
+ * index.html: Updated to latest version
+
+ * archive.html: Added revision for 2014-12-31.v2
+
+ * stage1hr.c: Fixed array overflow in segmentation procedure
+
+2016-01-14 twu
+
+ * uniqscan.c: Using new interface to Stage3hr_setup
+
+ * gsnap.c, stage3hr.c, stage3hr.h: Distinguishing between pairmax_linear and
+ pairmax_circular
+
+ * pair.c: Removed SOFT_CLIPS_AVOID_CIRCULARIZATION code in computing
+ circularpos, since it isn't needed
+
+ * substring.c, substring.h: Defining Substring_mandatory_trim_left and
+ Substring_mandatory_trim_right.
+
+ * stage3hr.c: Turning SOFT_CLIPS_AVOID_CIRCULARIZATION back on. Using
+ Substring_mandatory_left_trim and Substring_mandatory_right_trim.
+
+2016-01-13 twu
+
+ * gmap_select.c, gmapl_select.c, gsnap_select.c, gsnapl_select.c: Checking
+ for ENOENT instead of EACCES
+
+ * substring.c: Handling trim_left_action and trim_right_action, instead of
+ trim_left_p and trim_right_p
+
+ * substring.h: Using trim_left_action and trim_right_action, instead of
+ trim_left_p and trim_right_p
+
+ * stage3hr.c: Using trim_left_action and trim_right_action, instead of
+ trim_left_p and trim_right_p
2016-01-12 twu
- * stage3hr.c, substring.c: Reverting back to remove salvage procedure for
- terminal alignments
+ * gmap_select.c, gmapl_select.c, gsnap_select.c, gsnapl_select.c: Returning
+ return code from execvp
+
+ * gmap_select.c, gmapl_select.c, gsnap_select.c, gsnapl_select.c: Handling
+ case where no path is given, by using execvp to find the correct program
- * substring.c: Computing trim_left and trim_right, even when trim_left_p and
- trim_right_p are false
+ * stage3hr.c, substring.c: Computing coordinates correctly in salvage
+ procedure for terminal alignments with too many mismatches
- * stage3hr.c: Fixed coordinate calculations in salvage procedure for
- terminal alignments with too many mismatches
+2016-01-11 twu
+
+ * iit-read.c: Removed debugging code which was not adding .iit ending to
+ file suffix
2016-01-08 twu
- * gsnap.c, sarray-read.c, sarray-read.h: Not allowing ambiguous splicing in
- a circular chromosome
+ * dynprog_cdna.c, dynprog_end.c, dynprog_genome.c, dynprog_single.c: Added
+ parameters for Dynprog_standard in non-SIMD code
+
+ * samprint.c, stage3hr.c, stage3hr.h: Changed name of function from
+ Stage3end_substring2 to Stage3end_substringN
+
+ * gsnap.c, sarray-read.c, sarray-read.h: Not allowing for ambiguous splicing
+ on circular chromosomes
+
+ * dynprog_single.c: Added assertion
- * dynprog_single.c: Added assertion for glength > 0
+ * dynprog_genome.c: Checking for the case where no intron is found in a gap
2016-01-07 twu
- * dynprog_genome.c: Handling the case where dynamic programming does not
- find an intron solution
+ * stage1hr.c: Removed extra debugging code
- * VERSION: Updated version number
+ * sarray-read.c, stage3hr.c: Handling Junction_gc from within
+ Stage3end_new_substrings
- * stage1hr.c: Applied revision 181902 from trunk to use MAX_ANCHORS and keep
- track of both all_segments and anchor_segments
+ * stage1hr.c: Defining MAX_ANCHORS instead of EXHAUSTIVE_ANCHORS. Keeping
+ track of both all_segments and anchor_segments, and using whichever
+ satisfies MAX_ANCHORS.
- * stage3hr.c: Applied revision 181882 from trunk to turn off comparison of
- score_eventrim with cutoff_level in computing optimal_scores, and to
- recompute pos5 or pos3 in Stage3end_new_terminal if number of mismatches
- exceeds the number allowed.
+ * dynprog_cdna.c, dynprog_end.c, dynprog_genome.c, dynprog_simd.h,
+ dynprog_single.c: Replacing DEBUG14 and DEBUG16 with DEBUG_SIMD and
+ DEBUG_AVX2, respectively
- * sarray-read.c, stage3hr.c: Readjusting cutoff_levels in
- Stage3_pair_up_concordant. Handling Junction_gc within
- Stage3end_new_substrings.
+ * dynprog.c: Allocating space needed for AVX2 debugging
- * samprint.c, samprint.h: Made fixes to --add-paired-nomappers option
+ * dynprog.h: Providing SIMD variables for non-AVX2 debugging procedures
- * output.c: Using new interface to SAM_print_nomapping
+ * dynprog_simd.c: Fixed SIMD variables in non-AVX2 debugging procedures
-2015-12-09 twu
+ * dynprog_simd.c: Added code for AVX2
- * samprint.c: Fixed problem with --add-paired-nomappers option for unpaired
- multiple alignments
+ * dynprog_cdna.c, dynprog_end.c, dynprog_genome.c, dynprog_simd.h: Passing
+ debugging parameters for both SIMD and AVX2 debugging
-2015-11-20 twu
+ * dynprog.c: Generalized allocation procedures to use ALIGN_SIZE
- * VERSION: Updated version number
+ * stage3hr.c: In Stage3end_optimal_score and Stage3pair_optimal_score,
+ turning off comparison of score_eventrim with cutoff_level. In
+ Stage3end_new_terminal, if number of mismatches between pos5 and pos3
+ exceeds number allowed, then recomputing pos5 or pos3 that does fit within
+ the number allowed.
+
+ * stage1hr.c: Allowing for an exhaustive set of anchor segments
+
+2015-12-19 twu
+
+ * types.h: Revised comment
+
+ * dynprog.h: Moved definitions of infinite gap penalties here
+
+ * dynprog.c: Adjusting for negative infinity in last_nogap in F loop
+
+ * atoi.c, cmet.c: Added types to make sure 64 bits are used
- * samprint.c: Applied revision 179289 from trunk to fix some issues with
- --add-paired-nomappers option
+2015-12-18 twu
- * pair.c, stage3hr.c: Applied revisions 179286 and 179286 from trunk to
- exclude alignments to circular chromosomes that extend below the first
- copy or above the second copy
+ * dynprog_simd.c: Fixed initial conditions for all three types of initial
+ gap penalty
- * gsnap.c: Fixed check on floating point values for --min-coverage
+2015-12-15 twu
- * bitpack64-write.c, bitpack64-write.h: Changed variable type for n from
- UINT4 to Oligospace_T, to allow for k-mer of 16
+ * dynprog.c: Added initializtion for ZERO_INITIAL_GAP_PENALTY. Made fixes
+ for initial Fgap calculation for standard initial gap penalty, by
+ initializing last_nogap appropriately.
-2015-09-30 twu
+ * dynprog_simd.c: Using a filter on lband for the E calculation for the
+ first column when using a standard initial gap penalty
+
+ * dynprog_end.c: Added function needed for debugging
+
+ * dynprog_simd.c: For standard initial gap penalty, revising extend_ladder
+ for first column of values, in second and later blocks.
+
+ * dynprog_simd.c: Implemented code for ZERO_INITIAL_GAP_PENALTY and
+ INFINITE_INITIAL_GAP_PENALTY. Added filters on lband for first column of
+ values in ZERO_INITIAL_GAP_PENALTY.
+
+2015-12-11 twu
+
+ * dynprog.c, dynprog.h: Added upperp and lowerp parameters to
+ Dynprog_standard, to give it the same behavior as the SIMD upper and lower
+ procedures
+
+2015-12-10 twu
* VERSION: Updated version number
- * stage1hr.c: In converting segments to GMAP, ensuring that the pairs are
- monotonic in genomepos
+ * oligoindex_hr.h: Removed duplicate definition of Shortoligmer_T
+
+ * Makefile.gsnaptoo.am, Makefile.pmaptoo.am, alphabet.c, alphabet.h, atoi.h,
+ bitpack64-read.c, bitpack64-read.h, block.c, block.h, cmet.h,
+ compress-write.c, config.site.rescomp.tst, dynprog.c, dynprog_single.c,
+ gmap.c, gmapindex.c, indexdb-write.c, indexdb-write.h, indexdb.c,
+ indexdb.h, oligoindex.h, oligoindex_hr.c, oligoindex_pmap.c,
+ oligoindex_pmap.h, oligop.c, oligop.h, pair.c, pmap_select.c, pmapindex.c,
+ src, stage1.c, stage2.c, stage2.h, stage3.c, trunk, types.h: Merged
+ revisions 179384 through 180698 from branches/2015-11-20-pmap
+
+2015-12-09 twu
+
+ * indexdb.c: Defining blocksize for PMAP
+
+ * stage3hr.c: Adjusting cutoff levels in Stage3end_pair_up_concordant to
+ consider the best alignment on each end, if has mismatches that exceed the
+ given cutoff level. Added a field distant_splice_p, and using that for
+ filtering, rather than chrnum == 0.
+
+ * output.c, samprint.c, samprint.h: Printing NH to be the maximum of the two
+ npaths in --add-paired-nomappers option
+
+2015-12-07 twu
+
+ * Makefile.gsnaptoo.am, VERSION, atoi.c, atoi.h, atoiindex.c,
+ bitpack64-access.c, bitpack64-access.h, bitpack64-incr.c,
+ bitpack64-incr.h, bitpack64-read.c, bitpack64-read.h, bitpack64-readtwo.c,
+ bitpack64-readtwo.h, bitpack64-write.c, bitpack64-write.h, block.c,
+ block.h, cmet.c, cmet.h, cmetindex.c, config.site.rescomp.prd,
+ config.site.rescomp.tst, gdiag.c, genome_sites.c, gmap.c, gmapindex.c,
+ gsnap.c, indexdb-write.c, indexdb-write.h, indexdb.c, indexdb.h,
+ indexdb_hr.c, indexdb_hr.h, oligo.c, oligo.h, oligoindex_hr.c,
+ sarray-read.c, sarray-write.c, snpindex.c, spanningelt.c, spanningelt.h,
+ splicetrie_build.c, src, stage1.c, stage1hr.c, trunk, types.h: Merged
+ revisions 179335 through 180340 from branches/2015-11-20-16mers to allow
+ for genomic indices up to 18-mers
+
+ * index.html: Updated for latest version
+
+2015-12-04 twu
+
+ * samprint.c: Fixed printing under --add-paired-nomappers for unpaired
+ multiple alignments where npaths2 > npaths1
+
+2015-12-02 twu
+
+ * stage2.c: In looking back, skipping positions where no hits were found
+
+2015-12-01 twu
+
+ * configure.ac: Building only one level of SIMD
+
+ * ax_ext.m4: Added "no" flags for various SIMD levels
+
+2015-11-20 twu
+
+ * gsnap.c: Fixed incorrect check on floating-point values for --min-coverage
+
+ * gmap_select.c, gmapl_select.c, gsnap_select.c, gsnapl_select.c: Picking
+ best available program at run-time
+
+ * stage1hr.c: In computing gmap using segments, introducing a min_genomepos
+ and max_genomepos
+
+ * samread.c: Fixed incorrect parsing needed by sam_sort, resulting from
+ missing break commands in case statements
+
+ * samprint.c: Fixed some issues with --add-paired-nomappers option
* inbuffer.c: Initializing variables
+ * pair.c: Excluding alignments to circular chromosomes that extend below the
+ first copy or above the second copy
+
+ * stage3hr.c: Excluding alignments to circular chromosomes that extend below
+ the first copy or above the second copy
+
+ * atoiindex.c, cmetindex.c, gmapindex.c: Using new interface to suffix array
+ write procedures
+
+ * sarray-write.h: Using a list of Cell_T objects to compute exceptions
+
+ * sarray-write.c: Using a list of Cell_T objects to compute exceptions
+
+ * bytecoding.c, bytecoding.h: Implemented procedures for writing bytes file
+ and interleaving bytes files.
+
+2015-11-19 twu
+
+ * Makefile.gsnaptoo.am: Removed uinttable.c and uinttable.h from programs
+ with bytecoding.c
+
+2015-11-13 twu
+
+ * Makefile.gsnaptoo.am: Added uinttable files needed by bytecoding
+
+2015-10-29 twu
+
+ * stage3hr.c: Turning off SOFT_CLIPS_AVOID_CIRCULARIZATION. Handling
+ deletions on minus strand that go beyond genomic position 0.
+
+2015-10-06 twu
+
+ * Makefile.gsnaptoo.am: Added "=1" to some pre-processor flags
+
+ * access.h: Added LOADED type for cases where IIT file is loaded from memory
+ instead of being read from file
+
+ * iit-write.c: Adding padding to character arrays in IIT file, so the
+ integer arrays are aligned.
+
+ * iit-read.c, iit-read.h: Added IIT_load function to obtain IIT from a
+ region of memory
+
2015-09-28 twu
- * oligoindex_hr.c, public-2015-07-23, src: Merged revision 175543 from trunk
- to handle the case where left_plus_length < indexsize
+ * oligoindex_hr.c: Handling the case where left_plus_length < indexsize
- * VERSION: Updated version number
+2015-09-24 twu
+
+ * gmap.c, gsnap.c: Revised explanation message for illegal instructions
- * stage1hr.c: Putting debugging statement inside debug macro
+ * datadir.c: Increased buffer size for dbversion file name
+
+ * access.c: Looping until we get a semaphore, either by creation or by using
+ existing one
2015-09-22 twu
- * dynprog_genome.c, pair.c, pair.h, public-2015-07-23, src, stage1hr.c,
- stage3.c, stage3hr.c: Merged revisions 174475 through 174480 from trunk to
- improve alignments involving microexons, splices at ends, bridging intron
- gaps, and multiple segments
+ * stage3hr.c: Using nsegments field for all alignment types. Filtering
+ results if nsegments is relatively high compared with the best result.
+
+ * stage3.c: Using higher standard for microexons. Using nmatches instead of
+ support for sufficient_splice_prob.
+
+ * stage1hr.c: Handling case of paired-end alignments where both ends do not
+ satisfy minimum coverage. Fixed debugging statements.
+
+ * splice.c: Using correct variable names inside FREEA calls
+
+ * pair.c, pair.h: Implemented Pair_maxnegscore
+
+ * dynprog_genome.c: Revised bridge_intron_gap procedures to make reasoning
+ clearer. Using weaker values for scoreI. Using maxnegscore to filter out
+ bad alignments.
+
+2015-09-16 twu
- * VERSION, public-2015-07-23, src, stage1hr.c, stage3hr.c: Merged revision
- 174117 from trunk to fix calls to Genome_get_segment_blocks_left
+ * stage1hr.c: Removed debugging comment
+
+ * stage1hr.c, stage3hr.c: Fixed calls to Genome_get_segment_blocks_left,
+ where we were providing the left coordinate instead of the right one.
+
+ * genome.c: Added comment
2015-09-12 twu
- * splice.c: Fixed FREEA statements
+ * cpuid.c: Added to repository
+
+2015-09-11 twu
+
+ * uniqscan.c: Using new interfaces to stage 1 procedures
+
+ * substring.c, substring.h: Removed reject_trimlength
+
+ * stage3hr.c, stage3hr.h: Added procedures for filtering by coverage
+
+ * stage1hr.h: Added --min-coverage and removed --terminal-threshold
+
+ * stage1hr.c: Added --min-coverage. Changed criteria for running
+ find_terminals.
- * gmap_build.pl.in, util: Merged revision 173888 from trunk to allow for
- spaces in destination directory
+ * gsnap.c: Added --min-coverage and removed --terminal-threshold
- * gsnap.c, src, stage1hr.c, stage1hr.h, stage3hr.c, stage3hr.h, substring.c,
- substring.h, uniqscan.c: Merged revisions 173889 through 173894 from trunk
- to add --min-coverage and remove --terminal-threshold and
- reject_trimlength. Changed criteria for running find_terminals.
+ * gmap_build.pl.in: Allowing for spaces in destination directory
+
+2015-09-09 twu
+
+ * stage3hr.c: Fixed debugging statement
2015-09-01 twu
- * VERSION, chimera.c, gmap.c, public-2015-07-23, src: Merged revisions
- 173188 and 173189 from trunk to set dinucleotides for out-of-bound
- chimeric breakpoints and to set some uninitialized variables
+ * gmap.c: Setting some uninitialized variables for chimera
+
+ * chimera.c: When chimeric breakpoint is beyond chromosomal bounds,
+ returning NN for dinucleotides
- * stage3hr.c: Merged revision 173165 from trunk to favor non-zero sensedirs
- when sorting results
+ * stage3hr.c: Favoring non-zero sensedirs when sorting results
- * splice.c: Merged revision 173164 from trunk to fix variable names for
- FREEA
+ * splice.c: Fixed variable names for FREEA command, which was observed by
+ compiler only when alloca is not available.
- * oligoindex_hr.c: Merged revision 173163 from trunk to initialize some
- return variables when exiting trimming procedure early
+ * oligoindex_hr.c: Initializing some return variables when exiting trimming
+ procedure early
- * chimera.c, chimera.h, gmap.c, pair.c: Merged revision 173162 from trunk to
- fix issues when chimeras extend to beginning or end of chromosomes
+ * chimera.c, chimera.h, gmap.c, pair.c: Fixed issues when chimeras extend to
+ beginning or end of chromosomes, causing a search for donor and acceptor
+ nucleotides beyond chromosomal bounds. Fixed Pair_pathscores to extend to
+ last pair of path.
- * dynprog_genome.c: Merged revision 173161 from trunk to fix bridging intron
- gaps when no probabilities are found
+ * dynprog_genome.c: Resolved fatal bug in bridging intron gaps when when no
+ probabilities are found
2015-08-31 twu
- * gmap.c, outbuffer.c, src, stage1.c, stage3.c: Merged revision 173034 to
- not use alloca for array of Batch_T objects
+ * stage1.c: No longer using alloca for array of Batch_T objects
+
+2015-08-28 twu
+
+ * gmap.c: Changed MALLOC of array to MALLOC_OUT. Fixed code for memusage.
+
+ * outbuffer.c: Changed FREE of outputs to FREE_KEEP
+
+ * stage3.c: Using known splices in pick_cdna_direction. Changed MALLOC of
+ Stage3_new to MALLOC_OUT.
2015-08-27 twu
- * stage3.c: Applied revision 172740 from trunk to change criterion for
- evaluating splice neighborhood to allow for short ends
+ * stage3.c: Changed criterion for evaluating splice neighborhood to allow
+ for short ends
+
+2015-08-24 twu
+
+ * sarray-read.c: Using max_mismatches_allowed from original call to suffix
+ array algorithm, and not allowing it to be unlimited
+
+ * splice.c: Added debugging statements
- * sarray-read.c: Applied revision 172478 from trunk to use
- max_mismatches_allowed from original call to suffix array algorithm, and
- not allowing it to be unlimited
+ * genome.c: Setting end of genomealt string to be NULL
- * stage3hr.c: Applied part of revision 172472 from trunk to call
- Genome_get_segment_blocks_left with chroffset and not chrhigh
+ * dynprog_genome.c: Changed loop end condition to avoid accessing
+ uninitialized variables
- * genome.c: Applied revision 172476 from trunk to set end of genomealt
- string to be NULL
+ * stage3hr.c: Calling Genome_get_segment_blocks_left with chroffset and not
+ chrhigh. Setting resolve value to be -1 in case of
+ AMB_UNRESOLVED_TOOCLOSE.
- * dynprog_genome.c: Applied revision 172475 from trunk to change loop end
- condition to avoid accessing uninitialized variables
+2015-08-19 twu
- * gsnap.c, samprint.c, samprint.h: Applied revisions 171145 and 171803 from
- trunk to add flags --add-paired-nomappers and
+ * gsnap.c: Removed extraneous space after newline
+
+ * access.c: Added header file
+
+2015-08-13 twu
+
+ * gsnap.c: Using new interface to SAM_setup
+
+ * oligoindex_hr.h: Changing Inquery_T types to be unsigned
+
+ * oligoindex_hr.c: Removed old code that caused counts to be incremented
+ twice
+
+ * access.c, access.h, atoiindex.c, cmetindex.c, genome.c, gmapindex.c,
+ indexdb-write.c, indexdb.c, sarray-read.c, sarray-write.c, snpindex.c:
+ Replaced Access_allocate with Access_allocate_private and
+ Access_allocate_shared
+
+ * gsnap.c, samprint.c, samprint.h: Added option
--paired-flag-means-concordant
- * oligoindex_hr.c: Applied revision 170792 from trunk to restore missing
- line in counting of 9-mers
+2015-08-11 twu
+
+ * genome.c, indexdb.c, indexdbdef.h, sarray-read.c: Storing keys from shared
+ memory to check semaphores to see if the memory should be retained
+
+ * access.c, access.h, gsnap.c: Added code for preloading and unloading of
+ shared memory
+
+ * configure.ac: No longer offering options to enable or disable CPU types
+
+ * ax_ext.m4: Various changes to handle CPU types and features
+
+ * oligoindex_hr.c, oligoindex_hr.h: Created Inquery_T type to handle both
+ SSE2 and non-SSE code
+
+ * genome128_hr.c: Fixed branch for clz/ctz for SSE4.2
+
+ * configure.ac: Removing mpi for now
+
+ * ax_ext.m4: Requiring BMI2 as part of AVX2
+
+ * sarray-read.c: Allowing stream_load of si128 only for HAVE_SSE4_1
+
+ * genome.c, genome.h, indexdb.c, indexdb.h, sarray-read.h: Commented unused
+ procedures for shmem_remove
+
+2015-08-10 twu
+
+ * Makefile.am, Makefile.gsnaptoo.am, acinclude.m4, ax_compiler_vendor.m4,
+ ax_ext.m4, config.site.rescomp.tst, configure.ac, cpuid.h, genome128_hr.c,
+ gmap.c, gmap_select.c, gmapindex.c, gmapl_select.c, gsnap.c,
+ gsnap_select.c, gsnapl_select.c, popcount.c, popcount.h, sarray-read.c,
+ src, trunk: Merged revisions 171384 through 171613 from
+ branches/2015-08-06-run-time-variants to allow for run-time variants
+
+ * VERSION, config.site.rescomp.tst, index.html, oligoindex_hr.c,
+ oligoindex_hr.h, sarray-read.c, src, trunk: Merged revisions 170634 to
+ 171595 to add code for AVX2
+
+2015-08-05 twu
+
+ * oligoindex_hr.c: Changed debugging statements
+
+2015-08-04 twu
+
+ * oligoindex_hr.c: Added debugging statements
+
+2015-08-03 twu
+
+ * gsnap.c, samprint.c, samprint.h: Added flag --add-paired-nomappers
+
+2015-07-28 twu
- * public-2015-07-23: Created release branch for 2015-07-23
+ * oligoindex_hr.c: Restored missing line in counting of 9-mers
2015-07-23 twu
diff --git a/Makefile.am b/Makefile.am
index 4e9c4d5..05fd12f 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,5 +1,6 @@
-SUBDIRS = src mpi util tests
+# Removed mpi for now
+SUBDIRS = src util tests
EXTRA_DIST = VERSION NOTICE config.site
diff --git a/Makefile.in b/Makefile.in
index 9dadef1..1def6ec 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -37,7 +37,7 @@ target_triplet = @target@
subdir = .
DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \
$(srcdir)/Makefile.in $(top_srcdir)/configure AUTHORS COPYING \
- ChangeLog INSTALL NEWS config/compile config/config.guess \
+ ChangeLog INSTALL NEWS TODO config/compile config/config.guess \
config/config.sub config/depcomp config/install-sh \
config/ltmain.sh config/missing
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
@@ -46,6 +46,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/ltsugar.m4 \
$(top_srcdir)/config/ltversion.m4 \
$(top_srcdir)/config/lt~obsolete.m4 $(top_srcdir)/acinclude.m4 \
+ $(top_srcdir)/config/ax_compiler_vendor.m4 \
$(top_srcdir)/config/pagesize.m4 \
$(top_srcdir)/config/madvise-flags.m4 \
$(top_srcdir)/config/mmap-flags.m4 \
@@ -54,7 +55,6 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/shm-flags.m4 \
$(top_srcdir)/config/ax_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
- $(top_srcdir)/config/builtin-popcount.m4 \
$(top_srcdir)/config/struct-stat64.m4 \
$(top_srcdir)/config/expand.m4 $(top_srcdir)/config/perl.m4 \
$(top_srcdir)/config/fopen.m4 $(top_srcdir)/config/asm-bsr.m4 \
@@ -185,7 +185,6 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
-POPCNT_CFLAGS = @POPCNT_CFLAGS@
PTHREAD_CC = @PTHREAD_CC@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
PTHREAD_LIBS = @PTHREAD_LIBS@
@@ -193,7 +192,11 @@ RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
-SIMD_CFLAGS = @SIMD_CFLAGS@
+SIMD_AVX2_CFLAGS = @SIMD_AVX2_CFLAGS@
+SIMD_SSE2_CFLAGS = @SIMD_SSE2_CFLAGS@
+SIMD_SSE4_1_CFLAGS = @SIMD_SSE4_1_CFLAGS@
+SIMD_SSE4_2_CFLAGS = @SIMD_SSE4_2_CFLAGS@
+SIMD_SSSE3_CFLAGS = @SIMD_SSSE3_CFLAGS@
STRIP = @STRIP@
VERSION = @VERSION@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -254,7 +257,9 @@ target_vendor = @target_vendor@
top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
-SUBDIRS = src mpi util tests
+
+# Removed mpi for now
+SUBDIRS = src util tests
EXTRA_DIST = VERSION NOTICE config.site
CLEANFILES = so_locations
ACLOCAL_AMFLAGS = -I config
diff --git a/TODO b/TODO
new file mode 100644
index 0000000..c5a7bd7
--- /dev/null
+++ b/TODO
@@ -0,0 +1,3 @@
+
+Add flag that allows for splitting afterwards.
+
diff --git a/VERSION b/VERSION
index 451087c..0918dc2 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2015-12-31
\ No newline at end of file
+2016-04-04
\ No newline at end of file
diff --git a/acinclude.m4 b/acinclude.m4
index 602b9cd..abe76eb 100644
--- a/acinclude.m4
+++ b/acinclude.m4
@@ -2,6 +2,8 @@ M4 Source Code
m4_define([DATE],['`date +%Y-%m-%d`'])
+m4_include([config/ax_compiler_vendor.m4])
+
m4_include([config/pagesize.m4])
m4_include([config/madvise-flags.m4])
m4_include([config/mmap-flags.m4])
@@ -12,7 +14,6 @@ m4_include([config/shm-flags.m4])
m4_include([config/ax_mpi.m4])
m4_include([config/acx_pthread.m4])
-m4_include([config/builtin-popcount.m4])
m4_include([config/struct-stat64.m4])
m4_include([config/expand.m4])
m4_include([config/perl.m4])
diff --git a/config/ax_compiler_vendor.m4 b/config/ax_compiler_vendor.m4
new file mode 100644
index 0000000..39ca3c0
--- /dev/null
+++ b/config/ax_compiler_vendor.m4
@@ -0,0 +1,87 @@
+# ===========================================================================
+# http://www.gnu.org/software/autoconf-archive/ax_compiler_vendor.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_COMPILER_VENDOR
+#
+# DESCRIPTION
+#
+# Determine the vendor of the C/C++ compiler, e.g., gnu, intel, ibm, sun,
+# hp, borland, comeau, dec, cray, kai, lcc, metrowerks, sgi, microsoft,
+# watcom, etc. The vendor is returned in the cache variable
+# $ax_cv_c_compiler_vendor for C and $ax_cv_cxx_compiler_vendor for C++.
+#
+# LICENSE
+#
+# Copyright (c) 2008 Steven G. Johnson <stevenj at alum.mit.edu>
+# Copyright (c) 2008 Matteo Frigo
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception, the respective Autoconf Macro's copyright owner
+# gives unlimited permission to copy, distribute and modify the configure
+# scripts that are the output of Autoconf when processing the Macro. You
+# need not follow the terms of the GNU General Public License when using
+# or distributing such scripts, even though portions of the text of the
+# Macro appear in them. The GNU General Public License (GPL) does govern
+# all other use of the material that constitutes the Autoconf Macro.
+#
+# This special exception to the GPL applies to versions of the Autoconf
+# Macro released by the Autoconf Archive. When you make and distribute a
+# modified version of the Autoconf Macro, you may extend this special
+# exception to the GPL to apply to your modified version as well.
+
+#serial 15
+
+AC_DEFUN([AX_COMPILER_VENDOR],
+[AC_CACHE_CHECK([for _AC_LANG compiler vendor], ax_cv_[]_AC_LANG_ABBREV[]_compiler_vendor,
+ dnl Please add if possible support to ax_compiler_version.m4
+ [# note: don't check for gcc first since some other compilers define __GNUC__
+ vendors="intel: __ICC,__ECC,__INTEL_COMPILER
+ ibm: __xlc__,__xlC__,__IBMC__,__IBMCPP__
+ pathscale: __PATHCC__,__PATHSCALE__
+ clang: __clang__
+ cray: _CRAYC
+ fujitsu: __FUJITSU
+ gnu: __GNUC__
+ sun: __SUNPRO_C,__SUNPRO_CC
+ hp: __HP_cc,__HP_aCC
+ dec: __DECC,__DECCXX,__DECC_VER,__DECCXX_VER
+ borland: __BORLANDC__,__CODEGEARC__,__TURBOC__
+ comeau: __COMO__
+ kai: __KCC
+ lcc: __LCC__
+ sgi: __sgi,sgi
+ microsoft: _MSC_VER
+ metrowerks: __MWERKS__
+ watcom: __WATCOMC__
+ portland: __PGI
+ tcc: __TINYC__
+ unknown: UNKNOWN"
+ for ventest in $vendors; do
+ case $ventest in
+ *:) vendor=$ventest; continue ;;
+ *) vencpp="defined("`echo $ventest | sed 's/,/) || defined(/g'`")" ;;
+ esac
+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM(,[
+ #if !($vencpp)
+ thisisanerror;
+ #endif
+ ])], [break])
+ done
+ ax_cv_[]_AC_LANG_ABBREV[]_compiler_vendor=`echo $vendor | cut -d: -f1`
+ ])
+])
diff --git a/config/ax_ext.m4 b/config/ax_ext.m4
index 1065623..1817b02 100644
--- a/config/ax_ext.m4
+++ b/config/ax_ext.m4
@@ -31,6 +31,8 @@
# and this notice are preserved. This file is offered as-is, without any
# warranty.
+# Assumes AX_COMPILER_VENDOR has been called to define ax_cv_c_compiler_vendor
+
#serial 13
AC_DEFUN([AX_EXT],
@@ -41,24 +43,23 @@ AC_DEFUN([AX_EXT],
case $host_cpu in
powerpc*)
- AC_CACHE_CHECK([whether altivec is enabled and supported], [ax_cv_cpu_have_altivec_ext],
+ AC_CACHE_CHECK([whether altivec is enabled and supported], [ax_cv_cpu_has_altivec_ext],
[
if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then
if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then
- ax_cv_cpu_have_altivec_ext=yes
+ ax_cv_cpu_has_altivec_ext=yes
fi
fi
])
- if test "$ax_cv_cpu_have_altivec_ext" = yes; then
- AC_DEFINE(HAVE_ALTIVEC,1,[Define to 1 if you support Altivec instructions])
+ if test x"$ax_cv_cpu_has_altivec_ext" = xyes; then
+# AC_DEFINE(HAVE_ALTIVEC,1,[Define to 1 if you support Altivec instructions]) -- Not used
AX_CHECK_COMPILE_FLAG(-faltivec, SIMD_CFLAGS="$SIMD_CFLAGS -faltivec", [])
fi
;;
i[[3456]]86*|x86_64*|amd64*)
-
AC_REQUIRE([AX_GCC_X86_CPUID])
AC_REQUIRE([AX_GCC_X86_AVX_XGETBV])
@@ -71,90 +72,71 @@ AC_DEFUN([AX_EXT],
edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
fi
- AC_CACHE_CHECK([whether mmx is enabled and supported by CPU], [ax_cv_cpu_have_mmx_ext],
+ AC_CACHE_CHECK([whether mmx is enabled and supported by CPU], [ax_cv_cpu_has_mmx_ext],
[
- ax_cv_cpu_have_mmx_ext=no
+ ax_cv_cpu_has_mmx_ext=no
if test "$((0x$edx>>23&0x01))" = 1; then
- ax_cv_cpu_have_mmx_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features mmx"
-
+ ax_cv_cpu_has_mmx_ext=yes
fi
])
- AC_CACHE_CHECK([whether sse is enabled and supported by CPU], [ax_cv_cpu_have_sse_ext],
+ AC_CACHE_CHECK([whether sse is enabled and supported by CPU], [ax_cv_cpu_has_sse_ext],
[
- ax_cv_cpu_have_sse_ext=no
+ ax_cv_cpu_has_sse_ext=no
if test "$((0x$edx>>25&0x01))" = 1; then
- ax_cv_cpu_have_sse_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features sse"
+ ax_cv_cpu_has_sse_ext=yes
fi
])
- AC_CACHE_CHECK([whether sse2 is enabled and supported by CPU], [ax_cv_cpu_have_sse2_ext],
+ AC_CACHE_CHECK([whether sse2 is enabled and supported by CPU], [ax_cv_cpu_has_sse2_ext],
[
- ax_cv_cpu_have_sse2_ext=no
+ ax_cv_cpu_has_sse2_ext=no
if test "$((0x$edx>>26&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse2"
- if test "$ax_cv_want_sse2_ext" = yes; then
- ax_cv_cpu_have_sse2_ext=yes
- fi
+ ax_cv_cpu_has_sse2_ext=yes
fi
])
- AC_CACHE_CHECK([whether sse3 is enabled and supported by CPU], [ax_cv_cpu_have_sse3_ext],
+ AC_CACHE_CHECK([whether sse3 is enabled and supported by CPU], [ax_cv_cpu_has_sse3_ext],
[
- ax_cv_cpu_have_sse3_ext=no
+ ax_cv_cpu_has_sse3_ext=no
if test "$((0x$ecx&0x01))" = 1; then
- ax_cv_cpu_have_sse3_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features sse3"
+ ax_cv_cpu_has_sse3_ext=yes
fi
])
- AC_CACHE_CHECK([whether ssse3 is enabled and supported by CPU], [ax_cv_cpu_have_ssse3_ext],
+ AC_CACHE_CHECK([whether ssse3 is enabled and supported by CPU], [ax_cv_cpu_has_ssse3_ext],
[
- ax_cv_cpu_have_ssse3_ext=no
+ ax_cv_cpu_has_ssse3_ext=no
if test "$((0x$ecx>>9&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features ssse3"
- if test "$ax_cv_want_ssse3_ext" = yes; then
- ax_cv_cpu_have_ssse3_ext=yes
- fi
+ ax_cv_cpu_has_ssse3_ext=yes
fi
])
- AC_CACHE_CHECK([whether sse4.1 is enabled and supported by CPU], [ax_cv_cpu_have_sse41_ext],
+ AC_CACHE_CHECK([whether sse4.1 is enabled and supported by CPU], [ax_cv_cpu_has_sse41_ext],
[
- ax_cv_cpu_have_sse41_ext=no
+ ax_cv_cpu_has_sse41_ext=no
if test "$((0x$ecx>>19&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse4.1"
- if test "$ax_cv_want_sse41_ext" = yes; then
- ax_cv_cpu_have_sse41_ext=yes
- fi
+ ax_cv_cpu_has_sse41_ext=yes
fi
])
- AC_CACHE_CHECK([whether sse4.2 is enabled and supported by CPU], [ax_cv_cpu_have_sse42_ext],
+ AC_CACHE_CHECK([whether sse4.2 is enabled and supported by CPU], [ax_cv_cpu_has_sse42_ext],
[
- ax_cv_cpu_have_sse42_ext=no
+ ax_cv_cpu_has_sse42_ext=no
if test "$((0x$ecx>>20&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse4.2"
- if test "$ax_cv_want_sse42_ext" = yes; then
- ax_cv_cpu_have_sse42_ext=yes
- fi
+ ax_cv_cpu_has_sse42_ext=yes
fi
])
- AC_CACHE_CHECK([whether avx is enabled and supported by CPU], [ax_cv_cpu_have_avx_ext],
+ AC_CACHE_CHECK([whether avx is enabled and supported by CPU], [ax_cv_cpu_has_avx_ext],
[
- ax_cv_cpu_have_avx_ext=no
+ ax_cv_cpu_has_avx_ext=no
if test "$((0x$ecx>>28&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features avx"
- if test "$ax_cv_want_avx_ext" = yes; then
- ax_cv_cpu_have_avx_ext=yes
- fi
+ ax_cv_cpu_has_avx_ext=yes
fi
])
- if test x"$ax_cv_cpu_have_avx_ext" = x"yes"; then
+ if test x"$ax_cv_cpu_has_avx_ext" = xyes; then
AX_GCC_X86_AVX_XGETBV(0x00000000)
xgetbv_eax="0"
@@ -178,11 +160,11 @@ AC_DEFUN([AX_EXT],
fi
- AC_CACHE_CHECK([whether popcnt is enabled and supported by CPU], [ax_cv_cpu_have_popcnt_ext],
+ AC_CACHE_CHECK([whether popcnt is enabled and supported by CPU], [ax_cv_cpu_has_popcnt_ext],
[
- ax_cv_cpu_have_popcnt_ext=no
+ ax_cv_cpu_has_popcnt_ext=no
if test "$((0x$ecx>>23&0x01))" = 1; then
- ax_cv_cpu_have_popcnt_ext=yes
+ ax_cv_cpu_has_popcnt_ext=yes
fi
])
@@ -191,11 +173,11 @@ AC_DEFUN([AX_EXT],
ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
- AC_CACHE_CHECK([whether lzcnt is enabled and supported by CPU], [ax_cv_cpu_have_lzcnt_ext],
+ AC_CACHE_CHECK([whether lzcnt is enabled and supported by CPU], [ax_cv_cpu_has_lzcnt_ext],
[
- ax_cv_cpu_have_lzcnt_ext=no
+ ax_cv_cpu_has_lzcnt_ext=no
if test "$((0x$ecx>>5&0x01))" = 1; then
- ax_cv_cpu_have_lzcnt_ext=yes
+ ax_cv_cpu_has_lzcnt_ext=yes
fi
])
@@ -205,283 +187,415 @@ AC_DEFUN([AX_EXT],
ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 3`
edx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 4`
- AC_CACHE_CHECK([whether avx2 is enabled and supported by CPU], [ax_cv_cpu_have_avx2_ext],
+ AC_CACHE_CHECK([whether avx2 is enabled and supported by CPU], [ax_cv_cpu_has_avx2_ext],
[
- ax_cv_cpu_have_avx2_ext=no
+ ax_cv_cpu_has_avx2_ext=no
if test "$((0x$ebx>>5&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features avx2"
- if test "$ax_cv_want_avx2_ext" = yes; then
- ax_cv_cpu_have_avx2_ext=yes
- fi
+ ax_cv_cpu_has_avx2_ext=yes
fi
])
- AC_CACHE_CHECK([whether bmi1 is enabled and supported by CPU], [ax_cv_cpu_have_bmi1_ext],
+ AC_CACHE_CHECK([whether bmi1 is enabled and supported by CPU], [ax_cv_cpu_has_bmi1_ext],
[
- ax_cv_cpu_have_bmi1_ext=no
+ ax_cv_cpu_has_bmi1_ext=no
if test "$((0x$ebx>>3&0x01))" = 1; then
- ax_cv_cpu_have_bmi1_ext=yes
+ ax_cv_cpu_has_bmi1_ext=yes
fi
])
- AC_CACHE_CHECK([whether bmi2 is enabled and supported by CPU], [ax_cv_cpu_have_bmi2_ext],
+ AC_CACHE_CHECK([whether bmi2 is enabled and supported by CPU], [ax_cv_cpu_has_bmi2_ext],
[
- ax_cv_cpu_have_bmi2_ext=no
+ ax_cv_cpu_has_bmi2_ext=no
if test "$((0x$ebx>>8&0x01))" = 1; then
- ax_cv_cpu_have_bmi2_ext=yes
+ ax_cv_cpu_has_bmi2_ext=yes
fi
])
- if test "$ax_cv_cpu_have_mmx_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mmmx, [ax_cv_compile_mmx_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_mmx_ext" != x"yes"; then
+
+ # AX_CHECK_COMPILE_FLAG tests CFLAGS EXTRA-FLAGS FLAG
+
+ if test x"$ax_cv_cpu_has_mmx_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-mmmx
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_mmx_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_mmx_ext" != xyes; then
AC_MSG_WARN([Your CPU supports MMX instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for mmintrin.h header file)
- CFLAGS=-mmmx
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <mmintrin.h>])],
[ax_cv_link_mmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_mmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_mmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports MMX instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -mmmx"
- AC_DEFINE(HAVE_MMX,1,[Define to 1 if you support MMX instructions])
+# AC_DEFINE(HAVE_MMX,1,[Define to 1 if you support MMX instructions]) -- Not used
fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse, [ax_cv_compile_sse_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_sse_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_sse_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-msse
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_sse_ext" != xyes; then
AC_MSG_WARN([Your CPU supports SSE instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for xmmintrin.h header file)
- CFLAGS=-msse
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <xmmintrin.h>])],
[ax_cv_link_xmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_xmmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_xmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -msse"
- AC_DEFINE(HAVE_SSE,1,[Define to 1 if you support SSE (Streaming SIMD Extensions) instructions])
+# AC_DEFINE(HAVE_SSE,1,[Define to 1 if you support SSE (Streaming SIMD Extensions) instructions]) -- Not used
fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse2_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse2, [ax_cv_compile_sse2_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_sse2_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_sse2_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-msse2
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse2_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_sse2_ext" != xyes; then
AC_MSG_WARN([Your CPU supports SSE2 instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for emmintrin.h header file)
- CFLAGS=-msse2
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <emmintrin.h>])],
[ax_cv_link_emmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_emmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_emmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -msse2"
- AC_DEFINE(HAVE_SSE2,1,[Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions])
+ ax_make_sse2=yes
+ SIMD_SSE2_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_SSE2,1,[Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions]) -- Not used
fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse3_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse3, [ax_cv_compile_sse3_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_sse3_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_sse3_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-msse3
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse3_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_sse3_ext" != xyes; then
AC_MSG_WARN([Your CPU supports SSE3 instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for pmmintrin.h header file)
- CFLAGS=-msse3
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <pmmintrin.h>])],
[ax_cv_link_pmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_pmmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_pmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE3 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -msse3"
- AC_DEFINE(HAVE_SSE3,1,[Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions])
+# AC_DEFINE(HAVE_SSE3,1,[Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions]) -- Not used
fi
fi
fi
-
- if test "$ax_cv_cpu_have_ssse3_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mssse3, [ax_cv_compile_ssse3_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_ssse3_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_ssse3_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-mssse3"
+ else
+ TEST_CFLAGS="$SIMD_SSE2_CFLAGS -mssse3"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-ssse3"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_ssse3_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_ssse3_ext" != xyes; then
AC_MSG_WARN([Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for tmmintrin.h header file)
- CFLAGS=-mssse3
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <tmmintrin.h>])],
[ax_cv_link_tmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_tmmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_tmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSSE3 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -mssse3"
- AC_DEFINE(HAVE_SSSE3,1,[Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions])
+ ax_make_ssse3=yes
+ SIMD_SSSE3_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_SSSE3,1,[Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions]) -- Defines run-type
fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse41_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse4.1, [ax_cv_compile_sse41_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_sse41_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_sse41_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-msse4.1"
+ else
+ TEST_CFLAGS="$SIMD_SSSE3_CFLAGS -msse4.1"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-sse4.1"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-sse4.1"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse41_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_sse41_ext" != xyes; then
AC_MSG_WARN([Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for smmintrin.h header file)
- CFLAGS=-msse4.1
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <smmintrin.h>])],
[ax_cv_link_smmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_smmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_smmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE4.1 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -msse4.1"
- AC_DEFINE(HAVE_SSE4_1,1,[Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1) instructions])
+ ax_make_sse41=yes
+ SIMD_SSE4_1_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_SSE4_1,1,[Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1) instructions]) -- Not used
fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse42_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-msse4.2, [ax_cv_compile_sse42_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_sse42_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_sse42_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-march=corei7"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_1_CFLAGS -msse4.2"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-sse4.2"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-sse4.2"
+ SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-sse4.2"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_sse42_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_sse42_ext" != xyes; then
AC_MSG_WARN([Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for nmmintrin.h header file)
- CFLAGS=-msse4.2
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <nmmintrin.h>])],
[ax_cv_link_nmmintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_nmmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_nmmintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports SSE4.2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -msse4.2"
- AC_DEFINE(HAVE_SSE4_2,1,[Define to 1 if you support SSE4.2 (Streaming SIMD Extensions 4.2) instructions])
-
- if test "$ax_cv_cpu_have_popcnt_ext" = yes; then
- AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[#include <nmmintrin.h>]],
- [[return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;]])],
- [ax_cv_run_mm_popcnt_ext=yes])
- if test x"$ax_cv_run_mm_popcnt_ext" = x"yes"; then
- AC_DEFINE(HAVE_MM_POPCNT,1,[Define to 1 if you support Intel intrinsic _mm_popcnt_u32/64 instructions])
- fi
- fi
- fi
+ ax_make_sse42=yes
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ fi
fi
fi
+ if test x"$ax_make_sse42" = xyes; then
+ AC_MSG_CHECKING(for mm_popcnt support)
+ if test x"$ax_cv_cpu_has_popcnt_ext" != xyes; then
+ AC_MSG_RESULT([no])
+ else
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[#include <nmmintrin.h>]],
+ [[return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE(HAVE_MM_POPCNT,1,[Define to 1 if you support Intel intrinsic _mm_popcnt_u32/64 instructions])],
+ [AC_MSG_RESULT(no)])
+ fi
+ fi
- if test "$ax_cv_cpu_have_avx_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mavx, [ax_cv_compile_avx_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_avx_ext" != x"yes"; then
- AC_MSG_WARN([Your CPU supports AVX instructions but not your compiler. Can you try another compiler or update yours?])
+ if test x"$ax_make_sse42" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
else
- AC_MSG_CHECKING(for immintrin.h header file)
- CFLAGS=-mavx
- AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <immintrin.h>])],
- [ax_cv_link_immintrin_h=yes],
- [ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_immintrin_h" != x"yes"; then
- AC_MSG_RESULT([no])
- AC_MSG_WARN([Your compiler supports AVX instructions but not your linker.])
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mpopcnt"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_popcnt_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_popcnt_ext" != xyes; then
+ AC_MSG_WARN([Your CPU supports POPCNT instructions but not your compiler. Can you try another compiler or update yours?])
+ else
+ CFLAGS=$TEST_CFLAGS
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
+ [ax_cv_link_popcnt=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_popcnt" != xyes; then
+ AC_MSG_WARN([Your compiler supports -mpopcnt but not your linker. Can you try another linker or update yours?])
else
- AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -mavx"
- AC_DEFINE(HAVE_AVX,1,[Define to 1 if you support AVX (Advanced Vector Extensions) instructions])
-
- if test "$ax_cv_cpu_have_popcnt_ext" = yes; then
- AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[#include <immintrin.h>]],
- [[return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;]])],
- [ax_cv_run_popcnt_ext=yes])
- if test x"$ax_cv_run_popcnt_ext" = x"yes"; then
- AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])
- fi
- fi
-
- if test "$ax_cv_cpu_have_lzcnt_ext" = yes; then
- AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[#include <immintrin.h>]],
- [[return (_lzcnt_u32(0xffffffffu) == 32) ? 0 : 9;]])],
- [ax_cv_run_lzcnt_ext=yes])
- if test x"$ax_cv_run_lzcnt_ext" = x"yes"; then
- AC_DEFINE(HAVE_LZCNT,1,[Define to 1 if you support Intel intrinsic _lzcnt instruction])
- fi
- fi
-
- if test "$ax_cv_cpu_have_bmi1_ext" = yes; then
- CFLAGS=-mbmi
- AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[#include <immintrin.h>]],
- [[return (_tzcnt_u32(0xffffffffu) == 32) ? 0 : 9;]])],
- [ax_cv_run_tzcnt_ext=yes])
- if test x"$ax_cv_run_tzcnt_ext" = x"yes"; then
- SIMD_CFLAGS="$SIMD_CFLAGS -mbmi"
- AC_DEFINE(HAVE_TZCNT,1,[Define to 1 if you support Intel intrinsic _tzcnt instruction])
- fi
- fi
-
- if test "$ax_cv_cpu_have_bmi2_ext" = yes; then
- SIMD_CFLAGS="$SIMD_CFLAGS -mbmi2"
- AC_DEFINE(HAVE_BMI2,1,[Define to 1 if you support BMI2 (Bit Manipulation Instruction set 2)])
- fi
-
- fi
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ # Test for functionality with the -mpopcnt compiler flag
+ AC_MSG_CHECKING(for __builtin_clz)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[]],
+ [[return (__builtin_clz(0x1u) == 31) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE([HAVE_BUILTIN_CLZ],[1],[Define to 1 if __builtin_clz works.])],
+ [AC_MSG_RESULT(no)])
+
+ AC_MSG_CHECKING(for __builtin_ctz)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[]],
+ [[return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE([HAVE_BUILTIN_CTZ],[1],[Define to 1 if __builtin_ctz works.])],
+ [AC_MSG_RESULT(no)])
+
+ AC_MSG_CHECKING(for __builtin_popcount)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[]],
+ [[return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE([HAVE_BUILTIN_POPCOUNT],[1],[Define to 1 if __builtin_popcount works])],
+ [AC_MSG_RESULT(no)])
+ fi
fi
fi
+ if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mabm"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_abm_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_abm_ext" != xyes; then
+ AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
+ else
+ CFLAGS=$TEST_CFLAGS
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
+ [ax_cv_link_abm=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_abm" != xyes; then
+ AC_MSG_WARN([Your compiler supports -mabm but not your linker])
+ else
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ # Test for functionality with the -mabm compiler flag
+ AC_MSG_CHECKING(for _popcnt32 support)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[#include <immintrin.h>]],
+ [[return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE(HAVE_POPCNT,1,[Define to 1 if you support Intel intrinsic _popcnt instruction])],
+ [AC_MSG_RESULT(no)])
+
+ AC_MSG_CHECKING(for _lzcnt support)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[#include <immintrin.h>]],
+ [[return (_lzcnt_u32(0x0fffffffu) == 4) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE(HAVE_LZCNT,1,[Define to 1 if you support Intel intrinsic _lzcnt instruction])],
+ [AC_MSG_RESULT(no)])
+ fi
+ fi
+ fi
- if test "$ax_cv_cpu_have_avx2_ext" = yes; then
- AX_CHECK_COMPILE_FLAG(-mavx2, [ax_cv_compile_avx2_ext=yes], [ax_cv_ext_compile_problem=yes])
- if test x"$ax_cv_compile_avx2_ext" != x"yes"; then
+ if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mbmi"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_bmi_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_bmi_ext" != xyes; then
+ AC_MSG_WARN([Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?])
+ else
+ CFLAGS=$TEST_CFLAGS
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
+ [ax_cv_link_bmi=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_bmi" != xyes; then
+ AC_MSG_WARN([Your compiler supports -mbmi but not your linker])
+ else
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ # Test for functionality with the -mbmi compiler flag
+ AC_MSG_CHECKING(for _tzcnt support)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[#include <immintrin.h>]],
+ [[return (_tzcnt_u32(0xfffffff0u) == 4) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE(HAVE_TZCNT,1,[Define to 1 if you support Intel intrinsic _tzcnt instruction])],
+ [AC_MSG_RESULT(no)])
+ fi
+ fi
+ fi
+
+ if test x"$ax_cv_cpu_has_avx2_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-march=core-avx2"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx2"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx2"
+ SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx2"
+ SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx2"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_avx2_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_avx2_ext" != xyes; then
AC_MSG_WARN([Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?])
else
+ CFLAGS=$TEST_CFLAGS
AC_MSG_CHECKING(for immintrin.h header file)
- CFLAGS=-mavx2
AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <immintrin.h>])],
[ax_cv_link_immintrin_h=yes],
[ax_cv_ext_linker_problem=yes])
- if test x"$ax_cv_link_immintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_immintrin_h" != xyes; then
AC_MSG_RESULT([no])
AC_MSG_WARN([Your compiler supports AVX2 instructions but not your linker.])
else
AC_MSG_RESULT([yes])
- SIMD_CFLAGS="$SIMD_CFLAGS -mavx2"
- AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions])
+ ax_make_avx2=yes
+ SIMD_AVX2_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions]) -- Defines run-type
+ fi
+ fi
+ fi
- fi
+ if test x"$ax_cv_cpu_has_bmi2_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_AVX2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mbmi2"
+ fi
+ AX_CHECK_COMPILE_FLAG([$TEST_CFLAGS], [ax_cv_compile_bmi2_ext=yes], [ax_cv_ext_compile_problem=yes])
+ if test x"$ax_cv_compile_bmi2_ext" != xyes; then
+ AC_MSG_WARN([Your CPU supports BMI2 instructions but not your compiler. Can you try another compiler or update yours?])
+ else
+ CFLAGS=$TEST_CFLAGS
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([])],
+ [ax_cv_link_bmi2=yes],
+ [ax_cv_ext_linker_problem=yes])
+ if test x"$ax_cv_link_bmi2" != xyes; then
+ AC_MSG_WARN([Your compiler supports -mbmi2 but not your linker. Can you try another linker or update yours?])
+ else
+ SIMD_AVX2_CFLAGS=$CFLAGS
+ AC_MSG_CHECKING(for _pext support)
+ AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([[#include <immintrin.h>]],
+ [[return (_pext_u32(0x01234567u,0x0f33aa55) == 0x00001b0b) ? 0 : 9;]])],
+ [AC_MSG_RESULT(yes)
+ AC_DEFINE(HAVE_PEXT,1,[Define to 1 if you support Intel intrinsic _pext instruction])],
+ [AC_MSG_RESULT(no)])
+ fi
fi
fi
- ;;
+ ;;
esac
CFLAGS=$CFLAGS_ORIG
- AC_SUBST(SIMD_CFLAGS)
+ AC_SUBST(SIMD_SSE2_CFLAGS)
+ AC_SUBST(SIMD_SSSE3_CFLAGS)
+ AC_SUBST(SIMD_SSE4_1_CFLAGS)
+ AC_SUBST(SIMD_SSE4_2_CFLAGS)
+ AC_SUBST(SIMD_AVX2_CFLAGS)
+
])
+
diff --git a/config/builtin-popcount.m4 b/config/builtin-popcount.m4
deleted file mode 100644
index b0e1825..0000000
--- a/config/builtin-popcount.m4
+++ /dev/null
@@ -1,58 +0,0 @@
-
-AC_DEFUN([ACX_BUILTIN_POPCOUNT], [
-AC_REQUIRE([AC_CANONICAL_HOST])
-AC_LANG_SAVE
-AC_LANG(C)
-
-CFLAGS_ORIG=$CFLAGS
-CFLAGS="$CFLAGS -mpopcnt"
-
-AC_MSG_CHECKING(whether -mpopcnt compiler flag works)
-AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[#include <stdio.h>
-#include <stdlib.h>]],
- [[unsigned int x = rand();
-printf("%08X ",x);
-printf("clz=%d ",__builtin_clz(x));
-printf("ctz=%d ",__builtin_ctz(x));
-printf("popcount=%d ",__builtin_popcount(x));
-]])],
- [AC_MSG_RESULT(yes)
- acx_mpopcnt_ok=yes],
- [AC_MSG_RESULT(no)])
-
-if test "x$acx_mpopcnt_ok" != xyes; then
- CFLAGS=$CFLAGS_ORIG
-fi
-
-# Test for __builtin functions with or without the -mpopcnt compiler flag
-AC_MSG_CHECKING(for __builtin_popcount)
-AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[]],
- [[return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;]])],
- [AC_MSG_RESULT(yes)
- AC_DEFINE([HAVE_BUILTIN_POPCOUNT],[1],[Define to 1 if __builtin_popcount works.])],
- [AC_MSG_RESULT(no)])
-
-AC_MSG_CHECKING(for __builtin_clz)
-AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[]],
- [[return (__builtin_clz(0x1u) == 31) ? 0 : 9;]])],
- [AC_MSG_RESULT(yes)
- AC_DEFINE([HAVE_BUILTIN_CLZ],[1],[Define to 1 if __builtin_clz works.])],
- [AC_MSG_RESULT(no)])
-
-AC_MSG_CHECKING(for __builtin_ctz)
-AC_RUN_IFELSE(
- [AC_LANG_PROGRAM([[]],
- [[return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;]])],
- [AC_MSG_RESULT(yes)
- AC_DEFINE([HAVE_BUILTIN_CTZ],[1],[Define to 1 if __builtin_ctz works.])],
- [AC_MSG_RESULT(no)])
-
-CFLAGS=$CFLAGS_ORIG
-
-AC_LANG_RESTORE
-])
-
-
diff --git a/configure b/configure
index a7ddd4a..9e5f972 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.63 for gmap 2015-12-31.
+# Generated by GNU Autoconf 2.63 for gmap 2016-04-04.
#
# Report bugs to <Thomas Wu <twu at gene.com>>.
#
@@ -745,8 +745,8 @@ SHELL=${CONFIG_SHELL-/bin/sh}
# Identity of this package.
PACKAGE_NAME='gmap'
PACKAGE_TARNAME='gmap'
-PACKAGE_VERSION='2015-12-31'
-PACKAGE_STRING='gmap 2015-12-31'
+PACKAGE_VERSION='2016-04-04'
+PACKAGE_STRING='gmap 2016-04-04'
PACKAGE_BUGREPORT='Thomas Wu <twu at gene.com>'
ac_unique_file="src/gmap.c"
@@ -794,8 +794,21 @@ BZLIB_LIBS
ZLIB_LIBS
MAX_READLENGTH
GMAPDB
-SIMD_CFLAGS
-POPCNT_CFLAGS
+MAKE_SSE2_FALSE
+MAKE_SSE2_TRUE
+MAKE_SSSE3_FALSE
+MAKE_SSSE3_TRUE
+MAKE_SSE4_1_FALSE
+MAKE_SSE4_1_TRUE
+MAKE_SSE4_2_FALSE
+MAKE_SSE4_2_TRUE
+MAKE_AVX2_FALSE
+MAKE_AVX2_TRUE
+SIMD_AVX2_CFLAGS
+SIMD_SSE4_2_CFLAGS
+SIMD_SSE4_1_CFLAGS
+SIMD_SSSE3_CFLAGS
+SIMD_SSE2_CFLAGS
ALLOCA
PTHREAD_CFLAGS
PTHREAD_LIBS
@@ -937,14 +950,6 @@ enable_mpi_file_input
enable_pthreads
enable_alloca
enable_mmap
-enable_builtin_popcount
-enable_sse2
-enable_ssse3
-enable_sse4_1
-enable_sse4_2
-enable_avx
-enable_avx2
-enable_simd
with_gmapdb
enable_zlib
enable_bzlib
@@ -1513,7 +1518,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures gmap 2015-12-31 to adapt to many kinds of systems.
+\`configure' configures gmap 2016-04-04 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1584,7 +1589,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of gmap 2015-12-31:";;
+ short | recursive ) echo "Configuration of gmap 2016-04-04:";;
esac
cat <<\_ACEOF
@@ -1610,24 +1615,6 @@ Optional Features:
allocation.
--enable-mmap Enable mmap (default=yes). Recommend that you do not
disable this unless absolutely necessary.
- --enable-builtin-popcount
- Enable -mpopcnt if it __builtin_popcount compiles
- and runs (default=yes). May want to disable if
- compiling on one machine and running on another.
- --enable-sse2 Enable sse2 simd commands if they compile and run
- (default=yes).
- --enable-ssse3 Enable ssse3 simd commands if they compile and run
- (default=yes). Requires that sse2 be enabled.
- --enable-sse4.1 Enable sse4.1 simd commands if they compile and run
- (default=yes). Requires that ssse3 be enabled.
- --enable-sse4.2 Enable sse4.2 simd commands if they compile and run
- (default=yes). Requires that sse4.1 be enabled.
- --enable-avx Enable avx simd commands if they compile and run
- (default=yes). Requires that sse4.2 be enabled.
- --enable-avx2 Enable avx2 simd commands if they compile and run
- (default=yes). Requires that avx be enabled.
- --enable-simd Enable simd commands in general if they compile and
- run (default=yes).
--enable-zlib Enable zlib support (option needed for uncompressing
gzip files) (default=yes)
--enable-bzlib Enable bzlib support (option needed for
@@ -1721,7 +1708,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-gmap configure 2015-12-31
+gmap configure 2016-04-04
generated by GNU Autoconf 2.63
Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
@@ -1735,7 +1722,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by gmap $as_me 2015-12-31, which was
+It was created by gmap $as_me 2016-04-04, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ $0 $@
@@ -2105,8 +2092,8 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu
{ $as_echo "$as_me:$LINENO: checking package version" >&5
$as_echo_n "checking package version... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: 2015-12-31" >&5
-$as_echo "2015-12-31" >&6; }
+{ $as_echo "$as_me:$LINENO: result: 2016-04-04" >&5
+$as_echo "2016-04-04" >&6; }
### Read defaults
@@ -4172,7 +4159,7 @@ fi
# Define the identity of the package.
PACKAGE='gmap'
- VERSION='2015-12-31'
+ VERSION='2016-04-04'
cat >>confdefs.h <<_ACEOF
@@ -5293,6 +5280,93 @@ if test "$am_t" != yes; then
fi
+{ $as_echo "$as_me:$LINENO: checking for C compiler vendor" >&5
+$as_echo_n "checking for C compiler vendor... " >&6; }
+if test "${ax_cv_c_compiler_vendor+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # note: don't check for gcc first since some other compilers define __GNUC__
+ vendors="intel: __ICC,__ECC,__INTEL_COMPILER
+ ibm: __xlc__,__xlC__,__IBMC__,__IBMCPP__
+ pathscale: __PATHCC__,__PATHSCALE__
+ clang: __clang__
+ cray: _CRAYC
+ fujitsu: __FUJITSU
+ gnu: __GNUC__
+ sun: __SUNPRO_C,__SUNPRO_CC
+ hp: __HP_cc,__HP_aCC
+ dec: __DECC,__DECCXX,__DECC_VER,__DECCXX_VER
+ borland: __BORLANDC__,__CODEGEARC__,__TURBOC__
+ comeau: __COMO__
+ kai: __KCC
+ lcc: __LCC__
+ sgi: __sgi,sgi
+ microsoft: _MSC_VER
+ metrowerks: __MWERKS__
+ watcom: __WATCOMC__
+ portland: __PGI
+ tcc: __TINYC__
+ unknown: UNKNOWN"
+ for ventest in $vendors; do
+ case $ventest in
+ *:) vendor=$ventest; continue ;;
+ *) vencpp="defined("`echo $ventest | sed 's/,/) || defined(/g'`")" ;;
+ esac
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ #if !($vencpp)
+ thisisanerror;
+ #endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+ ax_cv_c_compiler_vendor=`echo $vendor | cut -d: -f1`
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_c_compiler_vendor" >&5
+$as_echo "$ax_cv_c_compiler_vendor" >&6; }
+
+# AM_CONDITIONAL(INTEL_COMPILER,test "x$ax_cv_c_compiler_vendor" = xintel)
+
@@ -6281,13 +6355,13 @@ if test "${lt_cv_nm_interface+set}" = set; then
else
lt_cv_nm_interface="BSD nm"
echo "int some_variable = 0;" > conftest.$ac_ext
- (eval echo "\"\$as_me:6284: $ac_compile\"" >&5)
+ (eval echo "\"\$as_me:6358: $ac_compile\"" >&5)
(eval "$ac_compile" 2>conftest.err)
cat conftest.err >&5
- (eval echo "\"\$as_me:6287: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+ (eval echo "\"\$as_me:6361: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
(eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
cat conftest.err >&5
- (eval echo "\"\$as_me:6290: output\"" >&5)
+ (eval echo "\"\$as_me:6364: output\"" >&5)
cat conftest.out >&5
if $GREP 'External.*some_variable' conftest.out > /dev/null; then
lt_cv_nm_interface="MS dumpbin"
@@ -7492,7 +7566,7 @@ ia64-*-hpux*)
;;
*-*-irix6*)
# Find out which ABI we are using.
- echo '#line 7495 "configure"' > conftest.$ac_ext
+ echo '#line 7569 "configure"' > conftest.$ac_ext
if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
(eval $ac_compile) 2>&5
ac_status=$?
@@ -9349,11 +9423,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:9352: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9426: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:9356: \$? = $ac_status" >&5
+ echo "$as_me:9430: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -9688,11 +9762,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:9691: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9765: $lt_compile\"" >&5)
(eval "$lt_compile" 2>conftest.err)
ac_status=$?
cat conftest.err >&5
- echo "$as_me:9695: \$? = $ac_status" >&5
+ echo "$as_me:9769: \$? = $ac_status" >&5
if (exit $ac_status) && test -s "$ac_outfile"; then
# The compiler can only warn and ignore the option if not recognized
# So say no if there are warnings other than the usual output.
@@ -9793,11 +9867,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:9796: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9870: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:9800: \$? = $ac_status" >&5
+ echo "$as_me:9874: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -9848,11 +9922,11 @@ else
-e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
-e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
-e 's:$: $lt_compiler_flag:'`
- (eval echo "\"\$as_me:9851: $lt_compile\"" >&5)
+ (eval echo "\"\$as_me:9925: $lt_compile\"" >&5)
(eval "$lt_compile" 2>out/conftest.err)
ac_status=$?
cat out/conftest.err >&5
- echo "$as_me:9855: \$? = $ac_status" >&5
+ echo "$as_me:9929: \$? = $ac_status" >&5
if (exit $ac_status) && test -s out/conftest2.$ac_objext
then
# The compiler can only warn and ignore the option if not recognized
@@ -12651,7 +12725,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<_LT_EOF
-#line 12654 "configure"
+#line 12728 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -12747,7 +12821,7 @@ else
lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
lt_status=$lt_dlunknown
cat > conftest.$ac_ext <<_LT_EOF
-#line 12750 "configure"
+#line 12824 "configure"
#include "confdefs.h"
#if HAVE_DLFCN_H
@@ -19320,19 +19394,32 @@ _ACEOF
fi
-{ $as_echo "$as_me:$LINENO: checking for builtin popcount/clz/ctz features" >&5
-$as_echo_n "checking for builtin popcount/clz/ctz features... " >&6; }
-# Check whether --enable-builtin-popcount was given.
-if test "${enable_builtin_popcount+set}" = set; then
- enableval=$enable_builtin_popcount; answer="$enableval"
-else
- answer=""
-fi
+#AC_MSG_CHECKING(for builtin popcount/clz/ctz features)
+#AC_ARG_ENABLE([builtin-popcount],
+# AC_HELP_STRING([--enable-builtin-popcount],
+# [Enable -mpopcnt if it __builtin_popcount compiles and runs (default=yes). May want to disable if compiling on one machine and running on another.]),
+# [answer="$enableval"],
+# [answer=""])
+#case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ACX_BUILTIN_POPCOUNT
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled)
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ACX_BUILTIN_POPCOUNT
+# ;;
+#esac
+#if test x"$acx_mpopcnt_ok" = x"yes"; then
+# POPCNT_CFLAGS="$POPCNT_CFLAGS -mpopcnt"
+#fi
+#AC_SUBST(POPCNT_CFLAGS)
-case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
@@ -19343,236 +19430,325 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-CFLAGS_ORIG=$CFLAGS
-CFLAGS="$CFLAGS -mpopcnt"
-
-{ $as_echo "$as_me:$LINENO: checking whether -mpopcnt compiler flag works" >&5
-$as_echo_n "checking whether -mpopcnt compiler flag works... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
+{ $as_echo "$as_me:$LINENO: checking for bsr instruction in assembly" >&5
+$as_echo_n "checking for bsr instruction in assembly... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
-#include <stdlib.h>
+
int
main ()
{
-unsigned int x = rand();
-printf("%08X ",x);
-printf("clz=%d ",__builtin_clz(x));
-printf("ctz=%d ",__builtin_ctz(x));
-printf("popcount=%d ",__builtin_popcount(x));
-
+int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_compile") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
- acx_mpopcnt_ok=yes
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_ASM_BSR 1
+_ACEOF
+
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
+ { $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
-if test "x$acx_mpopcnt_ok" != xyes; then
- CFLAGS=$CFLAGS_ORIG
-fi
-# Test for __builtin functions with or without the -mpopcnt compiler flag
-{ $as_echo "$as_me:$LINENO: checking for __builtin_popcount" >&5
-$as_echo_n "checking for __builtin_popcount... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
+
+
+#AC_MSG_CHECKING(whether sse2 is enabled)
+#AC_ARG_ENABLE([sse2],
+# AC_HELP_STRING([--enable-sse2],
+# [Enable sse2 simd commands if they compile and run (default=yes).]),
+# [answer="$enableval"],
+# [answer=""])
+#case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_sse2_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_sse2_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_sse2_ext=yes
+# ;;
+#esac
+
+
+
+
+
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+ { $as_echo "$as_me:$LINENO: checking compiler is defective and requires an immediate in sse2 shift commands" >&5
+$as_echo_n "checking compiler is defective and requires an immediate in sse2 shift commands... " >&6; }
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <stdio.h>
+#include <stdlib.h>
+#include <emmintrin.h>
int
main ()
{
-return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;
+int nshift = rand() % 32;
+__m128i shifted;
+shifted = _mm_slli_epi32(_mm_set1_epi32(1),nshift);
+
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_compile") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BUILTIN_POPCOUNT 1
-_ACEOF
-
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ax_cv_sse2_shift_defect=no
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+ ax_cv_sse2_shift_defect=yes
fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ { $as_echo "$as_me:$LINENO: result: $ax_cv_sse2_shift_defect" >&5
+$as_echo "$ax_cv_sse2_shift_defect" >&6; }
+ if test "$ax_cv_sse2_shift_defect" = yes; then
-{ $as_echo "$as_me:$LINENO: checking for __builtin_clz" >&5
-$as_echo_n "checking for __builtin_clz... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
+cat >>confdefs.h <<\_ACEOF
+#define DEFECTIVE_SSE2_COMPILER 1
_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-int
-main ()
-{
-return (__builtin_clz(0x1u) == 31) ? 0 : 9;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
+ fi
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BUILTIN_CLZ 1
-_ACEOF
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
+#AC_MSG_CHECKING(whether ssse3 is enabled)
+#AC_ARG_ENABLE([ssse3],
+# AC_HELP_STRING([--enable-ssse3],
+# [Enable ssse3 simd commands if they compile and run (default=yes). Requires that sse2 be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_sse2_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled sse2])
+# ax_cv_want_ssse3_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_ssse3_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_ssse3_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_ssse3_ext=yes
+# ;;
+# esac
+#fi
-{ $as_echo "$as_me:$LINENO: checking for __builtin_ctz" >&5
-$as_echo_n "checking for __builtin_ctz... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+
+
+#AC_MSG_CHECKING(whether sse4.1 is enabled)
+#AC_ARG_ENABLE([sse4.1],
+# AC_HELP_STRING([--enable-sse4.1],
+# [Enable sse4.1 simd commands if they compile and run (default=yes). Requires that ssse3 be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_ssse3_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled ssse3])
+# ax_cv_want_sse41_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_sse41_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_sse41_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_sse41_ext=yes
+# ;;
+# esac
+#fi
+
+
+#AC_MSG_CHECKING(whether sse4.2 is enabled)
+#AC_ARG_ENABLE([sse4.2],
+# AC_HELP_STRING([--enable-sse4.2],
+# [Enable sse4.2 simd commands if they compile and run (default=yes). Requires that sse4.1 be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_sse41_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled sse4.1])
+# ax_cv_want_sse42_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_sse42_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_sse42_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_sse42_ext=yes
+# ;;
+# esac
+#fi
+
+
+#AC_MSG_CHECKING(whether avx2 is enabled)
+#AC_ARG_ENABLE([avx2],
+# AC_HELP_STRING([--enable-avx2],
+# [Enable avx2 simd commands if they compile and run (default=yes). Requires that avx be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_avx_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled avx])
+# ax_cv_want_avx2_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_avx2_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_avx2_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_avx2_ext=yes
+# ;;
+# esac
+#fi
+
+
+
+#AC_MSG_CHECKING(for whether simd is enabled)
+#AC_ARG_ENABLE([simd],
+# AC_HELP_STRING([--enable-simd],
+# [Enable simd commands in general if they compile and run (default=yes).]),
+# [answer="$enableval"],
+# [answer=""])
+#case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# AX_EXT # Sets various SIMD_xxx_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX2
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled)
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# AX_EXT # Sets various SIMD_xxx_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX2
+# ;;
+#esac
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+{ $as_echo "$as_me:$LINENO: checking for x86 cpuid output" >&5
+$as_echo_n "checking for x86 cpuid output... " >&6; }
+if test "${ax_cv_gcc_x86_cpuid_+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ ax_cv_gcc_x86_cpuid_=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -19580,11 +19756,21 @@ _ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <stdio.h>
int
main ()
{
-return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;
+
+ int op = , eax, ebx, ecx, edx;
+ FILE *f;
+ __asm__("cpuid"
+ : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
+ : "a" (op));
+ f = fopen("conftest_cpuid", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
+ fclose(f);
+ return 0;
+
;
return 0;
}
@@ -19611,30 +19797,23 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BUILTIN_CTZ 1
-_ACEOF
-
+ ax_cv_gcc_x86_cpuid_=`cat conftest_cpuid`; rm -f conftest_cpuid
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
+ax_cv_gcc_x86_cpuid_=unknown; rm -f conftest_cpuid
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
-
-CFLAGS=$CFLAGS_ORIG
-
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_" >&5
+$as_echo "$ax_cv_gcc_x86_cpuid_" >&6; }
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -19642,18 +19821,6 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled" >&5
-$as_echo "disabled" >&6; }
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
-
-
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
@@ -19661,20 +19828,13 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-CFLAGS_ORIG=$CFLAGS
-CFLAGS="$CFLAGS -mpopcnt"
-
-{ $as_echo "$as_me:$LINENO: checking whether -mpopcnt compiler flag works" >&5
-$as_echo_n "checking whether -mpopcnt compiler flag works... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+{ $as_echo "$as_me:$LINENO: checking for x86-AVX xgetbv output" >&5
+$as_echo_n "checking for x86-AVX xgetbv output... " >&6; }
+if test "${ax_cv_gcc_x86_avx_xgetbv_+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ ax_cv_gcc_x86_avx_xgetbv_=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -19683,15 +19843,20 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
#include <stdio.h>
-#include <stdlib.h>
int
main ()
{
-unsigned int x = rand();
-printf("%08X ",x);
-printf("clz=%d ",__builtin_clz(x));
-printf("ctz=%d ",__builtin_ctz(x));
-printf("popcount=%d ",__builtin_popcount(x));
+
+ int op = , eax, edx;
+ FILE *f;
+ /* Opcodes for xgetbv */
+ __asm__(".byte 0x0f, 0x01, 0xd0"
+ : "=a" (eax), "=d" (edx)
+ : "c" (op));
+ f = fopen("conftest_xgetbv", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x\n", eax, edx);
+ fclose(f);
+ return 0;
;
return 0;
@@ -19719,40 +19884,63 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- acx_mpopcnt_ok=yes
+ ax_cv_gcc_x86_avx_xgetbv_=`cat conftest_xgetbv`; rm -f conftest_xgetbv
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
+ax_cv_gcc_x86_avx_xgetbv_=unknown; rm -f conftest_xgetbv
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_avx_xgetbv_" >&5
+$as_echo "$ax_cv_gcc_x86_avx_xgetbv_" >&6; }
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+
+
+
+ CFLAGS_ORIG=$CFLAGS
+
+ case $host_cpu in
+ powerpc*)
+ { $as_echo "$as_me:$LINENO: checking whether altivec is enabled and supported" >&5
+$as_echo_n "checking whether altivec is enabled and supported... " >&6; }
+if test "${ax_cv_cpu_has_altivec_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then
+ if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then
+ ax_cv_cpu_has_altivec_ext=yes
+ fi
+ fi
-if test "x$acx_mpopcnt_ok" != xyes; then
- CFLAGS=$CFLAGS_ORIG
fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_altivec_ext" >&5
+$as_echo "$ax_cv_cpu_has_altivec_ext" >&6; }
-# Test for __builtin functions with or without the -mpopcnt compiler flag
-{ $as_echo "$as_me:$LINENO: checking for __builtin_popcount" >&5
-$as_echo_n "checking for __builtin_popcount... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+ if test x"$ax_cv_cpu_has_altivec_ext" = xyes; then
+# AC_DEFINE(HAVE_ALTIVEC,1,[Define to 1 if you support Altivec instructions]) -- Not used
+ { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -faltivec" >&5
+$as_echo_n "checking whether C compiler accepts -faltivec... " >&6; }
+if test "${ax_cv_check_cflags___faltivec+set}" = set; then
+ $as_echo_n "(cached) " >&6
else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -faltivec"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -19763,65 +19951,71 @@ cat >>conftest.$ac_ext <<_ACEOF
int
main ()
{
-return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;
+
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_compile") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BUILTIN_POPCOUNT 1
-_ACEOF
-
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ax_cv_check_cflags___faltivec=yes
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
+ ax_cv_check_cflags___faltivec=no
fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ CFLAGS=$ax_check_save_flags
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___faltivec" >&5
+$as_echo "$ax_cv_check_cflags___faltivec" >&6; }
+if test x"$ax_cv_check_cflags___faltivec" = xyes; then
+ SIMD_CFLAGS="$SIMD_CFLAGS -faltivec"
+else
+ :
fi
+ fi
+ ;;
-{ $as_echo "$as_me:$LINENO: checking for __builtin_clz" >&5
-$as_echo_n "checking for __builtin_clz... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+
+ i[3456]86*|x86_64*|amd64*)
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x00000001 output" >&5
+$as_echo_n "checking for x86 cpuid 0x00000001 output... " >&6; }
+if test "${ax_cv_gcc_x86_cpuid_0x00000001+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ ax_cv_gcc_x86_cpuid_0x00000001=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -19829,11 +20023,21 @@ _ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <stdio.h>
int
main ()
{
-return (__builtin_clz(0x1u) == 31) ? 0 : 9;
+
+ int op = 0x00000001, eax, ebx, ecx, edx;
+ FILE *f;
+ __asm__("cpuid"
+ : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
+ : "a" (op));
+ f = fopen("conftest_cpuid", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
+ fclose(f);
+ return 0;
+
;
return 0;
}
@@ -19860,38 +20064,173 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BUILTIN_CLZ 1
-_ACEOF
-
+ ax_cv_gcc_x86_cpuid_0x00000001=`cat conftest_cpuid`; rm -f conftest_cpuid
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
+ax_cv_gcc_x86_cpuid_0x00000001=unknown; rm -f conftest_cpuid
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000001" >&5
+$as_echo "$ax_cv_gcc_x86_cpuid_0x00000001" >&6; }
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:$LINENO: checking for __builtin_ctz" >&5
-$as_echo_n "checking for __builtin_ctz... " >&6; }
-if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+
+ ecx=0
+ edx=0
+ if test "$ax_cv_gcc_x86_cpuid_0x00000001" != "unknown";
+ then
+ ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 3`
+ edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
+ fi
+
+ { $as_echo "$as_me:$LINENO: checking whether mmx is enabled and supported by CPU" >&5
+$as_echo_n "checking whether mmx is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_mmx_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_mmx_ext=no
+ if test "$((0x$edx>>23&0x01))" = 1; then
+ ax_cv_cpu_has_mmx_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_mmx_ext" >&5
+$as_echo "$ax_cv_cpu_has_mmx_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether sse is enabled and supported by CPU" >&5
+$as_echo_n "checking whether sse is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_sse_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_sse_ext=no
+ if test "$((0x$edx>>25&0x01))" = 1; then
+ ax_cv_cpu_has_sse_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_sse_ext" >&5
+$as_echo "$ax_cv_cpu_has_sse_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether sse2 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether sse2 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_sse2_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_sse2_ext=no
+ if test "$((0x$edx>>26&0x01))" = 1; then
+ ax_cv_cpu_has_sse2_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_sse2_ext" >&5
+$as_echo "$ax_cv_cpu_has_sse2_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether sse3 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether sse3 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_sse3_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_sse3_ext=no
+ if test "$((0x$ecx&0x01))" = 1; then
+ ax_cv_cpu_has_sse3_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_sse3_ext" >&5
+$as_echo "$ax_cv_cpu_has_sse3_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether ssse3 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether ssse3 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_ssse3_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_ssse3_ext=no
+ if test "$((0x$ecx>>9&0x01))" = 1; then
+ ax_cv_cpu_has_ssse3_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_ssse3_ext" >&5
+$as_echo "$ax_cv_cpu_has_ssse3_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether sse4.1 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether sse4.1 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_sse41_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_sse41_ext=no
+ if test "$((0x$ecx>>19&0x01))" = 1; then
+ ax_cv_cpu_has_sse41_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_sse41_ext" >&5
+$as_echo "$ax_cv_cpu_has_sse41_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether sse4.2 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether sse4.2 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_sse42_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_sse42_ext=no
+ if test "$((0x$ecx>>20&0x01))" = 1; then
+ ax_cv_cpu_has_sse42_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_sse42_ext" >&5
+$as_echo "$ax_cv_cpu_has_sse42_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether avx is enabled and supported by CPU" >&5
+$as_echo_n "checking whether avx is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_avx_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_avx_ext=no
+ if test "$((0x$ecx>>28&0x01))" = 1; then
+ ax_cv_cpu_has_avx_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_avx_ext" >&5
+$as_echo "$ax_cv_cpu_has_avx_ext" >&6; }
+
+ if test x"$ax_cv_cpu_has_avx_ext" = xyes; then
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+{ $as_echo "$as_me:$LINENO: checking for x86-AVX xgetbv 0x00000000 output" >&5
+$as_echo_n "checking for x86-AVX xgetbv 0x00000000 output... " >&6; }
+if test "${ax_cv_gcc_x86_avx_xgetbv_0x00000000+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -19899,11 +20238,22 @@ _ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <stdio.h>
int
main ()
{
-return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;
+
+ int op = 0x00000000, eax, edx;
+ FILE *f;
+ /* Opcodes for xgetbv */
+ __asm__(".byte 0x0f, 0x01, 0xd0"
+ : "=a" (eax), "=d" (edx)
+ : "c" (op));
+ f = fopen("conftest_xgetbv", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x\n", eax, edx);
+ fclose(f);
+ return 0;
+
;
return 0;
}
@@ -19930,30 +20280,23 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BUILTIN_CTZ 1
-_ACEOF
-
+ ax_cv_gcc_x86_avx_xgetbv_0x00000000=`cat conftest_xgetbv`; rm -f conftest_xgetbv
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
( exit $ac_status )
-{ $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
+ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown; rm -f conftest_xgetbv
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
-
-CFLAGS=$CFLAGS_ORIG
-
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&5
+$as_echo "$ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&6; }
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -19961,12 +20304,50 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
- ;;
-esac
-if test x"$acx_mpopcnt_ok" = x"yes"; then
- POPCNT_CFLAGS="$POPCNT_CFLAGS -mpopcnt"
+
+ xgetbv_eax="0"
+ if test x"$ax_cv_gcc_x86_avx_xgetbv_0x00000000" != x"unknown"; then
+ xgetbv_eax=`echo $ax_cv_gcc_x86_avx_xgetbv_0x00000000 | cut -d ":" -f 1`
+ fi
+
+ { $as_echo "$as_me:$LINENO: checking whether avx is supported by operating system" >&5
+$as_echo_n "checking whether avx is supported by operating system... " >&6; }
+if test "${ax_cv_have_avx_os_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_have_avx_os_ext=no
+
+ if test "$((0x$ecx>>27&0x01))" = 1; then
+ if test "$((0x$xgetbv_eax&0x6))" = 6; then
+ ax_cv_have_avx_os_ext=yes
+ fi
+ fi
+
fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx_os_ext" >&5
+$as_echo "$ax_cv_have_avx_os_ext" >&6; }
+ if test x"$ax_cv_have_avx_os_ext" = x"no"; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your processor supports AVX, but your operating system doesn't" >&5
+$as_echo "$as_me: WARNING: Your processor supports AVX, but your operating system doesn't" >&2;}
+ fi
+ fi
+
+
+ { $as_echo "$as_me:$LINENO: checking whether popcnt is enabled and supported by CPU" >&5
+$as_echo_n "checking whether popcnt is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_popcnt_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_popcnt_ext=no
+ if test "$((0x$ecx>>23&0x01))" = 1; then
+ ax_cv_cpu_has_popcnt_ext=yes
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_popcnt_ext" >&5
+$as_echo "$ax_cv_cpu_has_popcnt_ext" >&6; }
@@ -19976,169 +20357,78 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for bsr instruction in assembly" >&5
-$as_echo_n "checking for bsr instruction in assembly... " >&6; }
-cat >conftest.$ac_ext <<_ACEOF
+{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x80000001 output" >&5
+$as_echo_n "checking for x86 cpuid 0x80000001 output... " >&6; }
+if test "${ax_cv_gcc_x86_cpuid_0x80000001+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ ax_cv_gcc_x86_cpuid_0x80000001=unknown
+else
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <stdio.h>
int
main ()
{
-int msb; unsigned int x = rand(); asm("bsr %1,%0" : "=r"(msb) : "r"(x));
+
+ int op = 0x80000001, eax, ebx, ecx, edx;
+ FILE *f;
+ __asm__("cpuid"
+ : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
+ : "a" (op));
+ f = fopen("conftest_cpuid", "w"); if (!f) return 1;
+ fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
+ fclose(f);
+ return 0;
+
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
+ (eval "$ac_link") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_ASM_BSR 1
-_ACEOF
-
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-
-
-{ $as_echo "$as_me:$LINENO: checking whether sse2 is enabled" >&5
-$as_echo_n "checking whether sse2 is enabled... " >&6; }
-# Check whether --enable-sse2 was given.
-if test "${enable_sse2+set}" = set; then
- enableval=$enable_sse2; answer="$enableval"
-else
- answer=""
-fi
-
-case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
- ax_cv_want_sse2_ext=yes
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled by user" >&5
-$as_echo "disabled by user" >&6; }
- ax_cv_want_sse2_ext=no
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
- ax_cv_want_sse2_ext=yes
- ;;
-esac
-
-ax_cv_sse2_shift_defect=no
-if test "$ax_cv_want_sse2_ext" = yes; then
-
-
-
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
- { $as_echo "$as_me:$LINENO: checking compiler is defective and requires an immediate in sse2 shift commands" >&5
-$as_echo_n "checking compiler is defective and requires an immediate in sse2 shift commands... " >&6; }
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <stdio.h>
-#include <stdlib.h>
-#include <emmintrin.h>
-int
-main ()
-{
-int nshift = rand() % 32;
-__m128i shifted;
-shifted = _mm_slli_epi32(_mm_set1_epi32(1),nshift);
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
+ (eval "$ac_try") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_sse2_shift_defect=no
+ (exit $ac_status); }; }; then
+ ax_cv_gcc_x86_cpuid_0x80000001=`cat conftest_cpuid`; rm -f conftest_cpuid
else
- $as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_sse2_shift_defect=yes
+( exit $ac_status )
+ax_cv_gcc_x86_cpuid_0x80000001=unknown; rm -f conftest_cpuid
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-
- { $as_echo "$as_me:$LINENO: result: $ax_cv_sse2_shift_defect" >&5
-$as_echo "$ax_cv_sse2_shift_defect" >&6; }
- if test "$ax_cv_sse2_shift_defect" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define DEFECTIVE_SSE2_COMPILER 1
-_ACEOF
-
- fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x80000001" >&5
+$as_echo "$ax_cv_gcc_x86_cpuid_0x80000001" >&6; }
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -20146,203 +20436,25 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-fi
-
-
-{ $as_echo "$as_me:$LINENO: checking whether ssse3 is enabled" >&5
-$as_echo_n "checking whether ssse3 is enabled... " >&6; }
-# Check whether --enable-ssse3 was given.
-if test "${enable_ssse3+set}" = set; then
- enableval=$enable_ssse3; answer="$enableval"
-else
- answer=""
-fi
-
-if test "$ax_cv_want_sse2_ext" = no; then
- { $as_echo "$as_me:$LINENO: result: disabled because the user disabled sse2" >&5
-$as_echo "disabled because the user disabled sse2" >&6; }
- ax_cv_want_ssse3_ext=no
-else
- case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
- ax_cv_want_ssse3_ext=yes
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled by user" >&5
-$as_echo "disabled by user" >&6; }
- ax_cv_want_ssse3_ext=no
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
- ax_cv_want_ssse3_ext=yes
- ;;
- esac
-fi
-
-
-
-{ $as_echo "$as_me:$LINENO: checking whether sse4.1 is enabled" >&5
-$as_echo_n "checking whether sse4.1 is enabled... " >&6; }
-# Check whether --enable-sse4.1 was given.
-if test "${enable_sse4_1+set}" = set; then
- enableval=$enable_sse4_1; answer="$enableval"
-else
- answer=""
-fi
-
-if test "$ax_cv_want_ssse3_ext" = no; then
- { $as_echo "$as_me:$LINENO: result: disabled because the user disabled ssse3" >&5
-$as_echo "disabled because the user disabled ssse3" >&6; }
- ax_cv_want_sse41_ext=no
-else
- case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
- ax_cv_want_sse41_ext=yes
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled by user" >&5
-$as_echo "disabled by user" >&6; }
- ax_cv_want_sse41_ext=no
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
- ax_cv_want_sse41_ext=yes
- ;;
- esac
-fi
-
-
-{ $as_echo "$as_me:$LINENO: checking whether sse4.2 is enabled" >&5
-$as_echo_n "checking whether sse4.2 is enabled... " >&6; }
-# Check whether --enable-sse4.2 was given.
-if test "${enable_sse4_2+set}" = set; then
- enableval=$enable_sse4_2; answer="$enableval"
-else
- answer=""
-fi
-
-if test "$ax_cv_want_sse41_ext" = no; then
- { $as_echo "$as_me:$LINENO: result: disabled because the user disabled sse4.1" >&5
-$as_echo "disabled because the user disabled sse4.1" >&6; }
- ax_cv_want_sse42_ext=no
-else
- case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
- ax_cv_want_sse42_ext=yes
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled by user" >&5
-$as_echo "disabled by user" >&6; }
- ax_cv_want_sse42_ext=no
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
- ax_cv_want_sse42_ext=yes
- ;;
- esac
-fi
-
-
-{ $as_echo "$as_me:$LINENO: checking whether avx is enabled" >&5
-$as_echo_n "checking whether avx is enabled... " >&6; }
-# Check whether --enable-avx was given.
-if test "${enable_avx+set}" = set; then
- enableval=$enable_avx; answer="$enableval"
-else
- answer=""
-fi
-
-if test "$ax_cv_want_sse42_ext" = no; then
- { $as_echo "$as_me:$LINENO: result: disabled because the user disabled sse4.2" >&5
-$as_echo "disabled because the user disabled sse4.2" >&6; }
- ax_cv_want_avx_ext=no
-else
- case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
- ax_cv_want_avx_ext=yes
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled by user" >&5
-$as_echo "disabled by user" >&6; }
- ax_cv_want_avx_ext=no
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
- ax_cv_want_avx_ext=yes
- ;;
- esac
-fi
-
-
-{ $as_echo "$as_me:$LINENO: checking whether avx2 is enabled" >&5
-$as_echo_n "checking whether avx2 is enabled... " >&6; }
-# Check whether --enable-avx2 was given.
-if test "${enable_avx2+set}" = set; then
- enableval=$enable_avx2; answer="$enableval"
-else
- answer=""
-fi
+ ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
+ edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
-if test "$ax_cv_want_avx_ext" = no; then
- { $as_echo "$as_me:$LINENO: result: disabled because the user disabled avx" >&5
-$as_echo "disabled because the user disabled avx" >&6; }
- ax_cv_want_avx2_ext=no
+ { $as_echo "$as_me:$LINENO: checking whether lzcnt is enabled and supported by CPU" >&5
+$as_echo_n "checking whether lzcnt is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_lzcnt_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
else
- case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
- ax_cv_want_avx2_ext=yes
- ;;
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled by user" >&5
-$as_echo "disabled by user" >&6; }
- ax_cv_want_avx2_ext=no
- ;;
+ ax_cv_cpu_has_lzcnt_ext=no
+ if test "$((0x$ecx>>5&0x01))" = 1; then
+ ax_cv_cpu_has_lzcnt_ext=yes
+ fi
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
- ax_cv_want_avx2_ext=yes
- ;;
- esac
fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_lzcnt_ext" >&5
+$as_echo "$ax_cv_cpu_has_lzcnt_ext" >&6; }
-{ $as_echo "$as_me:$LINENO: checking whether simd is enabled" >&5
-$as_echo_n "checking whether simd is enabled... " >&6; }
-# Check whether --enable-simd was given.
-if test "${enable_simd+set}" = set; then
- enableval=$enable_simd; answer="$enableval"
-else
- answer=""
-fi
-
-case x"$answer" in
- xyes)
- { $as_echo "$as_me:$LINENO: result: enabled" >&5
-$as_echo "enabled" >&6; }
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
@@ -20350,13 +20462,13 @@ ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid output" >&5
-$as_echo_n "checking for x86 cpuid output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_+set}" = set; then
+{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x00000007 output" >&5
+$as_echo_n "checking for x86 cpuid 0x00000007 output... " >&6; }
+if test "${ax_cv_gcc_x86_cpuid_0x00000007+set}" = set; then
$as_echo_n "(cached) " >&6
else
if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_=unknown
+ ax_cv_gcc_x86_cpuid_0x00000007=unknown
else
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
@@ -20369,7 +20481,7 @@ int
main ()
{
- int op = , eax, ebx, ecx, edx;
+ int op = 0x00000007, eax, ebx, ecx, edx;
FILE *f;
__asm__("cpuid"
: "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
@@ -20405,14 +20517,14 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_=`cat conftest_cpuid`; rm -f conftest_cpuid
+ ax_cv_gcc_x86_cpuid_0x00000007=`cat conftest_cpuid`; rm -f conftest_cpuid
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
( exit $ac_status )
-ax_cv_gcc_x86_cpuid_=unknown; rm -f conftest_cpuid
+ax_cv_gcc_x86_cpuid_0x00000007=unknown; rm -f conftest_cpuid
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
@@ -20420,8 +20532,8 @@ fi
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_" >&6; }
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000007" >&5
+$as_echo "$ax_cv_gcc_x86_cpuid_0x00000007" >&6; }
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -20429,130 +20541,205 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ ebx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 2`
+ ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 3`
+ edx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 4`
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ { $as_echo "$as_me:$LINENO: checking whether avx2 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether avx2 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_avx2_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
-{ $as_echo "$as_me:$LINENO: checking for x86-AVX xgetbv output" >&5
-$as_echo_n "checking for x86-AVX xgetbv output... " >&6; }
-if test "${ax_cv_gcc_x86_avx_xgetbv_+set}" = set; then
+ ax_cv_cpu_has_avx2_ext=no
+ if test "$((0x$ebx>>5&0x01))" = 1; then
+ ax_cv_cpu_has_avx2_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_avx2_ext" >&5
+$as_echo "$ax_cv_cpu_has_avx2_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether bmi1 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether bmi1 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_bmi1_ext+set}" = set; then
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_avx_xgetbv_=unknown
+
+ ax_cv_cpu_has_bmi1_ext=no
+ if test "$((0x$ebx>>3&0x01))" = 1; then
+ ax_cv_cpu_has_bmi1_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_bmi1_ext" >&5
+$as_echo "$ax_cv_cpu_has_bmi1_ext" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether bmi2 is enabled and supported by CPU" >&5
+$as_echo_n "checking whether bmi2 is enabled and supported by CPU... " >&6; }
+if test "${ax_cv_cpu_has_bmi2_ext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_cv_cpu_has_bmi2_ext=no
+ if test "$((0x$ebx>>8&0x01))" = 1; then
+ ax_cv_cpu_has_bmi2_ext=yes
+ fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_has_bmi2_ext" >&5
+$as_echo "$ax_cv_cpu_has_bmi2_ext" >&6; }
+
+
+ # AX_CHECK_COMPILE_FLAG tests CFLAGS EXTRA-FLAGS FLAG
+
+ if test x"$ax_cv_cpu_has_mmx_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-mmmx
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+
int
main ()
{
- int op = , eax, edx;
- FILE *f;
- /* Opcodes for xgetbv */
- __asm__(".byte 0x0f, 0x01, 0xd0"
- : "=a" (eax), "=d" (edx)
- : "c" (op));
- f = fopen("conftest_xgetbv", "w"); if (!f) return 1;
- fprintf(f, "%x:%x\n", eax, edx);
- fclose(f);
- return 0;
-
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_compile") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_avx_xgetbv_=`cat conftest_xgetbv`; rm -f conftest_xgetbv
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_CACHEVAR=yes"
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-ax_cv_gcc_x86_avx_xgetbv_=unknown; rm -f conftest_xgetbv
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+ eval "$as_CACHEVAR=no"
fi
-
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ CFLAGS=$ax_check_save_flags
+fi
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_mmx_ext=yes
+else
+ ax_cv_ext_compile_problem=yes
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_avx_xgetbv_" >&5
-$as_echo "$ax_cv_gcc_x86_avx_xgetbv_" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-
- CFLAGS_ORIG=$CFLAGS
+ if test x"$ax_cv_compile_mmx_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports MMX instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports MMX instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for mmintrin.h header file" >&5
+$as_echo_n "checking for mmintrin.h header file... " >&6; }
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <mmintrin.h>
+int
+main ()
+{
- case $host_cpu in
- powerpc*)
- { $as_echo "$as_me:$LINENO: checking whether altivec is enabled and supported" >&5
-$as_echo_n "checking whether altivec is enabled and supported... " >&6; }
-if test "${ax_cv_cpu_have_altivec_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ax_cv_link_mmintrin_h=yes
else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
- if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then
- if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then
- ax_cv_cpu_have_altivec_ext=yes
- fi
- fi
-
+ ax_cv_ext_linker_problem=yes
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_altivec_ext" >&5
-$as_echo "$ax_cv_cpu_have_altivec_ext" >&6; }
- if test "$ax_cv_cpu_have_altivec_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_ALTIVEC 1
-_ACEOF
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_mmintrin_h" != xyes; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports MMX instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports MMX instructions but not your linker." >&2;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+# AC_DEFINE(HAVE_MMX,1,[Define to 1 if you support MMX instructions]) -- Not used
+ fi
+ fi
+ fi
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -faltivec" >&5
-$as_echo_n "checking whether C compiler accepts -faltivec... " >&6; }
-if test "${ax_cv_check_cflags___faltivec+set}" = set; then
+ if test x"$ax_cv_cpu_has_sse_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-msse
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -faltivec"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -20586,76 +20773,52 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___faltivec=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___faltivec=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___faltivec" >&5
-$as_echo "$ax_cv_check_cflags___faltivec" >&6; }
-if test x"$ax_cv_check_cflags___faltivec" = xyes; then
- SIMD_CFLAGS="$SIMD_CFLAGS -faltivec"
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_sse_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- fi
- ;;
-
-
- i[3456]86*|x86_64*|amd64*)
-
-
-
-
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x00000001 output" >&5
-$as_echo_n "checking for x86 cpuid 0x00000001 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x00000001+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_0x00000001=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
+ if test x"$ax_cv_compile_sse_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports SSE instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for xmmintrin.h header file" >&5
+$as_echo_n "checking for xmmintrin.h header file... " >&6; }
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+#include <xmmintrin.h>
int
main ()
{
- int op = 0x00000001, eax, ebx, ecx, edx;
- FILE *f;
- __asm__("cpuid"
- : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
- : "a" (op));
- f = fopen("conftest_cpuid", "w"); if (!f) return 1;
- fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
- fclose(f);
- return 0;
-
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
+rm -f conftest.$ac_objext conftest$ac_exeext
if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
@@ -20663,2029 +20826,11 @@ case "(($ac_try" in
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x00000001=`cat conftest_cpuid`; rm -f conftest_cpuid
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-( exit $ac_status )
-ax_cv_gcc_x86_cpuid_0x00000001=unknown; rm -f conftest_cpuid
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000001" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x00000001" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
- ecx=0
- edx=0
- if test "$ax_cv_gcc_x86_cpuid_0x00000001" != "unknown";
- then
- ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 3`
- edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
- fi
-
- { $as_echo "$as_me:$LINENO: checking whether mmx is enabled and supported by CPU" >&5
-$as_echo_n "checking whether mmx is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_mmx_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_mmx_ext=no
- if test "$((0x$edx>>23&0x01))" = 1; then
- ax_cv_cpu_have_mmx_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features mmx"
-
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_mmx_ext" >&5
-$as_echo "$ax_cv_cpu_have_mmx_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse_ext=no
- if test "$((0x$edx>>25&0x01))" = 1; then
- ax_cv_cpu_have_sse_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features sse"
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse2 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse2 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse2_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse2_ext=no
- if test "$((0x$edx>>26&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse2"
- if test "$ax_cv_want_sse2_ext" = yes; then
- ax_cv_cpu_have_sse2_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse2_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse2_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse3 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse3 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse3_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse3_ext=no
- if test "$((0x$ecx&0x01))" = 1; then
- ax_cv_cpu_have_sse3_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features sse3"
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse3_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse3_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether ssse3 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether ssse3 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_ssse3_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_ssse3_ext=no
- if test "$((0x$ecx>>9&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features ssse3"
- if test "$ax_cv_want_ssse3_ext" = yes; then
- ax_cv_cpu_have_ssse3_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_ssse3_ext" >&5
-$as_echo "$ax_cv_cpu_have_ssse3_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse4.1 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse4.1 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse41_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse41_ext=no
- if test "$((0x$ecx>>19&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse4.1"
- if test "$ax_cv_want_sse41_ext" = yes; then
- ax_cv_cpu_have_sse41_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse41_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse41_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse4.2 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse4.2 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse42_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse42_ext=no
- if test "$((0x$ecx>>20&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse4.2"
- if test "$ax_cv_want_sse42_ext" = yes; then
- ax_cv_cpu_have_sse42_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse42_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse42_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether avx is enabled and supported by CPU" >&5
-$as_echo_n "checking whether avx is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_avx_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_avx_ext=no
- if test "$((0x$ecx>>28&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features avx"
- if test "$ax_cv_want_avx_ext" = yes; then
- ax_cv_cpu_have_avx_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_avx_ext" >&5
-$as_echo "$ax_cv_cpu_have_avx_ext" >&6; }
-
- if test x"$ax_cv_cpu_have_avx_ext" = x"yes"; then
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for x86-AVX xgetbv 0x00000000 output" >&5
-$as_echo_n "checking for x86-AVX xgetbv 0x00000000 output... " >&6; }
-if test "${ax_cv_gcc_x86_avx_xgetbv_0x00000000+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <stdio.h>
-int
-main ()
-{
-
- int op = 0x00000000, eax, edx;
- FILE *f;
- /* Opcodes for xgetbv */
- __asm__(".byte 0x0f, 0x01, 0xd0"
- : "=a" (eax), "=d" (edx)
- : "c" (op));
- f = fopen("conftest_xgetbv", "w"); if (!f) return 1;
- fprintf(f, "%x:%x\n", eax, edx);
- fclose(f);
- return 0;
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_avx_xgetbv_0x00000000=`cat conftest_xgetbv`; rm -f conftest_xgetbv
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-( exit $ac_status )
-ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown; rm -f conftest_xgetbv
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&5
-$as_echo "$ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-
- xgetbv_eax="0"
- if test x"$ax_cv_gcc_x86_avx_xgetbv_0x00000000" != x"unknown"; then
- xgetbv_eax=`echo $ax_cv_gcc_x86_avx_xgetbv_0x00000000 | cut -d ":" -f 1`
- fi
-
- { $as_echo "$as_me:$LINENO: checking whether avx is supported by operating system" >&5
-$as_echo_n "checking whether avx is supported by operating system... " >&6; }
-if test "${ax_cv_have_avx_os_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_have_avx_os_ext=no
-
- if test "$((0x$ecx>>27&0x01))" = 1; then
- if test "$((0x$xgetbv_eax&0x6))" = 6; then
- ax_cv_have_avx_os_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx_os_ext" >&5
-$as_echo "$ax_cv_have_avx_os_ext" >&6; }
- if test x"$ax_cv_have_avx_os_ext" = x"no"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports AVX, but your operating system doesn't" >&5
-$as_echo "$as_me: WARNING: Your processor supports AVX, but your operating system doesn't" >&2;}
- fi
- fi
-
-
- { $as_echo "$as_me:$LINENO: checking whether popcnt is enabled and supported by CPU" >&5
-$as_echo_n "checking whether popcnt is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_popcnt_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_popcnt_ext=no
- if test "$((0x$ecx>>23&0x01))" = 1; then
- ax_cv_cpu_have_popcnt_ext=yes
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_popcnt_ext" >&5
-$as_echo "$ax_cv_cpu_have_popcnt_ext" >&6; }
-
-
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x80000001 output" >&5
-$as_echo_n "checking for x86 cpuid 0x80000001 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x80000001+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_0x80000001=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <stdio.h>
-int
-main ()
-{
-
- int op = 0x80000001, eax, ebx, ecx, edx;
- FILE *f;
- __asm__("cpuid"
- : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
- : "a" (op));
- f = fopen("conftest_cpuid", "w"); if (!f) return 1;
- fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
- fclose(f);
- return 0;
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x80000001=`cat conftest_cpuid`; rm -f conftest_cpuid
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-( exit $ac_status )
-ax_cv_gcc_x86_cpuid_0x80000001=unknown; rm -f conftest_cpuid
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x80000001" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x80000001" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
- ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
- edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
-
- { $as_echo "$as_me:$LINENO: checking whether lzcnt is enabled and supported by CPU" >&5
-$as_echo_n "checking whether lzcnt is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_lzcnt_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_lzcnt_ext=no
- if test "$((0x$ecx>>5&0x01))" = 1; then
- ax_cv_cpu_have_lzcnt_ext=yes
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_lzcnt_ext" >&5
-$as_echo "$ax_cv_cpu_have_lzcnt_ext" >&6; }
-
-
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x00000007 output" >&5
-$as_echo_n "checking for x86 cpuid 0x00000007 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x00000007+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_0x00000007=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <stdio.h>
-int
-main ()
-{
-
- int op = 0x00000007, eax, ebx, ecx, edx;
- FILE *f;
- __asm__("cpuid"
- : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
- : "a" (op));
- f = fopen("conftest_cpuid", "w"); if (!f) return 1;
- fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
- fclose(f);
- return 0;
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
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-( exit $ac_status )
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-
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000007" >&5
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-
-
- ebx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 2`
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-
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_avx2_ext" >&5
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-
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_bmi1_ext" >&5
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-
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_bmi2_ext" >&5
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-{
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mmmx" >&5
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-
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-{
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-cat >>confdefs.h <<\_ACEOF
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-_ACEOF
-
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- ax_check_save_flags=$CFLAGS
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-{
-
- ;
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse" >&5
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-{
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- ;
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-_ACEOF
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-cat >>confdefs.h <<\_ACEOF
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-_ACEOF
-
- fi
- fi
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- ax_check_save_flags=$CFLAGS
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse2" >&5
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-{
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- ;
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-
- fi
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- ax_check_save_flags=$CFLAGS
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-int
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-
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- $as_echo "$as_me: failed program was:" >&5
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-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse3" >&5
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- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
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- }; then
- ax_cv_link_pmmintrin_h=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_ext_linker_problem=yes
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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- if test x"$ax_cv_link_pmmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE3 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE3 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse3"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE3 1
-_ACEOF
-
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_ssse3_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mssse3" >&5
-$as_echo_n "checking whether C compiler accepts -mssse3... " >&6; }
-if test "${ax_cv_check_cflags___mssse3+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mssse3"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
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- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
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-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
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- ac_status=$?
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- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
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- } && test -s conftest.$ac_objext; then
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- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___mssse3=no
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-
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- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mssse3" >&5
-$as_echo "$ax_cv_check_cflags___mssse3" >&6; }
-if test x"$ax_cv_check_cflags___mssse3" = xyes; then
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- ax_cv_ext_compile_problem=yes
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-
-
- if test x"$ax_cv_compile_ssse3_ext" != x"yes"; then
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-$as_echo "$as_me: WARNING: Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for tmmintrin.h header file" >&5
-$as_echo_n "checking for tmmintrin.h header file... " >&6; }
- CFLAGS=-mssse3
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <tmmintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
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-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
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- ac_status=$?
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- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
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- }; then
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-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_ext_linker_problem=yes
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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- if test x"$ax_cv_link_tmmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSSE3 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSSE3 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mssse3"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSSE3 1
-_ACEOF
-
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_sse41_ext" = yes; then
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-$as_echo_n "checking whether C compiler accepts -msse4.1... " >&6; }
-if test "${ax_cv_check_cflags___msse4_1+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse4.1"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse4_1=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___msse4_1=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse4_1" >&5
-$as_echo "$ax_cv_check_cflags___msse4_1" >&6; }
-if test x"$ax_cv_check_cflags___msse4_1" = xyes; then
- ax_cv_compile_sse41_ext=yes
-else
- ax_cv_ext_compile_problem=yes
-fi
-
-
- if test x"$ax_cv_compile_sse41_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for smmintrin.h header file" >&5
-$as_echo_n "checking for smmintrin.h header file... " >&6; }
- CFLAGS=-msse4.1
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <smmintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
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-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
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- }; then
- ax_cv_link_smmintrin_h=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_ext_linker_problem=yes
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_smmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE4.1 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE4.1 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse4.1"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_1 1
-_ACEOF
-
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_sse42_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -msse4.2" >&5
-$as_echo_n "checking whether C compiler accepts -msse4.2... " >&6; }
-if test "${ax_cv_check_cflags___msse4_2+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse4.2"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
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- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse4_2=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___msse4_2=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse4_2" >&5
-$as_echo "$ax_cv_check_cflags___msse4_2" >&6; }
-if test x"$ax_cv_check_cflags___msse4_2" = xyes; then
- ax_cv_compile_sse42_ext=yes
-else
- ax_cv_ext_compile_problem=yes
-fi
-
-
- if test x"$ax_cv_compile_sse42_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for nmmintrin.h header file" >&5
-$as_echo_n "checking for nmmintrin.h header file... " >&6; }
- CFLAGS=-msse4.2
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <nmmintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ax_cv_link_nmmintrin_h=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_ext_linker_problem=yes
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
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- if test x"$ax_cv_link_nmmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE4.2 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE4.2 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse4.2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_2 1
-_ACEOF
-
-
- if test "$ax_cv_cpu_have_popcnt_ext" = yes; then
- if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <nmmintrin.h>
-int
-main ()
-{
-return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_run_mm_popcnt_ext=yes
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
- if test x"$ax_cv_run_mm_popcnt_ext" = x"yes"; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_MM_POPCNT 1
-_ACEOF
-
- fi
- fi
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_avx_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mavx" >&5
-$as_echo_n "checking whether C compiler accepts -mavx... " >&6; }
-if test "${ax_cv_check_cflags___mavx+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mavx"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mavx=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___mavx=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mavx" >&5
-$as_echo "$ax_cv_check_cflags___mavx" >&6; }
-if test x"$ax_cv_check_cflags___mavx" = xyes; then
- ax_cv_compile_avx_ext=yes
-else
- ax_cv_ext_compile_problem=yes
-fi
-
-
- if test x"$ax_cv_compile_avx_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports AVX instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports AVX instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
-$as_echo_n "checking for immintrin.h header file... " >&6; }
- CFLAGS=-mavx
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <immintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ax_cv_link_immintrin_h=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_ext_linker_problem=yes
-fi
-
-rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_immintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports AVX instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports AVX instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mavx"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_AVX 1
-_ACEOF
-
-
- if test "$ax_cv_cpu_have_popcnt_ext" = yes; then
- if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <immintrin.h>
-int
-main ()
-{
-return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_run_popcnt_ext=yes
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
- if test x"$ax_cv_run_popcnt_ext" = x"yes"; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_POPCNT 1
-_ACEOF
-
- fi
- fi
-
- if test "$ax_cv_cpu_have_lzcnt_ext" = yes; then
- if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <immintrin.h>
-int
-main ()
-{
-return (_lzcnt_u32(0xffffffffu) == 32) ? 0 : 9;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_run_lzcnt_ext=yes
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
- if test x"$ax_cv_run_lzcnt_ext" = x"yes"; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_LZCNT 1
-_ACEOF
-
- fi
- fi
-
- if test "$ax_cv_cpu_have_bmi1_ext" = yes; then
- CFLAGS=-mbmi
- if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <immintrin.h>
-int
-main ()
-{
-return (_tzcnt_u32(0xffffffffu) == 32) ? 0 : 9;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_run_tzcnt_ext=yes
-else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
- if test x"$ax_cv_run_tzcnt_ext" = x"yes"; then
- SIMD_CFLAGS="$SIMD_CFLAGS -mbmi"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_TZCNT 1
-_ACEOF
-
- fi
- fi
-
- if test "$ax_cv_cpu_have_bmi2_ext" = yes; then
- SIMD_CFLAGS="$SIMD_CFLAGS -mbmi2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BMI2 1
-_ACEOF
-
- fi
-
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_avx2_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mavx2" >&5
-$as_echo_n "checking whether C compiler accepts -mavx2... " >&6; }
-if test "${ax_cv_check_cflags___mavx2+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mavx2"
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mavx2=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___mavx2=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mavx2" >&5
-$as_echo "$ax_cv_check_cflags___mavx2" >&6; }
-if test x"$ax_cv_check_cflags___mavx2" = xyes; then
- ax_cv_compile_avx2_ext=yes
-else
- ax_cv_ext_compile_problem=yes
-fi
-
-
- if test x"$ax_cv_compile_avx2_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
-$as_echo_n "checking for immintrin.h header file... " >&6; }
- CFLAGS=-mavx2
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <immintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
- ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); } && {
test -z "$ac_c_werror_flag" ||
@@ -22694,7 +20839,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_immintrin_h=yes
+ ax_cv_link_xmmintrin_h=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -22705,79 +20850,31 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_immintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_xmmintrin_h" != xyes; then
{ $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports AVX2 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports AVX2 instructions but not your linker." >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports SSE instructions but not your linker." >&2;}
else
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mavx2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_AVX2 1
-_ACEOF
-
-
+# AC_DEFINE(HAVE_SSE,1,[Define to 1 if you support SSE (Streaming SIMD Extensions) instructions]) -- Not used
fi
fi
fi
- ;;
- esac
-
- CFLAGS=$CFLAGS_ORIG
-
-
- # Sets SIMD_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX
- ;;
-
- xno)
- { $as_echo "$as_me:$LINENO: result: disabled" >&5
-$as_echo "disabled" >&6; }
- ;;
-
- x)
- { $as_echo "$as_me:$LINENO: result: not specified so enabled by default" >&5
-$as_echo "not specified so enabled by default" >&6; }
-
-
-
- CFLAGS_ORIG=$CFLAGS
-
- case $host_cpu in
- powerpc*)
- { $as_echo "$as_me:$LINENO: checking whether altivec is enabled and supported" >&5
-$as_echo_n "checking whether altivec is enabled and supported... " >&6; }
-if test "${ax_cv_cpu_have_altivec_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- if test `/usr/sbin/sysctl -a 2>/dev/null| grep -c hw.optional.altivec` != 0; then
- if test `/usr/sbin/sysctl -n hw.optional.altivec` = 1; then
- ax_cv_cpu_have_altivec_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_altivec_ext" >&5
-$as_echo "$ax_cv_cpu_have_altivec_ext" >&6; }
-
- if test "$ax_cv_cpu_have_altivec_ext" = yes; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_ALTIVEC 1
-_ACEOF
-
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -faltivec" >&5
-$as_echo_n "checking whether C compiler accepts -faltivec... " >&6; }
-if test "${ax_cv_check_cflags___faltivec+set}" = set; then
+ if test x"$ax_cv_cpu_has_sse2_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-msse2
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -faltivec"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -22811,76 +20908,52 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___faltivec=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___faltivec=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___faltivec" >&5
-$as_echo "$ax_cv_check_cflags___faltivec" >&6; }
-if test x"$ax_cv_check_cflags___faltivec" = xyes; then
- SIMD_CFLAGS="$SIMD_CFLAGS -faltivec"
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_sse2_ext=yes
else
- :
+ ax_cv_ext_compile_problem=yes
fi
- fi
- ;;
-
-
- i[3456]86*|x86_64*|amd64*)
-
-
-
-
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x00000001 output" >&5
-$as_echo_n "checking for x86 cpuid 0x00000001 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x00000001+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_0x00000001=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
+ if test x"$ax_cv_compile_sse2_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports SSE2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for emmintrin.h header file" >&5
+$as_echo_n "checking for emmintrin.h header file... " >&6; }
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+#include <emmintrin.h>
int
main ()
{
- int op = 0x00000001, eax, ebx, ecx, edx;
- FILE *f;
- __asm__("cpuid"
- : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
- : "a" (op));
- f = fopen("conftest_cpuid", "w"); if (!f) return 1;
- fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
- fclose(f);
- return 0;
-
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
+rm -f conftest.$ac_objext conftest$ac_exeext
if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
@@ -22888,366 +20961,136 @@ case "(($ac_try" in
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x00000001=`cat conftest_cpuid`; rm -f conftest_cpuid
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ax_cv_link_emmintrin_h=yes
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-ax_cv_gcc_x86_cpuid_0x00000001=unknown; rm -f conftest_cpuid
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000001" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x00000001" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
- ecx=0
- edx=0
- if test "$ax_cv_gcc_x86_cpuid_0x00000001" != "unknown";
- then
- ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 3`
- edx=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
- fi
-
- { $as_echo "$as_me:$LINENO: checking whether mmx is enabled and supported by CPU" >&5
-$as_echo_n "checking whether mmx is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_mmx_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_mmx_ext=no
- if test "$((0x$edx>>23&0x01))" = 1; then
- ax_cv_cpu_have_mmx_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features mmx"
-
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_mmx_ext" >&5
-$as_echo "$ax_cv_cpu_have_mmx_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse_ext=no
- if test "$((0x$edx>>25&0x01))" = 1; then
- ax_cv_cpu_have_sse_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features sse"
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse2 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse2 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse2_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse2_ext=no
- if test "$((0x$edx>>26&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse2"
- if test "$ax_cv_want_sse2_ext" = yes; then
- ax_cv_cpu_have_sse2_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse2_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse2_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse3 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse3 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse3_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse3_ext=no
- if test "$((0x$ecx&0x01))" = 1; then
- ax_cv_cpu_have_sse3_ext=yes
- ax_cv_cpu_features="$ax_cv_cpu_features sse3"
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse3_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse3_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether ssse3 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether ssse3 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_ssse3_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_ssse3_ext=no
- if test "$((0x$ecx>>9&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features ssse3"
- if test "$ax_cv_want_ssse3_ext" = yes; then
- ax_cv_cpu_have_ssse3_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_ssse3_ext" >&5
-$as_echo "$ax_cv_cpu_have_ssse3_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse4.1 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse4.1 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse41_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse41_ext=no
- if test "$((0x$ecx>>19&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse4.1"
- if test "$ax_cv_want_sse41_ext" = yes; then
- ax_cv_cpu_have_sse41_ext=yes
- fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse41_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse41_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether sse4.2 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether sse4.2 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_sse42_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_sse42_ext=no
- if test "$((0x$ecx>>20&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features sse4.2"
- if test "$ax_cv_want_sse42_ext" = yes; then
- ax_cv_cpu_have_sse42_ext=yes
- fi
- fi
-
+ ax_cv_ext_linker_problem=yes
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_sse42_ext" >&5
-$as_echo "$ax_cv_cpu_have_sse42_ext" >&6; }
- { $as_echo "$as_me:$LINENO: checking whether avx is enabled and supported by CPU" >&5
-$as_echo_n "checking whether avx is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_avx_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_avx_ext=no
- if test "$((0x$ecx>>28&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features avx"
- if test "$ax_cv_want_avx_ext" = yes; then
- ax_cv_cpu_have_avx_ext=yes
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_emmintrin_h" != xyes; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE2 instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports SSE2 instructions but not your linker." >&2;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ ax_make_sse2=yes
+ SIMD_SSE2_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_SSE2,1,[Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions]) -- Not used
fi
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_avx_ext" >&5
-$as_echo "$ax_cv_cpu_have_avx_ext" >&6; }
-
- if test x"$ax_cv_cpu_have_avx_ext" = x"yes"; then
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ fi
+ fi
-{ $as_echo "$as_me:$LINENO: checking for x86-AVX xgetbv 0x00000000 output" >&5
-$as_echo_n "checking for x86-AVX xgetbv 0x00000000 output... " >&6; }
-if test "${ax_cv_gcc_x86_avx_xgetbv_0x00000000+set}" = set; then
+ if test x"$ax_cv_cpu_has_sse3_ext" = xyes; then
+ CFLAGS=
+ TEST_CFLAGS=-msse3
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown
-else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+
int
main ()
{
- int op = 0x00000000, eax, edx;
- FILE *f;
- /* Opcodes for xgetbv */
- __asm__(".byte 0x0f, 0x01, 0xd0"
- : "=a" (eax), "=d" (edx)
- : "c" (op));
- f = fopen("conftest_xgetbv", "w"); if (!f) return 1;
- fprintf(f, "%x:%x\n", eax, edx);
- fclose(f);
- return 0;
-
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_compile") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_avx_xgetbv_0x00000000=`cat conftest_xgetbv`; rm -f conftest_xgetbv
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_CACHEVAR=yes"
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-ax_cv_gcc_x86_avx_xgetbv_0x00000000=unknown; rm -f conftest_xgetbv
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
+ eval "$as_CACHEVAR=no"
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&5
-$as_echo "$ax_cv_gcc_x86_avx_xgetbv_0x00000000" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-
- xgetbv_eax="0"
- if test x"$ax_cv_gcc_x86_avx_xgetbv_0x00000000" != x"unknown"; then
- xgetbv_eax=`echo $ax_cv_gcc_x86_avx_xgetbv_0x00000000 | cut -d ":" -f 1`
- fi
-
- { $as_echo "$as_me:$LINENO: checking whether avx is supported by operating system" >&5
-$as_echo_n "checking whether avx is supported by operating system... " >&6; }
-if test "${ax_cv_have_avx_os_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_have_avx_os_ext=no
-
- if test "$((0x$ecx>>27&0x01))" = 1; then
- if test "$((0x$xgetbv_eax&0x6))" = 6; then
- ax_cv_have_avx_os_ext=yes
- fi
- fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_have_avx_os_ext" >&5
-$as_echo "$ax_cv_have_avx_os_ext" >&6; }
- if test x"$ax_cv_have_avx_os_ext" = x"no"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your processor supports AVX, but your operating system doesn't" >&5
-$as_echo "$as_me: WARNING: Your processor supports AVX, but your operating system doesn't" >&2;}
- fi
- fi
-
-
- { $as_echo "$as_me:$LINENO: checking whether popcnt is enabled and supported by CPU" >&5
-$as_echo_n "checking whether popcnt is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_popcnt_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_sse3_ext=yes
else
-
- ax_cv_cpu_have_popcnt_ext=no
- if test "$((0x$ecx>>23&0x01))" = 1; then
- ax_cv_cpu_have_popcnt_ext=yes
- fi
-
+ ax_cv_ext_compile_problem=yes
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_popcnt_ext" >&5
-$as_echo "$ax_cv_cpu_have_popcnt_ext" >&6; }
-
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x80000001 output" >&5
-$as_echo_n "checking for x86 cpuid 0x80000001 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x80000001+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_0x80000001=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
+ if test x"$ax_cv_compile_sse3_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports SSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for pmmintrin.h header file" >&5
+$as_echo_n "checking for pmmintrin.h header file... " >&6; }
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+#include <pmmintrin.h>
int
main ()
{
- int op = 0x80000001, eax, ebx, ecx, edx;
- FILE *f;
- __asm__("cpuid"
- : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
- : "a" (op));
- f = fopen("conftest_cpuid", "w"); if (!f) return 1;
- fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
- fclose(f);
- return 0;
-
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
+rm -f conftest.$ac_objext conftest$ac_exeext
if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
@@ -23255,104 +21098,139 @@ case "(($ac_try" in
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x80000001=`cat conftest_cpuid`; rm -f conftest_cpuid
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ax_cv_link_pmmintrin_h=yes
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-ax_cv_gcc_x86_cpuid_0x80000001=unknown; rm -f conftest_cpuid
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+ ax_cv_ext_linker_problem=yes
fi
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_pmmintrin_h" != xyes; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE3 instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports SSE3 instructions but not your linker." >&2;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+# AC_DEFINE(HAVE_SSE3,1,[Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions]) -- Not used
+ fi
+ fi
+ fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x80000001" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x80000001" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
+ if test x"$ax_cv_cpu_has_ssse3_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-mssse3"
+ else
+ TEST_CFLAGS="$SIMD_SSE2_CFLAGS -mssse3"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-ssse3"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
- ecx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
- edx=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
+int
+main ()
+{
- { $as_echo "$as_me:$LINENO: checking whether lzcnt is enabled and supported by CPU" >&5
-$as_echo_n "checking whether lzcnt is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_lzcnt_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_CACHEVAR=yes"
else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_cpu_have_lzcnt_ext=no
- if test "$((0x$ecx>>5&0x01))" = 1; then
- ax_cv_cpu_have_lzcnt_ext=yes
- fi
-
+ eval "$as_CACHEVAR=no"
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_lzcnt_ext" >&5
-$as_echo "$ax_cv_cpu_have_lzcnt_ext" >&6; }
-
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ CFLAGS=$ax_check_save_flags
+fi
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_ssse3_ext=yes
+else
+ ax_cv_ext_compile_problem=yes
+fi
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-{ $as_echo "$as_me:$LINENO: checking for x86 cpuid 0x00000007 output" >&5
-$as_echo_n "checking for x86 cpuid 0x00000007 output... " >&6; }
-if test "${ax_cv_gcc_x86_cpuid_0x00000007+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- if test "$cross_compiling" = yes; then
- ax_cv_gcc_x86_cpuid_0x00000007=unknown
-else
- cat >conftest.$ac_ext <<_ACEOF
+ if test x"$ax_cv_compile_ssse3_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for tmmintrin.h header file" >&5
+$as_echo_n "checking for tmmintrin.h header file... " >&6; }
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <stdio.h>
+#include <tmmintrin.h>
int
main ()
{
- int op = 0x00000007, eax, ebx, ecx, edx;
- FILE *f;
- __asm__("cpuid"
- : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
- : "a" (op));
- f = fopen("conftest_cpuid", "w"); if (!f) return 1;
- fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
- fclose(f);
- return 0;
-
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
+rm -f conftest.$ac_objext conftest$ac_exeext
if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
@@ -23360,105 +21238,63 @@ case "(($ac_try" in
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_gcc_x86_cpuid_0x00000007=`cat conftest_cpuid`; rm -f conftest_cpuid
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ax_cv_link_tmmintrin_h=yes
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
-( exit $ac_status )
-ax_cv_gcc_x86_cpuid_0x00000007=unknown; rm -f conftest_cpuid
-fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
+ ax_cv_ext_linker_problem=yes
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_gcc_x86_cpuid_0x00000007" >&5
-$as_echo "$ax_cv_gcc_x86_cpuid_0x00000007" >&6; }
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
- ebx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 2`
- ecx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 3`
- edx=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 4`
-
- { $as_echo "$as_me:$LINENO: checking whether avx2 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether avx2 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_avx2_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
- ax_cv_cpu_have_avx2_ext=no
- if test "$((0x$ebx>>5&0x01))" = 1; then
- ax_cv_cpu_features="$ax_cv_cpu_features avx2"
- if test "$ax_cv_want_avx2_ext" = yes; then
- ax_cv_cpu_have_avx2_ext=yes
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_tmmintrin_h" != xyes; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSSE3 instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports SSSE3 instructions but not your linker." >&2;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ ax_make_ssse3=yes
+ SIMD_SSSE3_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_SSSE3,1,[Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3) instructions]) -- Defines run-type
fi
fi
+ fi
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_avx2_ext" >&5
-$as_echo "$ax_cv_cpu_have_avx2_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether bmi1 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether bmi1 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_bmi1_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_bmi1_ext=no
- if test "$((0x$ebx>>3&0x01))" = 1; then
- ax_cv_cpu_have_bmi1_ext=yes
- fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_bmi1_ext" >&5
-$as_echo "$ax_cv_cpu_have_bmi1_ext" >&6; }
-
- { $as_echo "$as_me:$LINENO: checking whether bmi2 is enabled and supported by CPU" >&5
-$as_echo_n "checking whether bmi2 is enabled and supported by CPU... " >&6; }
-if test "${ax_cv_cpu_have_bmi2_ext+set}" = set; then
- $as_echo_n "(cached) " >&6
-else
-
- ax_cv_cpu_have_bmi2_ext=no
- if test "$((0x$ebx>>8&0x01))" = 1; then
- ax_cv_cpu_have_bmi2_ext=yes
+ if test x"$ax_cv_cpu_has_sse41_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-msse4.1"
+ else
+ TEST_CFLAGS="$SIMD_SSSE3_CFLAGS -msse4.1"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-sse4.1"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-sse4.1"
fi
-
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_have_bmi2_ext" >&5
-$as_echo "$ax_cv_cpu_have_bmi2_ext" >&6; }
-
- if test "$ax_cv_cpu_have_mmx_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mmmx" >&5
-$as_echo_n "checking whether C compiler accepts -mmmx... " >&6; }
-if test "${ax_cv_check_cflags___mmmx+set}" = set; then
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mmmx"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -23492,40 +21328,43 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mmmx=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___mmmx=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mmmx" >&5
-$as_echo "$ax_cv_check_cflags___mmmx" >&6; }
-if test x"$ax_cv_check_cflags___mmmx" = xyes; then
- ax_cv_compile_mmx_ext=yes
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_sse41_ext=yes
else
ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_compile_mmx_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports MMX instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports MMX instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for mmintrin.h header file" >&5
-$as_echo_n "checking for mmintrin.h header file... " >&6; }
- CFLAGS=-mmmx
+ if test x"$ax_cv_compile_sse41_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for smmintrin.h header file" >&5
+$as_echo_n "checking for smmintrin.h header file... " >&6; }
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <mmintrin.h>
+#include <smmintrin.h>
int
main ()
{
@@ -23555,7 +21394,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_mmintrin_h=yes
+ ax_cv_link_smmintrin_h=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -23566,34 +21405,40 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_mmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_smmintrin_h" != xyes; then
{ $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports MMX instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports MMX instructions but not your linker." >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE4.1 instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports SSE4.1 instructions but not your linker." >&2;}
else
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mmmx"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_MMX 1
-_ACEOF
-
+ ax_make_sse41=yes
+ SIMD_SSE4_1_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_SSE4_1,1,[Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1) instructions]) -- Not used
fi
- fi
+ fi
fi
-
- if test "$ax_cv_cpu_have_sse_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -msse" >&5
-$as_echo_n "checking whether C compiler accepts -msse... " >&6; }
-if test "${ax_cv_check_cflags___msse+set}" = set; then
+ if test x"$ax_cv_cpu_has_sse42_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-march=corei7"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_1_CFLAGS -msse4.2"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-sse4.2"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-sse4.2"
+ SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-sse4.2"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -23627,40 +21472,43 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___msse=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse" >&5
-$as_echo "$ax_cv_check_cflags___msse" >&6; }
-if test x"$ax_cv_check_cflags___msse" = xyes; then
- ax_cv_compile_sse_ext=yes
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_sse42_ext=yes
else
ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_compile_sse_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ if test x"$ax_cv_compile_sse42_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
else
- { $as_echo "$as_me:$LINENO: checking for xmmintrin.h header file" >&5
-$as_echo_n "checking for xmmintrin.h header file... " >&6; }
- CFLAGS=-msse
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for nmmintrin.h header file" >&5
+$as_echo_n "checking for nmmintrin.h header file... " >&6; }
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <xmmintrin.h>
+#include <nmmintrin.h>
int
main ()
{
@@ -23690,7 +21538,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_xmmintrin_h=yes
+ ax_cv_link_nmmintrin_h=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -23701,34 +21549,113 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_xmmintrin_h" != x"yes"; then
+ if test x"$ax_cv_link_nmmintrin_h" != xyes; then
{ $as_echo "$as_me:$LINENO: result: no" >&5
$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE instructions but not your linker." >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE4.2 instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports SSE4.2 instructions but not your linker." >&2;}
else
{ $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse"
+ ax_make_sse42=yes
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ fi
+ fi
+ fi
+
+ if test x"$ax_make_sse42" = xyes; then
+ { $as_echo "$as_me:$LINENO: checking for mm_popcnt support" >&5
+$as_echo_n "checking for mm_popcnt support... " >&6; }
+ if test x"$ax_cv_cpu_has_popcnt_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ else
+ if test "$cross_compiling" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <nmmintrin.h>
+int
+main ()
+{
+return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_MM_POPCNT 1
+_ACEOF
+
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE 1
-_ACEOF
- fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse2_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -msse2" >&5
-$as_echo_n "checking whether C compiler accepts -msse2... " >&6; }
-if test "${ax_cv_check_cflags___msse2+set}" = set; then
+ if test x"$ax_make_sse42" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mpopcnt"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse2"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -23762,40 +21689,41 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse2=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___msse2=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse2" >&5
-$as_echo "$ax_cv_check_cflags___msse2" >&6; }
-if test x"$ax_cv_check_cflags___msse2" = xyes; then
- ax_cv_compile_sse2_ext=yes
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_popcnt_ext=yes
else
ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_compile_sse2_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for emmintrin.h header file" >&5
-$as_echo_n "checking for emmintrin.h header file... " >&6; }
- CFLAGS=-msse2
+ if test x"$ax_cv_compile_popcnt_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports POPCNT instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports POPCNT instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <emmintrin.h>
+
int
main ()
{
@@ -23825,7 +21753,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_emmintrin_h=yes
+ ax_cv_link_popcnt=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -23836,34 +21764,23 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_emmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE2 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE2 instructions but not your linker." >&2;}
+ if test x"$ax_cv_link_popcnt" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports -mpopcnt but not your linker. Can you try another linker or update yours?" >&5
+$as_echo "$as_me: WARNING: Your compiler supports -mpopcnt but not your linker. Can you try another linker or update yours?" >&2;}
else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE2 1
-_ACEOF
-
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_sse3_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -msse3" >&5
-$as_echo_n "checking whether C compiler accepts -msse3... " >&6; }
-if test "${ax_cv_check_cflags___msse3+set}" = set; then
- $as_echo_n "(cached) " >&6
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ # Test for functionality with the -mpopcnt compiler flag
+ { $as_echo "$as_me:$LINENO: checking for __builtin_clz" >&5
+$as_echo_n "checking for __builtin_clz... " >&6; }
+ if test "$cross_compiling" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse3"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -23874,131 +21791,66 @@ cat >>conftest.$ac_ext <<_ACEOF
int
main ()
{
-
+return (__builtin_clz(0x1u) == 31) ? 0 : 9;
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
+ (eval "$ac_link") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse3=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___msse3=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse3" >&5
-$as_echo "$ax_cv_check_cflags___msse3" >&6; }
-if test x"$ax_cv_check_cflags___msse3" = xyes; then
- ax_cv_compile_sse3_ext=yes
-else
- ax_cv_ext_compile_problem=yes
-fi
-
-
- if test x"$ax_cv_compile_sse3_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for pmmintrin.h header file" >&5
-$as_echo_n "checking for pmmintrin.h header file... " >&6; }
- CFLAGS=-msse3
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <pmmintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
+ (eval "$ac_try") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ax_cv_link_pmmintrin_h=yes
+ (exit $ac_status); }; }; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BUILTIN_CLZ 1
+_ACEOF
+
else
- $as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_ext_linker_problem=yes
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
fi
-
rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_pmmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE3 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE3 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse3"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE3 1
-_ACEOF
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
- fi
- fi
- fi
- if test "$ax_cv_cpu_have_ssse3_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mssse3" >&5
-$as_echo_n "checking whether C compiler accepts -mssse3... " >&6; }
-if test "${ax_cv_check_cflags___mssse3+set}" = set; then
- $as_echo_n "(cached) " >&6
+ { $as_echo "$as_me:$LINENO: checking for __builtin_ctz" >&5
+$as_echo_n "checking for __builtin_ctz... " >&6; }
+ if test "$cross_compiling" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mssse3"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -24009,72 +21861,82 @@ cat >>conftest.$ac_ext <<_ACEOF
int
main ()
{
-
+return (__builtin_ctz(0x80000000u) == 31) ? 0 : 9;
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
+ (eval "$ac_link") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mssse3=yes
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BUILTIN_CTZ 1
+_ACEOF
+
else
- $as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___mssse3=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mssse3" >&5
-$as_echo "$ax_cv_check_cflags___mssse3" >&6; }
-if test x"$ax_cv_check_cflags___mssse3" = xyes; then
- ax_cv_compile_ssse3_ext=yes
-else
- ax_cv_ext_compile_problem=yes
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
- if test x"$ax_cv_compile_ssse3_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSSE3 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for tmmintrin.h header file" >&5
-$as_echo_n "checking for tmmintrin.h header file... " >&6; }
- CFLAGS=-mssse3
- cat >conftest.$ac_ext <<_ACEOF
+
+ { $as_echo "$as_me:$LINENO: checking for __builtin_popcount" >&5
+$as_echo_n "checking for __builtin_popcount... " >&6; }
+ if test "$cross_compiling" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+else
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <tmmintrin.h>
+
int
main ()
{
-
+return (__builtin_popcount(0xffffffffu) == 32) ? 0 : 9;
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
+rm -f conftest$ac_exeext
if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
@@ -24082,58 +21944,61 @@ case "(($ac_try" in
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
+ (eval "$ac_link") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ax_cv_link_tmmintrin_h=yes
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_BUILTIN_POPCOUNT 1
+_ACEOF
+
else
- $as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_ext_linker_problem=yes
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
fi
-
rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_tmmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSSE3 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSSE3 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mssse3"
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSSE3 1
-_ACEOF
fi
fi
fi
-
- if test "$ax_cv_cpu_have_sse41_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -msse4.1" >&5
-$as_echo_n "checking whether C compiler accepts -msse4.1... " >&6; }
-if test "${ax_cv_check_cflags___msse4_1+set}" = set; then
+ if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mabm"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse4.1"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -24167,40 +22032,41 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse4_1=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___msse4_1=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse4_1" >&5
-$as_echo "$ax_cv_check_cflags___msse4_1" >&6; }
-if test x"$ax_cv_check_cflags___msse4_1" = xyes; then
- ax_cv_compile_sse41_ext=yes
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_abm_ext=yes
else
ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_compile_sse41_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE4.1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for smmintrin.h header file" >&5
-$as_echo_n "checking for smmintrin.h header file... " >&6; }
- CFLAGS=-msse4.1
+ if test x"$ax_cv_compile_abm_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <smmintrin.h>
+
int
main ()
{
@@ -24230,7 +22096,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_smmintrin_h=yes
+ ax_cv_link_abm=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -24241,158 +22107,85 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_smmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE4.1 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE4.1 instructions but not your linker." >&2;}
+ if test x"$ax_cv_link_abm" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports -mabm but not your linker" >&5
+$as_echo "$as_me: WARNING: Your compiler supports -mabm but not your linker" >&2;}
else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse4.1"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_1 1
-_ACEOF
-
- fi
- fi
- fi
-
-
- if test "$ax_cv_cpu_have_sse42_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -msse4.2" >&5
-$as_echo_n "checking whether C compiler accepts -msse4.2... " >&6; }
-if test "${ax_cv_check_cflags___msse4_2+set}" = set; then
- $as_echo_n "(cached) " >&6
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ # Test for functionality with the -mabm compiler flag
+ { $as_echo "$as_me:$LINENO: checking for _popcnt32 support" >&5
+$as_echo_n "checking for _popcnt32 support... " >&6; }
+ if test "$cross_compiling" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -msse4.2"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-
+#include <immintrin.h>
int
main ()
{
-
+return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;
;
return 0;
}
_ACEOF
-rm -f conftest.$ac_objext
-if { (ac_try="$ac_compile"
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_compile") 2>conftest.er1
+ (eval "$ac_link") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___msse4_2=yes
-else
- $as_echo "$as_me: failed program was:" >&5
-sed 's/^/| /' conftest.$ac_ext >&5
-
- ax_cv_check_cflags___msse4_2=no
-fi
-
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___msse4_2" >&5
-$as_echo "$ax_cv_check_cflags___msse4_2" >&6; }
-if test x"$ax_cv_check_cflags___msse4_2" = xyes; then
- ax_cv_compile_sse42_ext=yes
-else
- ax_cv_ext_compile_problem=yes
-fi
-
-
- if test x"$ax_cv_compile_sse42_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports SSE4.2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
- else
- { $as_echo "$as_me:$LINENO: checking for nmmintrin.h header file" >&5
-$as_echo_n "checking for nmmintrin.h header file... " >&6; }
- CFLAGS=-msse4.2
- cat >conftest.$ac_ext <<_ACEOF
-/* confdefs.h. */
-_ACEOF
-cat confdefs.h >>conftest.$ac_ext
-cat >>conftest.$ac_ext <<_ACEOF
-/* end confdefs.h. */
-#include <nmmintrin.h>
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest.$ac_objext conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>conftest.er1
+ (eval "$ac_try") 2>&5
ac_status=$?
- grep -v '^ *+' conftest.er1 >conftest.err
- rm -f conftest.er1
- cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && {
- test -z "$ac_c_werror_flag" ||
- test ! -s conftest.err
- } && test -s conftest$ac_exeext && {
- test "$cross_compiling" = yes ||
- $as_test_x conftest$ac_exeext
- }; then
- ax_cv_link_nmmintrin_h=yes
+ (exit $ac_status); }; }; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_POPCNT 1
+_ACEOF
+
else
- $as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_ext_linker_problem=yes
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
fi
-
rm -rf conftest.dSYM
-rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
- conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_nmmintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports SSE4.2 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports SSE4.2 instructions but not your linker." >&2;}
- else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -msse4.2"
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_SSE4_2 1
-_ACEOF
- if test "$ax_cv_cpu_have_popcnt_ext" = yes; then
- if test "$cross_compiling" = yes; then
+ { $as_echo "$as_me:$LINENO: checking for _lzcnt support" >&5
+$as_echo_n "checking for _lzcnt support... " >&6; }
+ if test "$cross_compiling" = yes; then
{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
@@ -24407,11 +22200,11 @@ _ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <nmmintrin.h>
+#include <immintrin.h>
int
main ()
{
-return (_mm_popcnt_u32(0xffffffffu) == 32) ? 0 : 9;
+return (_lzcnt_u32(0x0fffffffu) == 4) ? 0 : 9;
;
return 0;
}
@@ -24438,40 +22231,47 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_run_mm_popcnt_ext=yes
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LZCNT 1
+_ACEOF
+
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
- if test x"$ax_cv_run_mm_popcnt_ext" = x"yes"; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_MM_POPCNT 1
-_ACEOF
-
- fi
- fi
fi
- fi
+ fi
fi
-
- if test "$ax_cv_cpu_have_avx_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mavx" >&5
-$as_echo_n "checking whether C compiler accepts -mavx... " >&6; }
-if test "${ax_cv_check_cflags___mavx+set}" = set; then
+ if test x"$ax_cv_cpu_has_bmi1_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mbmi"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mavx"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -24505,40 +22305,41 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mavx=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___mavx=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mavx" >&5
-$as_echo "$ax_cv_check_cflags___mavx" >&6; }
-if test x"$ax_cv_check_cflags___mavx" = xyes; then
- ax_cv_compile_avx_ext=yes
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_bmi_ext=yes
else
ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_compile_avx_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports AVX instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports AVX instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ if test x"$ax_cv_compile_bmi_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports BMI1 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
else
- { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
-$as_echo_n "checking for immintrin.h header file... " >&6; }
- CFLAGS=-mavx
+ CFLAGS=$TEST_CFLAGS
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <immintrin.h>
+
int
main ()
{
@@ -24568,7 +22369,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_immintrin_h=yes
+ ax_cv_link_bmi=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -24579,23 +22380,15 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_immintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports AVX instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports AVX instructions but not your linker." >&2;}
+ if test x"$ax_cv_link_bmi" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports -mbmi but not your linker" >&5
+$as_echo "$as_me: WARNING: Your compiler supports -mbmi but not your linker" >&2;}
else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
-$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mavx"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_AVX 1
-_ACEOF
-
-
- if test "$ax_cv_cpu_have_popcnt_ext" = yes; then
- if test "$cross_compiling" = yes; then
+ SIMD_SSE4_2_CFLAGS=$CFLAGS
+ # Test for functionality with the -mbmi compiler flag
+ { $as_echo "$as_me:$LINENO: checking for _tzcnt support" >&5
+$as_echo_n "checking for _tzcnt support... " >&6; }
+ if test "$cross_compiling" = yes; then
{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
@@ -24614,7 +22407,7 @@ cat >>conftest.$ac_ext <<_ACEOF
int
main ()
{
-return (_popcnt32(0xffffffffu) == 32) ? 0 : 9;
+return (_tzcnt_u32(0xfffffff0u) == 4) ? 0 : 9;
;
return 0;
}
@@ -24641,107 +22434,115 @@ $as_echo "$ac_try_echo") >&5
ac_status=$?
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
(exit $ac_status); }; }; then
- ax_cv_run_popcnt_ext=yes
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_TZCNT 1
+_ACEOF
+
else
$as_echo "$as_me: program exited with status $ac_status" >&5
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
fi
rm -rf conftest.dSYM
rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
fi
- if test x"$ax_cv_run_popcnt_ext" = x"yes"; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_POPCNT 1
-_ACEOF
-
- fi
- fi
+ fi
+ fi
+ fi
- if test "$ax_cv_cpu_have_lzcnt_ext" = yes; then
- if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
+ if test x"$ax_cv_cpu_has_avx2_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="-march=core-avx2"
+ else
+ TEST_CFLAGS="$SIMD_SSE4_2_CFLAGS -mavx2"
+ SIMD_SSE2_CFLAGS="$SIMD_SSE2_CFLAGS -mno-avx2"
+ SIMD_SSSE3_CFLAGS="$SIMD_SSSE3_CFLAGS -mno-avx2"
+ SIMD_SSE4_1_CFLAGS="$SIMD_SSE4_1_CFLAGS -mno-avx2"
+ SIMD_SSE4_2_CFLAGS="$SIMD_SSE4_2_CFLAGS -mno-avx2"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <immintrin.h>
+
int
main ()
-{
-return (_lzcnt_u32(0xffffffffu) == 32) ? 0 : 9;
- ;
- return 0;
-}
-_ACEOF
-rm -f conftest$ac_exeext
-if { (ac_try="$ac_link"
-case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
*) ac_try_echo=$ac_try;;
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_compile") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_run_lzcnt_ext=yes
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_CACHEVAR=yes"
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
+ eval "$as_CACHEVAR=no"
fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
- if test x"$ax_cv_run_lzcnt_ext" = x"yes"; then
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_LZCNT 1
-_ACEOF
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ CFLAGS=$ax_check_save_flags
+fi
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_avx2_ext=yes
+else
+ ax_cv_ext_compile_problem=yes
+fi
- fi
- fi
- if test "$ax_cv_cpu_have_bmi1_ext" = yes; then
- CFLAGS=-mbmi
- if test "$cross_compiling" = yes; then
- { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
-$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
-{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&5
-$as_echo "$as_me: error: cannot run test program while cross compiling
-See \`config.log' for more details." >&2;}
- { (exit 1); exit 1; }; }; }
-else
- cat >conftest.$ac_ext <<_ACEOF
+ if test x"$ax_cv_compile_avx2_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ else
+ CFLAGS=$TEST_CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
+$as_echo_n "checking for immintrin.h header file... " >&6; }
+ cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
@@ -24751,12 +22552,12 @@ cat >>conftest.$ac_ext <<_ACEOF
int
main ()
{
-return (_tzcnt_u32(0xffffffffu) == 32) ? 0 : 9;
+
;
return 0;
}
_ACEOF
-rm -f conftest$ac_exeext
+rm -f conftest.$ac_objext conftest$ac_exeext
if { (ac_try="$ac_link"
case "(($ac_try" in
*\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
@@ -24764,65 +22565,61 @@ case "(($ac_try" in
esac
eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
$as_echo "$ac_try_echo") >&5
- (eval "$ac_link") 2>&5
- ac_status=$?
- $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
- { (case "(($ac_try" in
- *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
- *) ac_try_echo=$ac_try;;
-esac
-eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
-$as_echo "$ac_try_echo") >&5
- (eval "$ac_try") 2>&5
+ (eval "$ac_link") 2>conftest.er1
ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
$as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
- (exit $ac_status); }; }; then
- ax_cv_run_tzcnt_ext=yes
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ax_cv_link_immintrin_h=yes
else
- $as_echo "$as_me: program exited with status $ac_status" >&5
-$as_echo "$as_me: failed program was:" >&5
+ $as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
+ ax_cv_ext_linker_problem=yes
fi
-rm -rf conftest.dSYM
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
-fi
-
-
- if test x"$ax_cv_run_tzcnt_ext" = x"yes"; then
- SIMD_CFLAGS="$SIMD_CFLAGS -mbmi"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_TZCNT 1
-_ACEOF
-
- fi
- fi
-
- if test "$ax_cv_cpu_have_bmi2_ext" = yes; then
- SIMD_CFLAGS="$SIMD_CFLAGS -mbmi2"
-
-cat >>confdefs.h <<\_ACEOF
-#define HAVE_BMI2 1
-_ACEOF
-
- fi
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ if test x"$ax_cv_link_immintrin_h" != xyes; then
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports AVX2 instructions but not your linker." >&5
+$as_echo "$as_me: WARNING: Your compiler supports AVX2 instructions but not your linker." >&2;}
+ else
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ ax_make_avx2=yes
+ SIMD_AVX2_CFLAGS=$CFLAGS
+# AC_DEFINE(HAVE_AVX2,1,[Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions]) -- Defines run-type
fi
fi
fi
-
- if test "$ax_cv_cpu_have_avx2_ext" = yes; then
- { $as_echo "$as_me:$LINENO: checking whether C compiler accepts -mavx2" >&5
-$as_echo_n "checking whether C compiler accepts -mavx2... " >&6; }
-if test "${ax_cv_check_cflags___mavx2+set}" = set; then
+ if test x"$ax_cv_cpu_has_bmi2_ext" = xyes; then
+ CFLAGS=
+ if test x"$ax_cv_c_compiler_vendor" = xintel; then
+ TEST_CFLAGS="$SIMD_AVX2_CFLAGS"
+ else
+ TEST_CFLAGS="$SIMD_AVX2_CFLAGS -mbmi2"
+ fi
+ as_CACHEVAR=`$as_echo "ax_cv_check_cflags__$TEST_CFLAGS" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking whether C compiler accepts $TEST_CFLAGS" >&5
+$as_echo_n "checking whether C compiler accepts $TEST_CFLAGS... " >&6; }
+if { as_var=$as_CACHEVAR; eval "test \"\${$as_var+set}\" = set"; }; then
$as_echo_n "(cached) " >&6
else
ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mavx2"
+ CFLAGS="$CFLAGS $TEST_CFLAGS"
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
@@ -24856,40 +22653,41 @@ $as_echo "$ac_try_echo") >&5
test -z "$ac_c_werror_flag" ||
test ! -s conftest.err
} && test -s conftest.$ac_objext; then
- ax_cv_check_cflags___mavx2=yes
+ eval "$as_CACHEVAR=yes"
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
- ax_cv_check_cflags___mavx2=no
+ eval "$as_CACHEVAR=no"
fi
rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
CFLAGS=$ax_check_save_flags
fi
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_check_cflags___mavx2" >&5
-$as_echo "$ax_cv_check_cflags___mavx2" >&6; }
-if test x"$ax_cv_check_cflags___mavx2" = xyes; then
- ax_cv_compile_avx2_ext=yes
+ac_res=`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+if test x"`eval 'as_val=${'$as_CACHEVAR'}
+ $as_echo "$as_val"'`" = xyes; then
+ ax_cv_compile_bmi2_ext=yes
else
ax_cv_ext_compile_problem=yes
fi
- if test x"$ax_cv_compile_avx2_ext" != x"yes"; then
- { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
-$as_echo "$as_me: WARNING: Your CPU supports AVX2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
+ if test x"$ax_cv_compile_bmi2_ext" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your CPU supports BMI2 instructions but not your compiler. Can you try another compiler or update yours?" >&5
+$as_echo "$as_me: WARNING: Your CPU supports BMI2 instructions but not your compiler. Can you try another compiler or update yours?" >&2;}
else
- { $as_echo "$as_me:$LINENO: checking for immintrin.h header file" >&5
-$as_echo_n "checking for immintrin.h header file... " >&6; }
- CFLAGS=-mavx2
+ CFLAGS=$TEST_CFLAGS
cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h. */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
-#include <immintrin.h>
+
int
main ()
{
@@ -24919,7 +22717,7 @@ $as_echo "$ac_try_echo") >&5
test "$cross_compiling" = yes ||
$as_test_x conftest$ac_exeext
}; then
- ax_cv_link_immintrin_h=yes
+ ax_cv_link_bmi2=yes
else
$as_echo "$as_me: failed program was:" >&5
sed 's/^/| /' conftest.$ac_ext >&5
@@ -24930,34 +22728,153 @@ fi
rm -rf conftest.dSYM
rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
conftest$ac_exeext conftest.$ac_ext
- if test x"$ax_cv_link_immintrin_h" != x"yes"; then
- { $as_echo "$as_me:$LINENO: result: no" >&5
-$as_echo "no" >&6; }
- { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports AVX2 instructions but not your linker." >&5
-$as_echo "$as_me: WARNING: Your compiler supports AVX2 instructions but not your linker." >&2;}
+ if test x"$ax_cv_link_bmi2" != xyes; then
+ { $as_echo "$as_me:$LINENO: WARNING: Your compiler supports -mbmi2 but not your linker. Can you try another linker or update yours?" >&5
+$as_echo "$as_me: WARNING: Your compiler supports -mbmi2 but not your linker. Can you try another linker or update yours?" >&2;}
else
- { $as_echo "$as_me:$LINENO: result: yes" >&5
+ SIMD_AVX2_CFLAGS=$CFLAGS
+ { $as_echo "$as_me:$LINENO: checking for _pext support" >&5
+$as_echo_n "checking for _pext support... " >&6; }
+ if test "$cross_compiling" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run test program while cross compiling
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <immintrin.h>
+int
+main ()
+{
+return (_pext_u32(0x01234567u,0x0f33aa55) == 0x00001b0b) ? 0 : 9;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
$as_echo "yes" >&6; }
- SIMD_CFLAGS="$SIMD_CFLAGS -mavx2"
cat >>confdefs.h <<\_ACEOF
-#define HAVE_AVX2 1
+#define HAVE_PEXT 1
_ACEOF
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+{ $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
fi
fi
fi
- ;;
+ ;;
esac
CFLAGS=$CFLAGS_ORIG
- # Sets SIMD_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX
- ;;
-esac
+
+
+
+
+
+
+
+if test "x$ax_make_avx2" = xyes; then
+ compile_level=avx2
+elif test "x$ax_make_sse42" = xyes; then
+ compile_level=sse42
+elif test "x$ax_make_sse41" = xyes; then
+ compile_level=sse41
+elif test "x$ax_make_ssse3" = xyes; then
+ compile_level=ssse3
+elif test "x$ax_make_sse2" = xyes; then
+ compile_level=sse2
+else
+ compile_level=none
+fi
+
+ if test "$compile_level" = avx2; then
+ MAKE_AVX2_TRUE=
+ MAKE_AVX2_FALSE='#'
+else
+ MAKE_AVX2_TRUE='#'
+ MAKE_AVX2_FALSE=
+fi
+
+ if test "$compile_level" = sse42; then
+ MAKE_SSE4_2_TRUE=
+ MAKE_SSE4_2_FALSE='#'
+else
+ MAKE_SSE4_2_TRUE='#'
+ MAKE_SSE4_2_FALSE=
+fi
+
+ if test "$compile_level" = sse41; then
+ MAKE_SSE4_1_TRUE=
+ MAKE_SSE4_1_FALSE='#'
+else
+ MAKE_SSE4_1_TRUE='#'
+ MAKE_SSE4_1_FALSE=
+fi
+
+ if test "$compile_level" = ssse3; then
+ MAKE_SSSE3_TRUE=
+ MAKE_SSSE3_FALSE='#'
+else
+ MAKE_SSSE3_TRUE='#'
+ MAKE_SSSE3_FALSE=
+fi
+
+ if test "$compile_level" = sse2; then
+ MAKE_SSE2_TRUE=
+ MAKE_SSE2_FALSE='#'
+else
+ MAKE_SSE2_TRUE='#'
+ MAKE_SSE2_FALSE=
+fi
+
+
+
# Genome directory
{ $as_echo "$as_me:$LINENO: checking gmapdb" >&5
@@ -26073,8 +23990,7 @@ ac_config_files="$ac_config_files Makefile"
ac_config_files="$ac_config_files src/Makefile"
-ac_config_files="$ac_config_files mpi/Makefile"
-
+#AC_CONFIG_FILES([mpi/Makefile])
ac_config_files="$ac_config_files util/Makefile"
ac_config_files="$ac_config_files util/gmap_compress.pl"
@@ -26269,6 +24185,41 @@ Usually this means the macro was only invoked conditionally." >&2;}
{ (exit 1); exit 1; }; }
fi
+if test -z "${MAKE_AVX2_TRUE}" && test -z "${MAKE_AVX2_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"MAKE_AVX2\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"MAKE_AVX2\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${MAKE_SSE4_2_TRUE}" && test -z "${MAKE_SSE4_2_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"MAKE_SSE4_2\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"MAKE_SSE4_2\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${MAKE_SSE4_1_TRUE}" && test -z "${MAKE_SSE4_1_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"MAKE_SSE4_1\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"MAKE_SSE4_1\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${MAKE_SSSE3_TRUE}" && test -z "${MAKE_SSSE3_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"MAKE_SSSE3\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"MAKE_SSSE3\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${MAKE_SSE2_TRUE}" && test -z "${MAKE_SSE2_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"MAKE_SSE2\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"MAKE_SSE2\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
: ${CONFIG_STATUS=./config.status}
ac_write_fail=0
@@ -26591,7 +24542,7 @@ exec 6>&1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by gmap $as_me 2015-12-31, which was
+This file was extended by gmap $as_me 2016-04-04, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -26654,7 +24605,7 @@ Report bugs to <bug-autoconf at gnu.org>."
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_version="\\
-gmap config.status 2015-12-31
+gmap config.status 2016-04-04
configured by $0, generated by GNU Autoconf 2.63,
with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
@@ -27037,7 +24988,6 @@ do
"libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
"Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
"src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
- "mpi/Makefile") CONFIG_FILES="$CONFIG_FILES mpi/Makefile" ;;
"util/Makefile") CONFIG_FILES="$CONFIG_FILES util/Makefile" ;;
"util/gmap_compress.pl") CONFIG_FILES="$CONFIG_FILES util/gmap_compress.pl" ;;
"util/gmap_uncompress.pl") CONFIG_FILES="$CONFIG_FILES util/gmap_uncompress.pl" ;;
@@ -28671,30 +26621,59 @@ $as_echo_n "checking Standard linker flags to be used... " >&6; }
{ $as_echo "$as_me:$LINENO: result: $LD_FLAGS" >&5
$as_echo "$LD_FLAGS" >&6; }
-{ $as_echo "$as_me:$LINENO: checking MPI compiler and flags to be used" >&5
-$as_echo_n "checking MPI compiler and flags to be used... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: $MPICC $MPI_CFLAGS" >&5
-$as_echo "$MPICC $MPI_CFLAGS" >&6; }
-{ $as_echo "$as_me:$LINENO: checking MPI linker flags to be used" >&5
-$as_echo_n "checking MPI linker flags to be used... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: $MPI_CLDFLAGS" >&5
-$as_echo "$MPI_CLDFLAGS" >&6; }
+#AC_MSG_CHECKING(MPI compiler and flags to be used)
+#AC_MSG_RESULT($MPICC $MPI_CFLAGS)
+#AC_MSG_CHECKING(MPI linker flags to be used)
+#AC_MSG_RESULT($MPI_CLDFLAGS)
{ $as_echo "$as_me:$LINENO: checking pthread compiler flags to be used" >&5
$as_echo_n "checking pthread compiler flags to be used... " >&6; }
{ $as_echo "$as_me:$LINENO: result: $PTHREAD_CFLAGS" >&5
$as_echo "$PTHREAD_CFLAGS" >&6; }
-{ $as_echo "$as_me:$LINENO: checking popcnt compiler flags to be used" >&5
-$as_echo_n "checking popcnt compiler flags to be used... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: $POPCNT_CFLAGS" >&5
-$as_echo "$POPCNT_CFLAGS" >&6; }
-
-{ $as_echo "$as_me:$LINENO: checking SIMD features available on computer" >&5
-$as_echo_n "checking SIMD features available on computer... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: $ax_cv_cpu_features" >&5
-$as_echo "$ax_cv_cpu_features" >&6; }
-{ $as_echo "$as_me:$LINENO: checking SIMD compiler flags to be used" >&5
-$as_echo_n "checking SIMD compiler flags to be used... " >&6; }
-{ $as_echo "$as_me:$LINENO: result: $SIMD_CFLAGS" >&5
-$as_echo "$SIMD_CFLAGS" >&6; }
+
+{ $as_echo "$as_me:$LINENO: checking compile level" >&5
+$as_echo_n "checking compile level... " >&6; }
+{ $as_echo "$as_me:$LINENO: result: $compile_level" >&5
+$as_echo "$compile_level" >&6; }
+
+if test "$compile_level" = avx2; then
+ { $as_echo "$as_me:$LINENO: checking AVX2 compiler flags to be used" >&5
+$as_echo_n "checking AVX2 compiler flags to be used... " >&6; }
+ { $as_echo "$as_me:$LINENO: result: $SIMD_AVX2_CFLAGS" >&5
+$as_echo "$SIMD_AVX2_CFLAGS" >&6; }
+fi
+
+if test "$compile_level" = sse42; then
+ { $as_echo "$as_me:$LINENO: checking SSE4.2 compiler flags to be used" >&5
+$as_echo_n "checking SSE4.2 compiler flags to be used... " >&6; }
+ { $as_echo "$as_me:$LINENO: result: $SIMD_SSE4_2_CFLAGS" >&5
+$as_echo "$SIMD_SSE4_2_CFLAGS" >&6; }
+fi
+
+if test "$compile_level" = sse41; then
+ { $as_echo "$as_me:$LINENO: checking SSE4.1 compiler flags to be used" >&5
+$as_echo_n "checking SSE4.1 compiler flags to be used... " >&6; }
+ { $as_echo "$as_me:$LINENO: result: $SIMD_SSE4_1_CFLAGS" >&5
+$as_echo "$SIMD_SSE4_1_CFLAGS" >&6; }
+fi
+
+if test "$compile_level" = ssse3; then
+ { $as_echo "$as_me:$LINENO: checking SSSE3 compiler flags to be used" >&5
+$as_echo_n "checking SSSE3 compiler flags to be used... " >&6; }
+ { $as_echo "$as_me:$LINENO: result: $SIMD_SSSE3_CFLAGS" >&5
+$as_echo "$SIMD_SSSE3_CFLAGS" >&6; }
+fi
+
+if test "$compile_level" = sse2; then
+ { $as_echo "$as_me:$LINENO: checking SSE2 compiler flags to be used" >&5
+$as_echo_n "checking SSE2 compiler flags to be used... " >&6; }
+ { $as_echo "$as_me:$LINENO: result: $SIMD_SSE2_CFLAGS" >&5
+$as_echo "$SIMD_SSE2_CFLAGS" >&6; }
+fi
+
+
+#AC_MSG_CHECKING(SIMD features available on computer)
+#AC_MSG_RESULT($ax_cv_cpu_features)
+#AC_MSG_CHECKING(SIMD compiler flags to be used)
+#AC_MSG_RESULT($SIMD_CFLAGS)
diff --git a/configure.ac b/configure.ac
index 153c7df..a0e9ee4 100644
--- a/configure.ac
+++ b/configure.ac
@@ -145,6 +145,9 @@ ACX_PATH_PERL
AC_PROG_CC
AM_PROG_CC_C_O
+AX_COMPILER_VENDOR
+# AM_CONDITIONAL(INTEL_COMPILER,test "x$ax_cv_c_compiler_vendor" = xintel)
+
AX_MPI # Sets MPICC to use for isolated source files that need it
# AC_PROG_CC_MPI # This sets CC to mpicc
@@ -310,231 +313,227 @@ ACX_FUNC_FOPEN_BINARY
ACX_FUNC_FOPEN_TEXT
-AC_MSG_CHECKING(for builtin popcount/clz/ctz features)
-AC_ARG_ENABLE([builtin-popcount],
- AC_HELP_STRING([--enable-builtin-popcount],
- [Enable -mpopcnt if it __builtin_popcount compiles and runs (default=yes). May want to disable if compiling on one machine and running on another.]),
- [answer="$enableval"],
- [answer=""])
-case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ACX_BUILTIN_POPCOUNT
- ;;
-
- xno)
- AC_MSG_RESULT(disabled)
- ;;
+#AC_MSG_CHECKING(for builtin popcount/clz/ctz features)
+#AC_ARG_ENABLE([builtin-popcount],
+# AC_HELP_STRING([--enable-builtin-popcount],
+# [Enable -mpopcnt if it __builtin_popcount compiles and runs (default=yes). May want to disable if compiling on one machine and running on another.]),
+# [answer="$enableval"],
+# [answer=""])
+#case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ACX_BUILTIN_POPCOUNT
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled)
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ACX_BUILTIN_POPCOUNT
+# ;;
+#esac
+#if test x"$acx_mpopcnt_ok" = x"yes"; then
+# POPCNT_CFLAGS="$POPCNT_CFLAGS -mpopcnt"
+#fi
+#AC_SUBST(POPCNT_CFLAGS)
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ACX_BUILTIN_POPCOUNT
- ;;
-esac
-if test x"$acx_mpopcnt_ok" = x"yes"; then
- POPCNT_CFLAGS="$POPCNT_CFLAGS -mpopcnt"
-fi
-AC_SUBST(POPCNT_CFLAGS)
ACX_ASM_BSR
-AC_MSG_CHECKING(whether sse2 is enabled)
-AC_ARG_ENABLE([sse2],
- AC_HELP_STRING([--enable-sse2],
- [Enable sse2 simd commands if they compile and run (default=yes).]),
- [answer="$enableval"],
- [answer=""])
-case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ax_cv_want_sse2_ext=yes
- ;;
-
- xno)
- AC_MSG_RESULT(disabled by user)
- ax_cv_want_sse2_ext=no
- ;;
+#AC_MSG_CHECKING(whether sse2 is enabled)
+#AC_ARG_ENABLE([sse2],
+# AC_HELP_STRING([--enable-sse2],
+# [Enable sse2 simd commands if they compile and run (default=yes).]),
+# [answer="$enableval"],
+# [answer=""])
+#case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_sse2_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_sse2_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_sse2_ext=yes
+# ;;
+#esac
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ax_cv_want_sse2_ext=yes
- ;;
-esac
-ax_cv_sse2_shift_defect=no
-if test "$ax_cv_want_sse2_ext" = yes; then
ACX_SSE2_SHIFT_DEFECT
-fi
-AC_MSG_CHECKING(whether ssse3 is enabled)
-AC_ARG_ENABLE([ssse3],
- AC_HELP_STRING([--enable-ssse3],
- [Enable ssse3 simd commands if they compile and run (default=yes). Requires that sse2 be enabled.]),
- [answer="$enableval"],
- [answer=""])
-if test "$ax_cv_want_sse2_ext" = no; then
- AC_MSG_RESULT([disabled because the user disabled sse2])
- ax_cv_want_ssse3_ext=no
-else
- case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ax_cv_want_ssse3_ext=yes
- ;;
-
- xno)
- AC_MSG_RESULT(disabled by user)
- ax_cv_want_ssse3_ext=no
- ;;
-
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ax_cv_want_ssse3_ext=yes
- ;;
- esac
-fi
+#AC_MSG_CHECKING(whether ssse3 is enabled)
+#AC_ARG_ENABLE([ssse3],
+# AC_HELP_STRING([--enable-ssse3],
+# [Enable ssse3 simd commands if they compile and run (default=yes). Requires that sse2 be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_sse2_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled sse2])
+# ax_cv_want_ssse3_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_ssse3_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_ssse3_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_ssse3_ext=yes
+# ;;
+# esac
+#fi
-AC_MSG_CHECKING(whether sse4.1 is enabled)
-AC_ARG_ENABLE([sse4.1],
- AC_HELP_STRING([--enable-sse4.1],
- [Enable sse4.1 simd commands if they compile and run (default=yes). Requires that ssse3 be enabled.]),
- [answer="$enableval"],
- [answer=""])
-if test "$ax_cv_want_ssse3_ext" = no; then
- AC_MSG_RESULT([disabled because the user disabled ssse3])
- ax_cv_want_sse41_ext=no
-else
- case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ax_cv_want_sse41_ext=yes
- ;;
-
- xno)
- AC_MSG_RESULT(disabled by user)
- ax_cv_want_sse41_ext=no
- ;;
-
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ax_cv_want_sse41_ext=yes
- ;;
- esac
-fi
+#AC_MSG_CHECKING(whether sse4.1 is enabled)
+#AC_ARG_ENABLE([sse4.1],
+# AC_HELP_STRING([--enable-sse4.1],
+# [Enable sse4.1 simd commands if they compile and run (default=yes). Requires that ssse3 be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_ssse3_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled ssse3])
+# ax_cv_want_sse41_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_sse41_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_sse41_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_sse41_ext=yes
+# ;;
+# esac
+#fi
-AC_MSG_CHECKING(whether sse4.2 is enabled)
-AC_ARG_ENABLE([sse4.2],
- AC_HELP_STRING([--enable-sse4.2],
- [Enable sse4.2 simd commands if they compile and run (default=yes). Requires that sse4.1 be enabled.]),
- [answer="$enableval"],
- [answer=""])
-if test "$ax_cv_want_sse41_ext" = no; then
- AC_MSG_RESULT([disabled because the user disabled sse4.1])
- ax_cv_want_sse42_ext=no
-else
- case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ax_cv_want_sse42_ext=yes
- ;;
-
- xno)
- AC_MSG_RESULT(disabled by user)
- ax_cv_want_sse42_ext=no
- ;;
-
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ax_cv_want_sse42_ext=yes
- ;;
- esac
-fi
+#AC_MSG_CHECKING(whether sse4.2 is enabled)
+#AC_ARG_ENABLE([sse4.2],
+# AC_HELP_STRING([--enable-sse4.2],
+# [Enable sse4.2 simd commands if they compile and run (default=yes). Requires that sse4.1 be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_sse41_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled sse4.1])
+# ax_cv_want_sse42_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_sse42_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_sse42_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_sse42_ext=yes
+# ;;
+# esac
+#fi
-AC_MSG_CHECKING(whether avx is enabled)
-AC_ARG_ENABLE([avx],
- AC_HELP_STRING([--enable-avx],
- [Enable avx simd commands if they compile and run (default=yes). Requires that sse4.2 be enabled.]),
- [answer="$enableval"],
- [answer=""])
-if test "$ax_cv_want_sse42_ext" = no; then
- AC_MSG_RESULT([disabled because the user disabled sse4.2])
- ax_cv_want_avx_ext=no
-else
- case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ax_cv_want_avx_ext=yes
- ;;
-
- xno)
- AC_MSG_RESULT(disabled by user)
- ax_cv_want_avx_ext=no
- ;;
-
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ax_cv_want_avx_ext=yes
- ;;
- esac
-fi
+#AC_MSG_CHECKING(whether avx2 is enabled)
+#AC_ARG_ENABLE([avx2],
+# AC_HELP_STRING([--enable-avx2],
+# [Enable avx2 simd commands if they compile and run (default=yes). Requires that avx be enabled.]),
+# [answer="$enableval"],
+# [answer=""])
+#if test "$ax_cv_want_avx_ext" = no; then
+# AC_MSG_RESULT([disabled because the user disabled avx])
+# ax_cv_want_avx2_ext=no
+#else
+# case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# ax_cv_want_avx2_ext=yes
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled by user)
+# ax_cv_want_avx2_ext=no
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# ax_cv_want_avx2_ext=yes
+# ;;
+# esac
+#fi
-AC_MSG_CHECKING(whether avx2 is enabled)
-AC_ARG_ENABLE([avx2],
- AC_HELP_STRING([--enable-avx2],
- [Enable avx2 simd commands if they compile and run (default=yes). Requires that avx be enabled.]),
- [answer="$enableval"],
- [answer=""])
-if test "$ax_cv_want_avx_ext" = no; then
- AC_MSG_RESULT([disabled because the user disabled avx])
- ax_cv_want_avx2_ext=no
+
+#AC_MSG_CHECKING(for whether simd is enabled)
+#AC_ARG_ENABLE([simd],
+# AC_HELP_STRING([--enable-simd],
+# [Enable simd commands in general if they compile and run (default=yes).]),
+# [answer="$enableval"],
+# [answer=""])
+#case x"$answer" in
+# xyes)
+# AC_MSG_RESULT(enabled)
+# AX_EXT # Sets various SIMD_xxx_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX2
+# ;;
+#
+# xno)
+# AC_MSG_RESULT(disabled)
+# ;;
+#
+# x)
+# AC_MSG_RESULT([not specified so enabled by default])
+# AX_EXT # Sets various SIMD_xxx_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX2
+# ;;
+#esac
+
+
+AX_EXT
+
+if test "x$ax_make_avx2" = xyes; then
+ compile_level=avx2
+elif test "x$ax_make_sse42" = xyes; then
+ compile_level=sse42
+elif test "x$ax_make_sse41" = xyes; then
+ compile_level=sse41
+elif test "x$ax_make_ssse3" = xyes; then
+ compile_level=ssse3
+elif test "x$ax_make_sse2" = xyes; then
+ compile_level=sse2
else
- case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- ax_cv_want_avx2_ext=yes
- ;;
-
- xno)
- AC_MSG_RESULT(disabled by user)
- ax_cv_want_avx2_ext=no
- ;;
-
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- ax_cv_want_avx2_ext=yes
- ;;
- esac
+ compile_level=none
fi
+AM_CONDITIONAL(MAKE_AVX2,[test "$compile_level" = avx2])
+AM_CONDITIONAL(MAKE_SSE4_2,[test "$compile_level" = sse42])
+AM_CONDITIONAL(MAKE_SSE4_1,[test "$compile_level" = sse41])
+AM_CONDITIONAL(MAKE_SSSE3,[test "$compile_level" = ssse3])
+AM_CONDITIONAL(MAKE_SSE2,[test "$compile_level" = sse2])
-AC_MSG_CHECKING(whether simd is enabled)
-AC_ARG_ENABLE([simd],
- AC_HELP_STRING([--enable-simd],
- [Enable simd commands in general if they compile and run (default=yes).]),
- [answer="$enableval"],
- [answer=""])
-case x"$answer" in
- xyes)
- AC_MSG_RESULT(enabled)
- AX_EXT # Sets SIMD_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX
- ;;
-
- xno)
- AC_MSG_RESULT(disabled)
- ;;
- x)
- AC_MSG_RESULT([not specified so enabled by default])
- AX_EXT # Sets SIMD_CFLAGS, and HAVE_ALTIVEC,HAVE_MMX,HAVE_SSE,HAVE_SSE2,HAVE_SSE3,HAVE_SSSE3,HAVE_SSE4_1,HAVE_SSE4_2,HAVE_AVX
- ;;
-esac
# Genome directory
AC_MSG_CHECKING(gmapdb)
@@ -653,7 +652,7 @@ AC_SUBST(BZLIB_LIBS)
AC_CONFIG_FILES([Makefile])
AC_CONFIG_FILES([src/Makefile])
-AC_CONFIG_FILES([mpi/Makefile])
+#AC_CONFIG_FILES([mpi/Makefile])
AC_CONFIG_FILES([util/Makefile])
AC_CONFIG_FILES([util/gmap_compress.pl])
AC_CONFIG_FILES([util/gmap_uncompress.pl])
@@ -762,18 +761,45 @@ AC_MSG_RESULT($CC $CFLAGS)
AC_MSG_CHECKING(Standard linker flags to be used)
AC_MSG_RESULT($LD_FLAGS)
-AC_MSG_CHECKING(MPI compiler and flags to be used)
-AC_MSG_RESULT($MPICC $MPI_CFLAGS)
-AC_MSG_CHECKING(MPI linker flags to be used)
-AC_MSG_RESULT($MPI_CLDFLAGS)
+#AC_MSG_CHECKING(MPI compiler and flags to be used)
+#AC_MSG_RESULT($MPICC $MPI_CFLAGS)
+#AC_MSG_CHECKING(MPI linker flags to be used)
+#AC_MSG_RESULT($MPI_CLDFLAGS)
AC_MSG_CHECKING(pthread compiler flags to be used)
AC_MSG_RESULT($PTHREAD_CFLAGS)
-AC_MSG_CHECKING(popcnt compiler flags to be used)
-AC_MSG_RESULT($POPCNT_CFLAGS)
-AC_MSG_CHECKING(SIMD features available on computer)
-AC_MSG_RESULT($ax_cv_cpu_features)
-AC_MSG_CHECKING(SIMD compiler flags to be used)
-AC_MSG_RESULT($SIMD_CFLAGS)
+AC_MSG_CHECKING(compile level)
+AC_MSG_RESULT($compile_level)
+
+if test "$compile_level" = avx2; then
+ AC_MSG_CHECKING(AVX2 compiler flags to be used)
+ AC_MSG_RESULT($SIMD_AVX2_CFLAGS)
+fi
+
+if test "$compile_level" = sse42; then
+ AC_MSG_CHECKING(SSE4.2 compiler flags to be used)
+ AC_MSG_RESULT($SIMD_SSE4_2_CFLAGS)
+fi
+
+if test "$compile_level" = sse41; then
+ AC_MSG_CHECKING(SSE4.1 compiler flags to be used)
+ AC_MSG_RESULT($SIMD_SSE4_1_CFLAGS)
+fi
+
+if test "$compile_level" = ssse3; then
+ AC_MSG_CHECKING(SSSE3 compiler flags to be used)
+ AC_MSG_RESULT($SIMD_SSSE3_CFLAGS)
+fi
+
+if test "$compile_level" = sse2; then
+ AC_MSG_CHECKING(SSE2 compiler flags to be used)
+ AC_MSG_RESULT($SIMD_SSE2_CFLAGS)
+fi
+
+
+#AC_MSG_CHECKING(SIMD features available on computer)
+#AC_MSG_RESULT($ax_cv_cpu_features)
+#AC_MSG_CHECKING(SIMD compiler flags to be used)
+#AC_MSG_RESULT($SIMD_CFLAGS)
diff --git a/mpi/Makefile.am b/mpi/Makefile.am
deleted file mode 100644
index 533cb61..0000000
--- a/mpi/Makefile.am
+++ /dev/null
@@ -1,111 +0,0 @@
-
-
-CC = $(MPICC)
-srcdir = $(top_srcdir)/src
-
-# This is a configure-time conditional
-if MPI_FOUND
-bin_PROGRAMS = mpi_gsnap
-endif
-
-
-MPI_GSNAP_FILES = $(srcdir)/mpidebug.c $(srcdir)/mpidebug.h \
- $(srcdir)/fopen.h $(srcdir)/bool.h $(srcdir)/types.h $(srcdir)/separator.h $(srcdir)/comp.h \
- $(srcdir)/except.c $(srcdir)/except.h $(srcdir)/assert.c $(srcdir)/assert.h $(srcdir)/mem.c $(srcdir)/mem.h \
- $(srcdir)/intlistdef.h $(srcdir)/intlist.c $(srcdir)/intlist.h $(srcdir)/listdef.h $(srcdir)/list.c $(srcdir)/list.h \
- $(srcdir)/littleendian.c $(srcdir)/littleendian.h $(srcdir)/bigendian.c $(srcdir)/bigendian.h \
- $(srcdir)/univinterval.c $(srcdir)/univinterval.h $(srcdir)/interval.c $(srcdir)/interval.h \
- $(srcdir)/uintlist.c $(srcdir)/uintlist.h \
- $(srcdir)/stopwatch.c $(srcdir)/stopwatch.h $(srcdir)/access.c $(srcdir)/access.h \
- $(srcdir)/filestring.c $(srcdir)/filestring.h \
- $(srcdir)/iit-read-univ.c $(srcdir)/iit-read-univ.h $(srcdir)/iitdef.h $(srcdir)/iit-read.c $(srcdir)/iit-read.h \
- $(srcdir)/md5.c $(srcdir)/md5.h $(srcdir)/complement.h $(srcdir)/bzip2.c $(srcdir)/bzip2.h $(srcdir)/sequence.c $(srcdir)/sequence.h $(srcdir)/reader.c $(srcdir)/reader.h \
- $(srcdir)/genomicpos.c $(srcdir)/genomicpos.h $(srcdir)/compress.c $(srcdir)/compress.h \
- $(srcdir)/genome.c $(srcdir)/genome.h \
- $(srcdir)/popcount.c $(srcdir)/popcount.h $(srcdir)/genome128_hr.c $(srcdir)/genome128_hr.h $(srcdir)/genome_sites.c $(srcdir)/genome_sites.h \
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diff --git a/mpi/Makefile.in b/mpi/Makefile.in
deleted file mode 100644
index eaafa03..0000000
--- a/mpi/Makefile.in
+++ /dev/null
@@ -1,2042 +0,0 @@
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-# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
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-# gives unlimited permission to copy and/or distribute it,
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-
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-
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-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
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diff --git a/src/ChangeLog b/src/ChangeLog
new file mode 100644
index 0000000..e69de29
diff --git a/src/Makefile.am b/src/Makefile.am
index 836fbff..46ac87c 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -11,6 +11,69 @@ EXTRA_DIST = mpidebug.c mpidebug.h master.c master.h
bin_PROGRAMS = gmap gmapl get-genome gmapindex iit_store iit_get iit_dump \
gsnap gsnapl uniqscan uniqscanl snpindex cmetindex atoiindex \
sam_sort
+bin_PROGRAMS += gmap.nosimd
+bin_PROGRAMS += gmapl.nosimd
+bin_PROGRAMS += gsnap.nosimd
+bin_PROGRAMS += gsnapl.nosimd
+if MAKE_SSE2
+ bin_PROGRAMS += gmap.sse2
+ bin_PROGRAMS += gmapl.sse2
+ bin_PROGRAMS += gsnap.sse2
+ bin_PROGRAMS += gsnapl.sse2
+endif
+if MAKE_SSSE3
+ bin_PROGRAMS += gmap.ssse3
+ bin_PROGRAMS += gmapl.ssse3
+ bin_PROGRAMS += gsnap.ssse3
+ bin_PROGRAMS += gsnapl.ssse3
+endif
+if MAKE_SSE4_1
+ bin_PROGRAMS += gmap.sse41
+ bin_PROGRAMS += gmapl.sse41
+ bin_PROGRAMS += gsnap.sse41
+ bin_PROGRAMS += gsnapl.sse41
+endif
+if MAKE_SSE4_2
+ bin_PROGRAMS += gmap.sse42
+ bin_PROGRAMS += gmapl.sse42
+ bin_PROGRAMS += gsnap.sse42
+ bin_PROGRAMS += gsnapl.sse42
+endif
+if MAKE_AVX2
+ bin_PROGRAMS += gmap.avx2
+ bin_PROGRAMS += gmapl.avx2
+ bin_PROGRAMS += gsnap.avx2
+ bin_PROGRAMS += gsnapl.avx2
+endif
+
+
+GMAP_SELECT_FILES = bool.h cpuid.c cpuid.h gmap_select.c
+gmap_CC = $(CC)
+gmap_CFLAGS = $(AM_CFLAGS)
+gmap_LDFLAGS = $(AM_LDFLAGS)
+gmap_LDADD =
+dist_gmap_SOURCES = $(GMAP_SELECT_FILES)
+
+GMAPL_SELECT_FILES = bool.h cpuid.c cpuid.h gmapl_select.c
+gmapl_CC = $(CC)
+gmapl_CFLAGS = $(AM_CFLAGS)
+gmapl_LDFLAGS = $(AM_LDFLAGS)
+gmapl_LDADD =
+dist_gmapl_SOURCES = $(GMAPL_SELECT_FILES)
+
+GSNAP_SELECT_FILES = bool.h cpuid.c cpuid.h gsnap_select.c
+gsnap_CC = $(CC)
+gsnap_CFLAGS = $(AM_CFLAGS)
+gsnap_LDFLAGS = $(AM_LDFLAGS)
+gsnap_LDADD =
+dist_gsnap_SOURCES = $(GSNAP_SELECT_FILES)
+
+GSNAPL_SELECT_FILES = bool.h cpuid.c cpuid.h gsnapl_select.c
+gsnapl_CC = $(CC)
+gsnapl_CFLAGS = $(AM_CFLAGS)
+gsnapl_LDFLAGS = $(AM_LDFLAGS)
+gsnapl_LDADD =
+dist_gsnapl_SOURCES = $(GSNAPL_SELECT_FILES)
GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
@@ -18,7 +81,7 @@ GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -47,18 +110,48 @@ GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
pbinom.c pbinom.h changepoint.c changepoint.h sense.h fastlog.h stage3.c stage3.h \
request.c request.h result.c result.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- chimera.c chimera.h datadir.c datadir.h \
+ chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gmap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-gmap_CC = $(PTHREAD_CC)
-gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
-gmap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gmap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+gmap_nosimd_CC = $(PTHREAD_CC)
+gmap_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
+gmap_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_nosimd_SOURCES = $(GMAP_FILES)
+
+gmap_sse2_CC = $(PTHREAD_CC)
+gmap_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gmap_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_sse2_SOURCES = $(GMAP_FILES)
+
+gmap_ssse3_CC = $(PTHREAD_CC)
+gmap_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gmap_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_ssse3_SOURCES = $(GMAP_FILES)
+
+gmap_sse41_CC = $(PTHREAD_CC)
+gmap_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gmap_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_sse41_SOURCES = $(GMAP_FILES)
+
+gmap_sse42_CC = $(PTHREAD_CC)
+gmap_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gmap_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_sse42_SOURCES = $(GMAP_FILES)
+
+gmap_avx2_CC = $(PTHREAD_CC)
+gmap_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gmap_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_avx2_SOURCES = $(GMAP_FILES)
-dist_gmap_SOURCES = $(GMAP_FILES)
GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
@@ -66,7 +159,7 @@ GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -95,19 +188,47 @@ GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
pbinom.c pbinom.h changepoint.c changepoint.h sense.h fastlog.h stage3.c stage3.h \
request.c request.h result.c result.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- chimera.c chimera.h datadir.c datadir.h \
+ chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gmap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-gmapl_CC = $(PTHREAD_CC)
-gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
-gmapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gmapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
-
-dist_gmapl_SOURCES = $(GMAPL_FILES)
-
+gmapl_nosimd_CC = $(PTHREAD_CC)
+gmapl_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
+gmapl_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_nosimd_SOURCES = $(GMAPL_FILES)
+
+gmapl_sse2_CC = $(PTHREAD_CC)
+gmapl_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gmapl_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_sse2_SOURCES = $(GMAPL_FILES)
+
+gmapl_ssse3_CC = $(PTHREAD_CC)
+gmapl_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gmapl_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_ssse3_SOURCES = $(GMAPL_FILES)
+
+gmapl_sse41_CC = $(PTHREAD_CC)
+gmapl_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gmapl_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_sse41_SOURCES = $(GMAPL_FILES)
+
+gmapl_sse42_CC = $(PTHREAD_CC)
+gmapl_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gmapl_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_sse42_SOURCES = $(GMAPL_FILES)
+
+gmapl_avx2_CC = $(PTHREAD_CC)
+gmapl_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gmapl_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_avx2_SOURCES = $(GMAPL_FILES)
GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
@@ -116,7 +237,7 @@ GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -141,23 +262,55 @@ GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
- bytecoding.c bytecoding.h univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
+ bytecoding.c bytecoding.h \
+ univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
stage1hr.c stage1hr.h \
request.c request.h resulthr.c resulthr.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gsnap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
# Previously included -lrt for shm_open, but we are not calling that
-gsnap_CC = $(PTHREAD_CC)
-gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
-gsnap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gsnap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+gsnap_nosimd_CC = $(PTHREAD_CC)
+gsnap_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+gsnap_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_nosimd_SOURCES = $(GSNAP_FILES)
+
+gsnap_sse2_CC = $(PTHREAD_CC)
+gsnap_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gsnap_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_sse2_SOURCES = $(GSNAP_FILES)
+
+gsnap_ssse3_CC = $(PTHREAD_CC)
+gsnap_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gsnap_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_ssse3_SOURCES = $(GSNAP_FILES)
+
+gsnap_sse41_CC = $(PTHREAD_CC)
+gsnap_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gsnap_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_sse41_SOURCES = $(GSNAP_FILES)
+
+gsnap_sse42_CC = $(PTHREAD_CC)
+gsnap_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gsnap_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_sse42_SOURCES = $(GSNAP_FILES)
+
+gsnap_avx2_CC = $(PTHREAD_CC)
+gsnap_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gsnap_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_avx2_SOURCES = $(GSNAP_FILES)
+
-dist_gsnap_SOURCES = $(GSNAP_FILES)
GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
@@ -166,7 +319,7 @@ GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h uint8list.c uint8list.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -194,26 +347,56 @@ GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
stage1hr.c stage1hr.h \
request.c request.h resulthr.c resulthr.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gsnap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-gsnapl_CC = $(PTHREAD_CC)
-gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
-gsnapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gsnapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
-
-dist_gsnapl_SOURCES = $(GSNAPL_FILES)
-
-
+gsnapl_nosimd_CC = $(PTHREAD_CC)
+gsnapl_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+gsnapl_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_nosimd_SOURCES = $(GSNAPL_FILES)
+
+gsnapl_sse2_CC = $(PTHREAD_CC)
+gsnapl_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gsnapl_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_sse2_SOURCES = $(GSNAPL_FILES)
+
+gsnapl_ssse3_CC = $(PTHREAD_CC)
+gsnapl_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gsnapl_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_ssse3_SOURCES = $(GSNAPL_FILES)
+
+gsnapl_sse41_CC = $(PTHREAD_CC)
+gsnapl_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gsnapl_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_sse41_SOURCES = $(GSNAPL_FILES)
+
+gsnapl_sse42_CC = $(PTHREAD_CC)
+gsnapl_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gsnapl_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_sse42_SOURCES = $(GSNAPL_FILES)
+
+gsnapl_avx2_CC = $(PTHREAD_CC)
+gsnapl_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gsnapl_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_avx2_SOURCES = $(GSNAPL_FILES)
+
+
+# Build as a non-SIMD program
UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -238,13 +421,14 @@ UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
- bytecoding.c bytecoding.h univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
+ bytecoding.c bytecoding.h \
+ univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
stage1hr.c stage1hr.h resulthr.c resulthr.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscan_CC = $(PTHREAD_CC)
-uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
uniqscan_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscan_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
@@ -256,7 +440,7 @@ UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h uint8list.c uint8list.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -282,23 +466,24 @@ UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
stage1hr.c stage1hr.h resulthr.c resulthr.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscanl_CC = $(PTHREAD_CC)
-uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
uniqscanl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscanl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_uniqscanl_SOURCES = $(UNIQSCANL_FILES)
+# Build utility programs as non-SIMD programs
GMAPINDEX_FILES = fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iit-write-univ.c iit-write-univ.h \
iitdef.h iit-read.c iit-read.h \
@@ -306,15 +491,18 @@ GMAPINDEX_FILES = fopen.h bool.h types.h \
genomicpos.c genomicpos.h compress-write.c compress-write.h genome-write.c genome-write.h \
compress.c compress.h popcount.c popcount.h genome128_hr.c genome128_hr.h \
bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
- bitpack64-access.c bitpack64-access.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.c indexdb.h indexdb-write.c indexdb-write.h \
- table.c table.h tableuint.c tableuint.h tableuint8.c tableuint8.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.c indexdb.h \
+ indexdb-write.c indexdb-write.h \
+ table.c table.h tableuint.c tableuint.h tableuint8.c tableuint8.h tableint.c tableint.h \
chrom.c chrom.h segmentpos.c segmentpos.h \
- saca-k.c saca-k.h uint8list.c uint8list.h bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ saca-k.c saca-k.h uint8list.c uint8list.h \
+ bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ parserange.c parserange.h \
gmapindex.c
gmapindex_CC = $(PTHREAD_CC)
-gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DUTILITYP=1
+gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
gmapindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapindex_SOURCES = $(GMAPINDEX_FILES)
@@ -325,20 +513,22 @@ SNPINDEX_FILES = fopen.h bool.h types.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
genomicpos.c genomicpos.h compress.c compress.h compress-write.c compress-write.h \
popcount.c popcount.h genome128_hr.c genome128_hr.h \
- bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.c indexdb.h indexdb-write.c indexdb-write.h \
+ bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.c indexdb.h \
+ indexdb-write.c indexdb-write.h \
chrom.c chrom.h \
complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
- datadir.c datadir.h \
+ datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h snpindex.c
snpindex_CC = $(PTHREAD_CC)
-snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
snpindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
snpindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_snpindex_SOURCES = $(SNPINDEX_FILES)
@@ -348,23 +538,26 @@ CMETINDEX_FILES = fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
genomicpos.c genomicpos.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
univinterval.c univinterval.h interval.h interval.c \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.h iit-read.c \
complement.h compress.c compress.h compress-write.c compress-write.h \
popcount.c popcount.h genome128_hr.c genome128_hr.h \
- bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.h indexdb.c indexdb-write.c indexdb-write.h \
+ bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.h indexdb.c \
+ indexdb-write.c indexdb-write.h \
cmet.c cmet.h \
complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
uintlist.c uintlist.h intlist.c intlist.h \
- saca-k.c saca-k.h uint8list.c uint8list.h bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
- list.c list.h listdef.h datadir.c datadir.h \
+ saca-k.c saca-k.h uint8list.c uint8list.h \
+ bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ list.c list.h listdef.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h cmetindex.c
cmetindex_CC = $(PTHREAD_CC)
-cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
cmetindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
cmetindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_cmetindex_SOURCES = $(CMETINDEX_FILES)
@@ -374,23 +567,26 @@ ATOIINDEX_FILES = fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
genomicpos.c genomicpos.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
univinterval.c univinterval.h interval.h interval.c \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.h iit-read.c \
complement.h compress.c compress.h compress-write.c compress-write.h \
popcount.c popcount.h genome128_hr.c genome128_hr.h \
- bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.h indexdb.c indexdb-write.c indexdb-write.h \
+ bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.h indexdb.c \
+ indexdb-write.c indexdb-write.h \
atoi.c atoi.h \
complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
uintlist.c uintlist.h intlist.c intlist.h \
- saca-k.c saca-k.h uint8list.c uint8list.h bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
- list.c list.h listdef.h datadir.c datadir.h \
+ saca-k.c saca-k.h uint8list.c uint8list.h \
+ bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ list.c list.h listdef.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h atoiindex.c
atoiindex_CC = $(PTHREAD_CC)
-atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
atoiindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
atoiindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_atoiindex_SOURCES = $(ATOIINDEX_FILES)
@@ -401,7 +597,7 @@ GET_GENOME_FILES = fopen.h bool.h types.h separator.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
@@ -424,7 +620,7 @@ IIT_STORE_FILES = fopen.h bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
doublelist.c doublelist.h \
iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
tableint.c tableint.h table.c table.h chrom.c chrom.h \
@@ -443,7 +639,7 @@ IIT_GET_FILES = fopen.h bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
complement.h parserange.c parserange.h getopt.c getopt1.c getopt.h iit_get.c
@@ -459,9 +655,9 @@ IIT_DUMP_FILES = fopen.h bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
intlistdef.h intlist.c intlist.h list.c list.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
- iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
+ iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h iit_dump.c
iit_dump_CC = $(PTHREAD_CC)
@@ -476,11 +672,11 @@ SAM_SORT_FILES = bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
genomicpos.h chrnum.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
filestring.c filestring.h \
- iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
+ parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
samflags.h samheader.c samheader.h samread.c samread.h \
datadir.c datadir.h \
getopt.c getopt1.c getopt.h sam_sort.c
@@ -490,3 +686,27 @@ sam_sort_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILIT
sam_sort_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
sam_sort_LDADD = $(PTHREAD_LIBS)
dist_sam_sort_SOURCES = $(SAM_SORT_FILES)
+
+
+
+#SPLICING_SCORE_FILES = fopen.h bool.h types.h \
+# except.c except.h assert.c assert.h mem.c mem.h \
+# intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
+# univinterval.c univinterval.h interval.c interval.h \
+# uintlist.c uintlist.h \
+# chrom.c chrom.h stopwatch.c stopwatch.h access.c access.h \
+# iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
+# filestring.c filestring.h \
+# md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
+# genome.c genome.h \
+# genomicpos.c genomicpos.h \
+# chrnum.c chrnum.h chrsubset.c chrsubset.h \
+# maxent.c maxent.h \
+# branchpoint.c branchpoint.h \
+# parserange.c parserange.h datadir.c datadir.h getopt.c getopt1.c getopt.h splicing-score.c
+#
+#splicing_score_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\"
+#splicing_score_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)
+#splicing_score_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+#dist_splicing_score_SOURCES =
+#nodist_splicing_score_SOURCES = $(SPLICING_SCORE_FILES)
diff --git a/src/Makefile.in b/src/Makefile.in
index 7e8d342..91032a9 100644
--- a/src/Makefile.in
+++ b/src/Makefile.in
@@ -39,16 +39,31 @@ bin_PROGRAMS = gmap$(EXEEXT) gmapl$(EXEEXT) get-genome$(EXEEXT) \
gmapindex$(EXEEXT) iit_store$(EXEEXT) iit_get$(EXEEXT) \
iit_dump$(EXEEXT) gsnap$(EXEEXT) gsnapl$(EXEEXT) \
uniqscan$(EXEEXT) uniqscanl$(EXEEXT) snpindex$(EXEEXT) \
- cmetindex$(EXEEXT) atoiindex$(EXEEXT) sam_sort$(EXEEXT)
+ cmetindex$(EXEEXT) atoiindex$(EXEEXT) sam_sort$(EXEEXT) \
+ gmap.nosimd$(EXEEXT) gmapl.nosimd$(EXEEXT) \
+ gsnap.nosimd$(EXEEXT) gsnapl.nosimd$(EXEEXT) $(am__EXEEXT_1) \
+ $(am__EXEEXT_2) $(am__EXEEXT_3) $(am__EXEEXT_4) \
+ $(am__EXEEXT_5)
+ at MAKE_SSE2_TRUE@am__append_1 = gmap.sse2 gmapl.sse2 gsnap.sse2 \
+ at MAKE_SSE2_TRUE@ gsnapl.sse2
+ at MAKE_SSSE3_TRUE@am__append_2 = gmap.ssse3 gmapl.ssse3 gsnap.ssse3 \
+ at MAKE_SSSE3_TRUE@ gsnapl.ssse3
+ at MAKE_SSE4_1_TRUE@am__append_3 = gmap.sse41 gmapl.sse41 gsnap.sse41 \
+ at MAKE_SSE4_1_TRUE@ gsnapl.sse41
+ at MAKE_SSE4_2_TRUE@am__append_4 = gmap.sse42 gmapl.sse42 gsnap.sse42 \
+ at MAKE_SSE4_2_TRUE@ gsnapl.sse42
+ at MAKE_AVX2_TRUE@am__append_5 = gmap.avx2 gmapl.avx2 gsnap.avx2 \
+ at MAKE_AVX2_TRUE@ gsnapl.avx2
subdir = src
DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in \
- $(srcdir)/config.h.in
+ $(srcdir)/config.h.in ChangeLog compile
ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/ltoptions.m4 \
$(top_srcdir)/config/ltsugar.m4 \
$(top_srcdir)/config/ltversion.m4 \
$(top_srcdir)/config/lt~obsolete.m4 $(top_srcdir)/acinclude.m4 \
+ $(top_srcdir)/config/ax_compiler_vendor.m4 \
$(top_srcdir)/config/pagesize.m4 \
$(top_srcdir)/config/madvise-flags.m4 \
$(top_srcdir)/config/mmap-flags.m4 \
@@ -57,7 +72,6 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/shm-flags.m4 \
$(top_srcdir)/config/ax_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
- $(top_srcdir)/config/builtin-popcount.m4 \
$(top_srcdir)/config/struct-stat64.m4 \
$(top_srcdir)/config/expand.m4 $(top_srcdir)/config/perl.m4 \
$(top_srcdir)/config/fopen.m4 $(top_srcdir)/config/asm-bsr.m4 \
@@ -72,20 +86,35 @@ mkinstalldirs = $(install_sh) -d
CONFIG_HEADER = config.h
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
+ at MAKE_SSE2_TRUE@am__EXEEXT_1 = gmap.sse2$(EXEEXT) gmapl.sse2$(EXEEXT) \
+ at MAKE_SSE2_TRUE@ gsnap.sse2$(EXEEXT) gsnapl.sse2$(EXEEXT)
+ at MAKE_SSSE3_TRUE@am__EXEEXT_2 = gmap.ssse3$(EXEEXT) \
+ at MAKE_SSSE3_TRUE@ gmapl.ssse3$(EXEEXT) gsnap.ssse3$(EXEEXT) \
+ at MAKE_SSSE3_TRUE@ gsnapl.ssse3$(EXEEXT)
+ at MAKE_SSE4_1_TRUE@am__EXEEXT_3 = gmap.sse41$(EXEEXT) \
+ at MAKE_SSE4_1_TRUE@ gmapl.sse41$(EXEEXT) gsnap.sse41$(EXEEXT) \
+ at MAKE_SSE4_1_TRUE@ gsnapl.sse41$(EXEEXT)
+ at MAKE_SSE4_2_TRUE@am__EXEEXT_4 = gmap.sse42$(EXEEXT) \
+ at MAKE_SSE4_2_TRUE@ gmapl.sse42$(EXEEXT) gsnap.sse42$(EXEEXT) \
+ at MAKE_SSE4_2_TRUE@ gsnapl.sse42$(EXEEXT)
+ at MAKE_AVX2_TRUE@am__EXEEXT_5 = gmap.avx2$(EXEEXT) gmapl.avx2$(EXEEXT) \
+ at MAKE_AVX2_TRUE@ gsnap.avx2$(EXEEXT) gsnapl.avx2$(EXEEXT)
am__installdirs = "$(DESTDIR)$(bindir)"
PROGRAMS = $(bin_PROGRAMS)
am__objects_1 = atoiindex-except.$(OBJEXT) atoiindex-assert.$(OBJEXT) \
atoiindex-mem.$(OBJEXT) atoiindex-littleendian.$(OBJEXT) \
atoiindex-bigendian.$(OBJEXT) atoiindex-genomicpos.$(OBJEXT) \
- atoiindex-stopwatch.$(OBJEXT) atoiindex-access.$(OBJEXT) \
- atoiindex-univinterval.$(OBJEXT) atoiindex-interval.$(OBJEXT) \
- atoiindex-filestring.$(OBJEXT) \
+ atoiindex-stopwatch.$(OBJEXT) atoiindex-semaphore.$(OBJEXT) \
+ atoiindex-access.$(OBJEXT) atoiindex-univinterval.$(OBJEXT) \
+ atoiindex-interval.$(OBJEXT) atoiindex-filestring.$(OBJEXT) \
atoiindex-iit-read-univ.$(OBJEXT) atoiindex-iit-read.$(OBJEXT) \
atoiindex-compress.$(OBJEXT) \
atoiindex-compress-write.$(OBJEXT) \
atoiindex-popcount.$(OBJEXT) atoiindex-genome128_hr.$(OBJEXT) \
atoiindex-bitpack64-read.$(OBJEXT) \
atoiindex-bitpack64-readtwo.$(OBJEXT) \
+ atoiindex-bitpack64-access.$(OBJEXT) \
+ atoiindex-bitpack64-incr.$(OBJEXT) \
atoiindex-bitpack64-write.$(OBJEXT) \
atoiindex-indexdb.$(OBJEXT) atoiindex-indexdb-write.$(OBJEXT) \
atoiindex-atoi.$(OBJEXT) atoiindex-md5.$(OBJEXT) \
@@ -94,8 +123,9 @@ am__objects_1 = atoiindex-except.$(OBJEXT) atoiindex-assert.$(OBJEXT) \
atoiindex-intlist.$(OBJEXT) atoiindex-saca-k.$(OBJEXT) \
atoiindex-uint8list.$(OBJEXT) atoiindex-bytecoding.$(OBJEXT) \
atoiindex-sarray-write.$(OBJEXT) atoiindex-list.$(OBJEXT) \
- atoiindex-datadir.$(OBJEXT) atoiindex-getopt.$(OBJEXT) \
- atoiindex-getopt1.$(OBJEXT) atoiindex-atoiindex.$(OBJEXT)
+ atoiindex-datadir.$(OBJEXT) atoiindex-parserange.$(OBJEXT) \
+ atoiindex-getopt.$(OBJEXT) atoiindex-getopt1.$(OBJEXT) \
+ atoiindex-atoiindex.$(OBJEXT)
dist_atoiindex_OBJECTS = $(am__objects_1)
atoiindex_OBJECTS = $(dist_atoiindex_OBJECTS)
am__DEPENDENCIES_1 =
@@ -107,15 +137,17 @@ atoiindex_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
am__objects_2 = cmetindex-except.$(OBJEXT) cmetindex-assert.$(OBJEXT) \
cmetindex-mem.$(OBJEXT) cmetindex-littleendian.$(OBJEXT) \
cmetindex-bigendian.$(OBJEXT) cmetindex-genomicpos.$(OBJEXT) \
- cmetindex-stopwatch.$(OBJEXT) cmetindex-access.$(OBJEXT) \
- cmetindex-univinterval.$(OBJEXT) cmetindex-interval.$(OBJEXT) \
- cmetindex-filestring.$(OBJEXT) \
+ cmetindex-stopwatch.$(OBJEXT) cmetindex-semaphore.$(OBJEXT) \
+ cmetindex-access.$(OBJEXT) cmetindex-univinterval.$(OBJEXT) \
+ cmetindex-interval.$(OBJEXT) cmetindex-filestring.$(OBJEXT) \
cmetindex-iit-read-univ.$(OBJEXT) cmetindex-iit-read.$(OBJEXT) \
cmetindex-compress.$(OBJEXT) \
cmetindex-compress-write.$(OBJEXT) \
cmetindex-popcount.$(OBJEXT) cmetindex-genome128_hr.$(OBJEXT) \
cmetindex-bitpack64-read.$(OBJEXT) \
cmetindex-bitpack64-readtwo.$(OBJEXT) \
+ cmetindex-bitpack64-access.$(OBJEXT) \
+ cmetindex-bitpack64-incr.$(OBJEXT) \
cmetindex-bitpack64-write.$(OBJEXT) \
cmetindex-indexdb.$(OBJEXT) cmetindex-indexdb-write.$(OBJEXT) \
cmetindex-cmet.$(OBJEXT) cmetindex-md5.$(OBJEXT) \
@@ -124,8 +156,9 @@ am__objects_2 = cmetindex-except.$(OBJEXT) cmetindex-assert.$(OBJEXT) \
cmetindex-intlist.$(OBJEXT) cmetindex-saca-k.$(OBJEXT) \
cmetindex-uint8list.$(OBJEXT) cmetindex-bytecoding.$(OBJEXT) \
cmetindex-sarray-write.$(OBJEXT) cmetindex-list.$(OBJEXT) \
- cmetindex-datadir.$(OBJEXT) cmetindex-getopt.$(OBJEXT) \
- cmetindex-getopt1.$(OBJEXT) cmetindex-cmetindex.$(OBJEXT)
+ cmetindex-datadir.$(OBJEXT) cmetindex-parserange.$(OBJEXT) \
+ cmetindex-getopt.$(OBJEXT) cmetindex-getopt1.$(OBJEXT) \
+ cmetindex-cmetindex.$(OBJEXT)
dist_cmetindex_OBJECTS = $(am__objects_2)
cmetindex_OBJECTS = $(dist_cmetindex_OBJECTS)
cmetindex_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
@@ -140,8 +173,8 @@ am__objects_3 = get_genome-except.$(OBJEXT) \
get_genome-bigendian.$(OBJEXT) \
get_genome-univinterval.$(OBJEXT) \
get_genome-interval.$(OBJEXT) get_genome-uintlist.$(OBJEXT) \
- get_genome-stopwatch.$(OBJEXT) get_genome-access.$(OBJEXT) \
- get_genome-filestring.$(OBJEXT) \
+ get_genome-stopwatch.$(OBJEXT) get_genome-semaphore.$(OBJEXT) \
+ get_genome-access.$(OBJEXT) get_genome-filestring.$(OBJEXT) \
get_genome-iit-read-univ.$(OBJEXT) \
get_genome-iit-read.$(OBJEXT) get_genome-md5.$(OBJEXT) \
get_genome-bzip2.$(OBJEXT) get_genome-sequence.$(OBJEXT) \
@@ -157,61 +190,375 @@ get_genome_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
get_genome_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(get_genome_CFLAGS) \
$(CFLAGS) $(get_genome_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_4 = gmap-except.$(OBJEXT) gmap-assert.$(OBJEXT) \
- gmap-mem.$(OBJEXT) gmap-intlist.$(OBJEXT) gmap-list.$(OBJEXT) \
- gmap-littleendian.$(OBJEXT) gmap-bigendian.$(OBJEXT) \
- gmap-univinterval.$(OBJEXT) gmap-interval.$(OBJEXT) \
- gmap-uintlist.$(OBJEXT) gmap-stopwatch.$(OBJEXT) \
- gmap-access.$(OBJEXT) gmap-filestring.$(OBJEXT) \
- gmap-iit-read-univ.$(OBJEXT) gmap-iit-read.$(OBJEXT) \
- gmap-md5.$(OBJEXT) gmap-bzip2.$(OBJEXT) \
- gmap-sequence.$(OBJEXT) gmap-reader.$(OBJEXT) \
- gmap-genomicpos.$(OBJEXT) gmap-compress.$(OBJEXT) \
- gmap-compress-write.$(OBJEXT) gmap-gbuffer.$(OBJEXT) \
- gmap-genome.$(OBJEXT) gmap-popcount.$(OBJEXT) \
- gmap-genome128_hr.$(OBJEXT) gmap-genome_sites.$(OBJEXT) \
- gmap-genome-write.$(OBJEXT) gmap-bitpack64-read.$(OBJEXT) \
- gmap-bitpack64-readtwo.$(OBJEXT) gmap-indexdb.$(OBJEXT) \
- gmap-indexdb_hr.$(OBJEXT) gmap-oligo.$(OBJEXT) \
- gmap-block.$(OBJEXT) gmap-chrom.$(OBJEXT) \
- gmap-segmentpos.$(OBJEXT) gmap-chrnum.$(OBJEXT) \
- gmap-uinttable.$(OBJEXT) gmap-gregion.$(OBJEXT) \
- gmap-match.$(OBJEXT) gmap-matchpool.$(OBJEXT) \
- gmap-diagnostic.$(OBJEXT) gmap-stage1.$(OBJEXT) \
- gmap-diag.$(OBJEXT) gmap-diagpool.$(OBJEXT) \
- gmap-cmet.$(OBJEXT) gmap-atoi.$(OBJEXT) \
- gmap-orderstat.$(OBJEXT) gmap-oligoindex_hr.$(OBJEXT) \
- gmap-intron.$(OBJEXT) gmap-maxent.$(OBJEXT) \
- gmap-maxent_hr.$(OBJEXT) gmap-pair.$(OBJEXT) \
- gmap-pairpool.$(OBJEXT) gmap-cellpool.$(OBJEXT) \
- gmap-stage2.$(OBJEXT) gmap-doublelist.$(OBJEXT) \
- gmap-smooth.$(OBJEXT) gmap-splicestringpool.$(OBJEXT) \
- gmap-splicetrie_build.$(OBJEXT) gmap-splicetrie.$(OBJEXT) \
- gmap-boyer-moore.$(OBJEXT) gmap-dynprog.$(OBJEXT) \
- gmap-dynprog_simd.$(OBJEXT) gmap-dynprog_single.$(OBJEXT) \
- gmap-dynprog_genome.$(OBJEXT) gmap-dynprog_cdna.$(OBJEXT) \
- gmap-dynprog_end.$(OBJEXT) gmap-translation.$(OBJEXT) \
- gmap-pbinom.$(OBJEXT) gmap-changepoint.$(OBJEXT) \
- gmap-stage3.$(OBJEXT) gmap-request.$(OBJEXT) \
- gmap-result.$(OBJEXT) gmap-output.$(OBJEXT) \
- gmap-inbuffer.$(OBJEXT) gmap-samheader.$(OBJEXT) \
- gmap-outbuffer.$(OBJEXT) gmap-chimera.$(OBJEXT) \
- gmap-datadir.$(OBJEXT) gmap-getopt.$(OBJEXT) \
- gmap-getopt1.$(OBJEXT) gmap-gmap.$(OBJEXT)
+am__objects_4 = gmap-cpuid.$(OBJEXT) gmap-gmap_select.$(OBJEXT)
dist_gmap_OBJECTS = $(am__objects_4)
gmap_OBJECTS = $(dist_gmap_OBJECTS)
-gmap_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
- $(am__DEPENDENCIES_1)
+gmap_DEPENDENCIES =
gmap_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(gmap_CFLAGS) $(CFLAGS) $(gmap_LDFLAGS) \
$(LDFLAGS) -o $@
-am__objects_5 = gmapindex-except.$(OBJEXT) gmapindex-assert.$(OBJEXT) \
+am__objects_5 = gmap_avx2-except.$(OBJEXT) gmap_avx2-assert.$(OBJEXT) \
+ gmap_avx2-mem.$(OBJEXT) gmap_avx2-intlist.$(OBJEXT) \
+ gmap_avx2-list.$(OBJEXT) gmap_avx2-littleendian.$(OBJEXT) \
+ gmap_avx2-bigendian.$(OBJEXT) gmap_avx2-univinterval.$(OBJEXT) \
+ gmap_avx2-interval.$(OBJEXT) gmap_avx2-uintlist.$(OBJEXT) \
+ gmap_avx2-stopwatch.$(OBJEXT) gmap_avx2-semaphore.$(OBJEXT) \
+ gmap_avx2-access.$(OBJEXT) gmap_avx2-filestring.$(OBJEXT) \
+ gmap_avx2-iit-read-univ.$(OBJEXT) gmap_avx2-iit-read.$(OBJEXT) \
+ gmap_avx2-md5.$(OBJEXT) gmap_avx2-bzip2.$(OBJEXT) \
+ gmap_avx2-sequence.$(OBJEXT) gmap_avx2-reader.$(OBJEXT) \
+ gmap_avx2-genomicpos.$(OBJEXT) gmap_avx2-compress.$(OBJEXT) \
+ gmap_avx2-compress-write.$(OBJEXT) gmap_avx2-gbuffer.$(OBJEXT) \
+ gmap_avx2-genome.$(OBJEXT) gmap_avx2-popcount.$(OBJEXT) \
+ gmap_avx2-genome128_hr.$(OBJEXT) \
+ gmap_avx2-genome_sites.$(OBJEXT) \
+ gmap_avx2-genome-write.$(OBJEXT) \
+ gmap_avx2-bitpack64-read.$(OBJEXT) \
+ gmap_avx2-bitpack64-readtwo.$(OBJEXT) \
+ gmap_avx2-indexdb.$(OBJEXT) gmap_avx2-indexdb_hr.$(OBJEXT) \
+ gmap_avx2-oligo.$(OBJEXT) gmap_avx2-block.$(OBJEXT) \
+ gmap_avx2-chrom.$(OBJEXT) gmap_avx2-segmentpos.$(OBJEXT) \
+ gmap_avx2-chrnum.$(OBJEXT) gmap_avx2-uinttable.$(OBJEXT) \
+ gmap_avx2-gregion.$(OBJEXT) gmap_avx2-match.$(OBJEXT) \
+ gmap_avx2-matchpool.$(OBJEXT) gmap_avx2-diagnostic.$(OBJEXT) \
+ gmap_avx2-stage1.$(OBJEXT) gmap_avx2-diag.$(OBJEXT) \
+ gmap_avx2-diagpool.$(OBJEXT) gmap_avx2-cmet.$(OBJEXT) \
+ gmap_avx2-atoi.$(OBJEXT) gmap_avx2-orderstat.$(OBJEXT) \
+ gmap_avx2-oligoindex_hr.$(OBJEXT) gmap_avx2-intron.$(OBJEXT) \
+ gmap_avx2-maxent.$(OBJEXT) gmap_avx2-maxent_hr.$(OBJEXT) \
+ gmap_avx2-pair.$(OBJEXT) gmap_avx2-pairpool.$(OBJEXT) \
+ gmap_avx2-cellpool.$(OBJEXT) gmap_avx2-stage2.$(OBJEXT) \
+ gmap_avx2-doublelist.$(OBJEXT) gmap_avx2-smooth.$(OBJEXT) \
+ gmap_avx2-splicestringpool.$(OBJEXT) \
+ gmap_avx2-splicetrie_build.$(OBJEXT) \
+ gmap_avx2-splicetrie.$(OBJEXT) gmap_avx2-boyer-moore.$(OBJEXT) \
+ gmap_avx2-dynprog.$(OBJEXT) gmap_avx2-dynprog_simd.$(OBJEXT) \
+ gmap_avx2-dynprog_single.$(OBJEXT) \
+ gmap_avx2-dynprog_genome.$(OBJEXT) \
+ gmap_avx2-dynprog_cdna.$(OBJEXT) \
+ gmap_avx2-dynprog_end.$(OBJEXT) \
+ gmap_avx2-translation.$(OBJEXT) gmap_avx2-pbinom.$(OBJEXT) \
+ gmap_avx2-changepoint.$(OBJEXT) gmap_avx2-stage3.$(OBJEXT) \
+ gmap_avx2-request.$(OBJEXT) gmap_avx2-result.$(OBJEXT) \
+ gmap_avx2-output.$(OBJEXT) gmap_avx2-inbuffer.$(OBJEXT) \
+ gmap_avx2-samheader.$(OBJEXT) gmap_avx2-outbuffer.$(OBJEXT) \
+ gmap_avx2-chimera.$(OBJEXT) gmap_avx2-datadir.$(OBJEXT) \
+ gmap_avx2-parserange.$(OBJEXT) gmap_avx2-getopt.$(OBJEXT) \
+ gmap_avx2-getopt1.$(OBJEXT) gmap_avx2-gmap.$(OBJEXT)
+dist_gmap_avx2_OBJECTS = $(am__objects_5)
+gmap_avx2_OBJECTS = $(dist_gmap_avx2_OBJECTS)
+gmap_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmap_avx2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_avx2_CFLAGS) \
+ $(CFLAGS) $(gmap_avx2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_6 = gmap_nosimd-except.$(OBJEXT) \
+ gmap_nosimd-assert.$(OBJEXT) gmap_nosimd-mem.$(OBJEXT) \
+ gmap_nosimd-intlist.$(OBJEXT) gmap_nosimd-list.$(OBJEXT) \
+ gmap_nosimd-littleendian.$(OBJEXT) \
+ gmap_nosimd-bigendian.$(OBJEXT) \
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+ gmap_nosimd-interval.$(OBJEXT) gmap_nosimd-uintlist.$(OBJEXT) \
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+ gmap_nosimd-semaphore.$(OBJEXT) gmap_nosimd-access.$(OBJEXT) \
+ gmap_nosimd-filestring.$(OBJEXT) \
+ gmap_nosimd-iit-read-univ.$(OBJEXT) \
+ gmap_nosimd-iit-read.$(OBJEXT) gmap_nosimd-md5.$(OBJEXT) \
+ gmap_nosimd-bzip2.$(OBJEXT) gmap_nosimd-sequence.$(OBJEXT) \
+ gmap_nosimd-reader.$(OBJEXT) gmap_nosimd-genomicpos.$(OBJEXT) \
+ gmap_nosimd-compress.$(OBJEXT) \
+ gmap_nosimd-compress-write.$(OBJEXT) \
+ gmap_nosimd-gbuffer.$(OBJEXT) gmap_nosimd-genome.$(OBJEXT) \
+ gmap_nosimd-popcount.$(OBJEXT) \
+ gmap_nosimd-genome128_hr.$(OBJEXT) \
+ gmap_nosimd-genome_sites.$(OBJEXT) \
+ gmap_nosimd-genome-write.$(OBJEXT) \
+ gmap_nosimd-bitpack64-read.$(OBJEXT) \
+ gmap_nosimd-bitpack64-readtwo.$(OBJEXT) \
+ gmap_nosimd-indexdb.$(OBJEXT) gmap_nosimd-indexdb_hr.$(OBJEXT) \
+ gmap_nosimd-oligo.$(OBJEXT) gmap_nosimd-block.$(OBJEXT) \
+ gmap_nosimd-chrom.$(OBJEXT) gmap_nosimd-segmentpos.$(OBJEXT) \
+ gmap_nosimd-chrnum.$(OBJEXT) gmap_nosimd-uinttable.$(OBJEXT) \
+ gmap_nosimd-gregion.$(OBJEXT) gmap_nosimd-match.$(OBJEXT) \
+ gmap_nosimd-matchpool.$(OBJEXT) \
+ gmap_nosimd-diagnostic.$(OBJEXT) gmap_nosimd-stage1.$(OBJEXT) \
+ gmap_nosimd-diag.$(OBJEXT) gmap_nosimd-diagpool.$(OBJEXT) \
+ gmap_nosimd-cmet.$(OBJEXT) gmap_nosimd-atoi.$(OBJEXT) \
+ gmap_nosimd-orderstat.$(OBJEXT) \
+ gmap_nosimd-oligoindex_hr.$(OBJEXT) \
+ gmap_nosimd-intron.$(OBJEXT) gmap_nosimd-maxent.$(OBJEXT) \
+ gmap_nosimd-maxent_hr.$(OBJEXT) gmap_nosimd-pair.$(OBJEXT) \
+ gmap_nosimd-pairpool.$(OBJEXT) gmap_nosimd-cellpool.$(OBJEXT) \
+ gmap_nosimd-stage2.$(OBJEXT) gmap_nosimd-doublelist.$(OBJEXT) \
+ gmap_nosimd-smooth.$(OBJEXT) \
+ gmap_nosimd-splicestringpool.$(OBJEXT) \
+ gmap_nosimd-splicetrie_build.$(OBJEXT) \
+ gmap_nosimd-splicetrie.$(OBJEXT) \
+ gmap_nosimd-boyer-moore.$(OBJEXT) \
+ gmap_nosimd-dynprog.$(OBJEXT) \
+ gmap_nosimd-dynprog_simd.$(OBJEXT) \
+ gmap_nosimd-dynprog_single.$(OBJEXT) \
+ gmap_nosimd-dynprog_genome.$(OBJEXT) \
+ gmap_nosimd-dynprog_cdna.$(OBJEXT) \
+ gmap_nosimd-dynprog_end.$(OBJEXT) \
+ gmap_nosimd-translation.$(OBJEXT) gmap_nosimd-pbinom.$(OBJEXT) \
+ gmap_nosimd-changepoint.$(OBJEXT) gmap_nosimd-stage3.$(OBJEXT) \
+ gmap_nosimd-request.$(OBJEXT) gmap_nosimd-result.$(OBJEXT) \
+ gmap_nosimd-output.$(OBJEXT) gmap_nosimd-inbuffer.$(OBJEXT) \
+ gmap_nosimd-samheader.$(OBJEXT) \
+ gmap_nosimd-outbuffer.$(OBJEXT) gmap_nosimd-chimera.$(OBJEXT) \
+ gmap_nosimd-datadir.$(OBJEXT) gmap_nosimd-parserange.$(OBJEXT) \
+ gmap_nosimd-getopt.$(OBJEXT) gmap_nosimd-getopt1.$(OBJEXT) \
+ gmap_nosimd-gmap.$(OBJEXT)
+dist_gmap_nosimd_OBJECTS = $(am__objects_6)
+gmap_nosimd_OBJECTS = $(dist_gmap_nosimd_OBJECTS)
+gmap_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmap_nosimd_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_nosimd_CFLAGS) \
+ $(CFLAGS) $(gmap_nosimd_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_7 = gmap_sse2-except.$(OBJEXT) gmap_sse2-assert.$(OBJEXT) \
+ gmap_sse2-mem.$(OBJEXT) gmap_sse2-intlist.$(OBJEXT) \
+ gmap_sse2-list.$(OBJEXT) gmap_sse2-littleendian.$(OBJEXT) \
+ gmap_sse2-bigendian.$(OBJEXT) gmap_sse2-univinterval.$(OBJEXT) \
+ gmap_sse2-interval.$(OBJEXT) gmap_sse2-uintlist.$(OBJEXT) \
+ gmap_sse2-stopwatch.$(OBJEXT) gmap_sse2-semaphore.$(OBJEXT) \
+ gmap_sse2-access.$(OBJEXT) gmap_sse2-filestring.$(OBJEXT) \
+ gmap_sse2-iit-read-univ.$(OBJEXT) gmap_sse2-iit-read.$(OBJEXT) \
+ gmap_sse2-md5.$(OBJEXT) gmap_sse2-bzip2.$(OBJEXT) \
+ gmap_sse2-sequence.$(OBJEXT) gmap_sse2-reader.$(OBJEXT) \
+ gmap_sse2-genomicpos.$(OBJEXT) gmap_sse2-compress.$(OBJEXT) \
+ gmap_sse2-compress-write.$(OBJEXT) gmap_sse2-gbuffer.$(OBJEXT) \
+ gmap_sse2-genome.$(OBJEXT) gmap_sse2-popcount.$(OBJEXT) \
+ gmap_sse2-genome128_hr.$(OBJEXT) \
+ gmap_sse2-genome_sites.$(OBJEXT) \
+ gmap_sse2-genome-write.$(OBJEXT) \
+ gmap_sse2-bitpack64-read.$(OBJEXT) \
+ gmap_sse2-bitpack64-readtwo.$(OBJEXT) \
+ gmap_sse2-indexdb.$(OBJEXT) gmap_sse2-indexdb_hr.$(OBJEXT) \
+ gmap_sse2-oligo.$(OBJEXT) gmap_sse2-block.$(OBJEXT) \
+ gmap_sse2-chrom.$(OBJEXT) gmap_sse2-segmentpos.$(OBJEXT) \
+ gmap_sse2-chrnum.$(OBJEXT) gmap_sse2-uinttable.$(OBJEXT) \
+ gmap_sse2-gregion.$(OBJEXT) gmap_sse2-match.$(OBJEXT) \
+ gmap_sse2-matchpool.$(OBJEXT) gmap_sse2-diagnostic.$(OBJEXT) \
+ gmap_sse2-stage1.$(OBJEXT) gmap_sse2-diag.$(OBJEXT) \
+ gmap_sse2-diagpool.$(OBJEXT) gmap_sse2-cmet.$(OBJEXT) \
+ gmap_sse2-atoi.$(OBJEXT) gmap_sse2-orderstat.$(OBJEXT) \
+ gmap_sse2-oligoindex_hr.$(OBJEXT) gmap_sse2-intron.$(OBJEXT) \
+ gmap_sse2-maxent.$(OBJEXT) gmap_sse2-maxent_hr.$(OBJEXT) \
+ gmap_sse2-pair.$(OBJEXT) gmap_sse2-pairpool.$(OBJEXT) \
+ gmap_sse2-cellpool.$(OBJEXT) gmap_sse2-stage2.$(OBJEXT) \
+ gmap_sse2-doublelist.$(OBJEXT) gmap_sse2-smooth.$(OBJEXT) \
+ gmap_sse2-splicestringpool.$(OBJEXT) \
+ gmap_sse2-splicetrie_build.$(OBJEXT) \
+ gmap_sse2-splicetrie.$(OBJEXT) gmap_sse2-boyer-moore.$(OBJEXT) \
+ gmap_sse2-dynprog.$(OBJEXT) gmap_sse2-dynprog_simd.$(OBJEXT) \
+ gmap_sse2-dynprog_single.$(OBJEXT) \
+ gmap_sse2-dynprog_genome.$(OBJEXT) \
+ gmap_sse2-dynprog_cdna.$(OBJEXT) \
+ gmap_sse2-dynprog_end.$(OBJEXT) \
+ gmap_sse2-translation.$(OBJEXT) gmap_sse2-pbinom.$(OBJEXT) \
+ gmap_sse2-changepoint.$(OBJEXT) gmap_sse2-stage3.$(OBJEXT) \
+ gmap_sse2-request.$(OBJEXT) gmap_sse2-result.$(OBJEXT) \
+ gmap_sse2-output.$(OBJEXT) gmap_sse2-inbuffer.$(OBJEXT) \
+ gmap_sse2-samheader.$(OBJEXT) gmap_sse2-outbuffer.$(OBJEXT) \
+ gmap_sse2-chimera.$(OBJEXT) gmap_sse2-datadir.$(OBJEXT) \
+ gmap_sse2-parserange.$(OBJEXT) gmap_sse2-getopt.$(OBJEXT) \
+ gmap_sse2-getopt1.$(OBJEXT) gmap_sse2-gmap.$(OBJEXT)
+dist_gmap_sse2_OBJECTS = $(am__objects_7)
+gmap_sse2_OBJECTS = $(dist_gmap_sse2_OBJECTS)
+gmap_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmap_sse2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_sse2_CFLAGS) \
+ $(CFLAGS) $(gmap_sse2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_8 = gmap_sse41-except.$(OBJEXT) \
+ gmap_sse41-assert.$(OBJEXT) gmap_sse41-mem.$(OBJEXT) \
+ gmap_sse41-intlist.$(OBJEXT) gmap_sse41-list.$(OBJEXT) \
+ gmap_sse41-littleendian.$(OBJEXT) \
+ gmap_sse41-bigendian.$(OBJEXT) \
+ gmap_sse41-univinterval.$(OBJEXT) \
+ gmap_sse41-interval.$(OBJEXT) gmap_sse41-uintlist.$(OBJEXT) \
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+ gmap_sse41-access.$(OBJEXT) gmap_sse41-filestring.$(OBJEXT) \
+ gmap_sse41-iit-read-univ.$(OBJEXT) \
+ gmap_sse41-iit-read.$(OBJEXT) gmap_sse41-md5.$(OBJEXT) \
+ gmap_sse41-bzip2.$(OBJEXT) gmap_sse41-sequence.$(OBJEXT) \
+ gmap_sse41-reader.$(OBJEXT) gmap_sse41-genomicpos.$(OBJEXT) \
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+ gmap_sse41-compress-write.$(OBJEXT) \
+ gmap_sse41-gbuffer.$(OBJEXT) gmap_sse41-genome.$(OBJEXT) \
+ gmap_sse41-popcount.$(OBJEXT) \
+ gmap_sse41-genome128_hr.$(OBJEXT) \
+ gmap_sse41-genome_sites.$(OBJEXT) \
+ gmap_sse41-genome-write.$(OBJEXT) \
+ gmap_sse41-bitpack64-read.$(OBJEXT) \
+ gmap_sse41-bitpack64-readtwo.$(OBJEXT) \
+ gmap_sse41-indexdb.$(OBJEXT) gmap_sse41-indexdb_hr.$(OBJEXT) \
+ gmap_sse41-oligo.$(OBJEXT) gmap_sse41-block.$(OBJEXT) \
+ gmap_sse41-chrom.$(OBJEXT) gmap_sse41-segmentpos.$(OBJEXT) \
+ gmap_sse41-chrnum.$(OBJEXT) gmap_sse41-uinttable.$(OBJEXT) \
+ gmap_sse41-gregion.$(OBJEXT) gmap_sse41-match.$(OBJEXT) \
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+ gmap_sse41-atoi.$(OBJEXT) gmap_sse41-orderstat.$(OBJEXT) \
+ gmap_sse41-oligoindex_hr.$(OBJEXT) gmap_sse41-intron.$(OBJEXT) \
+ gmap_sse41-maxent.$(OBJEXT) gmap_sse41-maxent_hr.$(OBJEXT) \
+ gmap_sse41-pair.$(OBJEXT) gmap_sse41-pairpool.$(OBJEXT) \
+ gmap_sse41-cellpool.$(OBJEXT) gmap_sse41-stage2.$(OBJEXT) \
+ gmap_sse41-doublelist.$(OBJEXT) gmap_sse41-smooth.$(OBJEXT) \
+ gmap_sse41-splicestringpool.$(OBJEXT) \
+ gmap_sse41-splicetrie_build.$(OBJEXT) \
+ gmap_sse41-splicetrie.$(OBJEXT) \
+ gmap_sse41-boyer-moore.$(OBJEXT) gmap_sse41-dynprog.$(OBJEXT) \
+ gmap_sse41-dynprog_simd.$(OBJEXT) \
+ gmap_sse41-dynprog_single.$(OBJEXT) \
+ gmap_sse41-dynprog_genome.$(OBJEXT) \
+ gmap_sse41-dynprog_cdna.$(OBJEXT) \
+ gmap_sse41-dynprog_end.$(OBJEXT) \
+ gmap_sse41-translation.$(OBJEXT) gmap_sse41-pbinom.$(OBJEXT) \
+ gmap_sse41-changepoint.$(OBJEXT) gmap_sse41-stage3.$(OBJEXT) \
+ gmap_sse41-request.$(OBJEXT) gmap_sse41-result.$(OBJEXT) \
+ gmap_sse41-output.$(OBJEXT) gmap_sse41-inbuffer.$(OBJEXT) \
+ gmap_sse41-samheader.$(OBJEXT) gmap_sse41-outbuffer.$(OBJEXT) \
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+ gmap_sse41-parserange.$(OBJEXT) gmap_sse41-getopt.$(OBJEXT) \
+ gmap_sse41-getopt1.$(OBJEXT) gmap_sse41-gmap.$(OBJEXT)
+dist_gmap_sse41_OBJECTS = $(am__objects_8)
+gmap_sse41_OBJECTS = $(dist_gmap_sse41_OBJECTS)
+gmap_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmap_sse41_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_sse41_CFLAGS) \
+ $(CFLAGS) $(gmap_sse41_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_9 = gmap_sse42-except.$(OBJEXT) \
+ gmap_sse42-assert.$(OBJEXT) gmap_sse42-mem.$(OBJEXT) \
+ gmap_sse42-intlist.$(OBJEXT) gmap_sse42-list.$(OBJEXT) \
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+ gmap_sse42-bigendian.$(OBJEXT) \
+ gmap_sse42-univinterval.$(OBJEXT) \
+ gmap_sse42-interval.$(OBJEXT) gmap_sse42-uintlist.$(OBJEXT) \
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+ gmap_sse42-access.$(OBJEXT) gmap_sse42-filestring.$(OBJEXT) \
+ gmap_sse42-iit-read-univ.$(OBJEXT) \
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+ gmap_sse42-genome_sites.$(OBJEXT) \
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+ gmap_sse42-bitpack64-readtwo.$(OBJEXT) \
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+ gmap_sse42-doublelist.$(OBJEXT) gmap_sse42-smooth.$(OBJEXT) \
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+ gmap_sse42-splicetrie_build.$(OBJEXT) \
+ gmap_sse42-splicetrie.$(OBJEXT) \
+ gmap_sse42-boyer-moore.$(OBJEXT) gmap_sse42-dynprog.$(OBJEXT) \
+ gmap_sse42-dynprog_simd.$(OBJEXT) \
+ gmap_sse42-dynprog_single.$(OBJEXT) \
+ gmap_sse42-dynprog_genome.$(OBJEXT) \
+ gmap_sse42-dynprog_cdna.$(OBJEXT) \
+ gmap_sse42-dynprog_end.$(OBJEXT) \
+ gmap_sse42-translation.$(OBJEXT) gmap_sse42-pbinom.$(OBJEXT) \
+ gmap_sse42-changepoint.$(OBJEXT) gmap_sse42-stage3.$(OBJEXT) \
+ gmap_sse42-request.$(OBJEXT) gmap_sse42-result.$(OBJEXT) \
+ gmap_sse42-output.$(OBJEXT) gmap_sse42-inbuffer.$(OBJEXT) \
+ gmap_sse42-samheader.$(OBJEXT) gmap_sse42-outbuffer.$(OBJEXT) \
+ gmap_sse42-chimera.$(OBJEXT) gmap_sse42-datadir.$(OBJEXT) \
+ gmap_sse42-parserange.$(OBJEXT) gmap_sse42-getopt.$(OBJEXT) \
+ gmap_sse42-getopt1.$(OBJEXT) gmap_sse42-gmap.$(OBJEXT)
+dist_gmap_sse42_OBJECTS = $(am__objects_9)
+gmap_sse42_OBJECTS = $(dist_gmap_sse42_OBJECTS)
+gmap_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmap_sse42_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_sse42_CFLAGS) \
+ $(CFLAGS) $(gmap_sse42_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_10 = gmap_ssse3-except.$(OBJEXT) \
+ gmap_ssse3-assert.$(OBJEXT) gmap_ssse3-mem.$(OBJEXT) \
+ gmap_ssse3-intlist.$(OBJEXT) gmap_ssse3-list.$(OBJEXT) \
+ gmap_ssse3-littleendian.$(OBJEXT) \
+ gmap_ssse3-bigendian.$(OBJEXT) \
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+ gmap_ssse3-access.$(OBJEXT) gmap_ssse3-filestring.$(OBJEXT) \
+ gmap_ssse3-iit-read-univ.$(OBJEXT) \
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+ gmap_ssse3-reader.$(OBJEXT) gmap_ssse3-genomicpos.$(OBJEXT) \
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+ gmap_ssse3-compress-write.$(OBJEXT) \
+ gmap_ssse3-gbuffer.$(OBJEXT) gmap_ssse3-genome.$(OBJEXT) \
+ gmap_ssse3-popcount.$(OBJEXT) \
+ gmap_ssse3-genome128_hr.$(OBJEXT) \
+ gmap_ssse3-genome_sites.$(OBJEXT) \
+ gmap_ssse3-genome-write.$(OBJEXT) \
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+ gmap_ssse3-bitpack64-readtwo.$(OBJEXT) \
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+ gmap_ssse3-doublelist.$(OBJEXT) gmap_ssse3-smooth.$(OBJEXT) \
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+ gmap_ssse3-splicetrie_build.$(OBJEXT) \
+ gmap_ssse3-splicetrie.$(OBJEXT) \
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+ gmap_ssse3-dynprog_simd.$(OBJEXT) \
+ gmap_ssse3-dynprog_single.$(OBJEXT) \
+ gmap_ssse3-dynprog_genome.$(OBJEXT) \
+ gmap_ssse3-dynprog_cdna.$(OBJEXT) \
+ gmap_ssse3-dynprog_end.$(OBJEXT) \
+ gmap_ssse3-translation.$(OBJEXT) gmap_ssse3-pbinom.$(OBJEXT) \
+ gmap_ssse3-changepoint.$(OBJEXT) gmap_ssse3-stage3.$(OBJEXT) \
+ gmap_ssse3-request.$(OBJEXT) gmap_ssse3-result.$(OBJEXT) \
+ gmap_ssse3-output.$(OBJEXT) gmap_ssse3-inbuffer.$(OBJEXT) \
+ gmap_ssse3-samheader.$(OBJEXT) gmap_ssse3-outbuffer.$(OBJEXT) \
+ gmap_ssse3-chimera.$(OBJEXT) gmap_ssse3-datadir.$(OBJEXT) \
+ gmap_ssse3-parserange.$(OBJEXT) gmap_ssse3-getopt.$(OBJEXT) \
+ gmap_ssse3-getopt1.$(OBJEXT) gmap_ssse3-gmap.$(OBJEXT)
+dist_gmap_ssse3_OBJECTS = $(am__objects_10)
+gmap_ssse3_OBJECTS = $(dist_gmap_ssse3_OBJECTS)
+gmap_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmap_ssse3_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmap_ssse3_CFLAGS) \
+ $(CFLAGS) $(gmap_ssse3_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_11 = gmapindex-except.$(OBJEXT) gmapindex-assert.$(OBJEXT) \
gmapindex-mem.$(OBJEXT) gmapindex-intlist.$(OBJEXT) \
gmapindex-list.$(OBJEXT) gmapindex-littleendian.$(OBJEXT) \
gmapindex-bigendian.$(OBJEXT) gmapindex-univinterval.$(OBJEXT) \
gmapindex-interval.$(OBJEXT) gmapindex-uintlist.$(OBJEXT) \
- gmapindex-stopwatch.$(OBJEXT) gmapindex-access.$(OBJEXT) \
- gmapindex-filestring.$(OBJEXT) \
+ gmapindex-stopwatch.$(OBJEXT) gmapindex-semaphore.$(OBJEXT) \
+ gmapindex-access.$(OBJEXT) gmapindex-filestring.$(OBJEXT) \
gmapindex-iit-read-univ.$(OBJEXT) \
gmapindex-iit-write-univ.$(OBJEXT) \
gmapindex-iit-read.$(OBJEXT) gmapindex-md5.$(OBJEXT) \
@@ -223,275 +570,1375 @@ am__objects_5 = gmapindex-except.$(OBJEXT) gmapindex-assert.$(OBJEXT) \
gmapindex-bitpack64-read.$(OBJEXT) \
gmapindex-bitpack64-readtwo.$(OBJEXT) \
gmapindex-bitpack64-access.$(OBJEXT) \
+ gmapindex-bitpack64-incr.$(OBJEXT) \
gmapindex-bitpack64-write.$(OBJEXT) \
gmapindex-indexdb.$(OBJEXT) gmapindex-indexdb-write.$(OBJEXT) \
gmapindex-table.$(OBJEXT) gmapindex-tableuint.$(OBJEXT) \
- gmapindex-tableuint8.$(OBJEXT) gmapindex-chrom.$(OBJEXT) \
- gmapindex-segmentpos.$(OBJEXT) gmapindex-saca-k.$(OBJEXT) \
- gmapindex-uint8list.$(OBJEXT) gmapindex-bytecoding.$(OBJEXT) \
- gmapindex-sarray-write.$(OBJEXT) gmapindex-gmapindex.$(OBJEXT)
-dist_gmapindex_OBJECTS = $(am__objects_5)
+ gmapindex-tableuint8.$(OBJEXT) gmapindex-tableint.$(OBJEXT) \
+ gmapindex-chrom.$(OBJEXT) gmapindex-segmentpos.$(OBJEXT) \
+ gmapindex-saca-k.$(OBJEXT) gmapindex-uint8list.$(OBJEXT) \
+ gmapindex-bytecoding.$(OBJEXT) \
+ gmapindex-sarray-write.$(OBJEXT) \
+ gmapindex-parserange.$(OBJEXT) gmapindex-gmapindex.$(OBJEXT)
+dist_gmapindex_OBJECTS = $(am__objects_11)
gmapindex_OBJECTS = $(dist_gmapindex_OBJECTS)
gmapindex_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
gmapindex_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapindex_CFLAGS) \
$(CFLAGS) $(gmapindex_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_6 = gmapl-except.$(OBJEXT) gmapl-assert.$(OBJEXT) \
- gmapl-mem.$(OBJEXT) gmapl-intlist.$(OBJEXT) \
- gmapl-list.$(OBJEXT) gmapl-littleendian.$(OBJEXT) \
- gmapl-bigendian.$(OBJEXT) gmapl-univinterval.$(OBJEXT) \
- gmapl-interval.$(OBJEXT) gmapl-uintlist.$(OBJEXT) \
- gmapl-stopwatch.$(OBJEXT) gmapl-access.$(OBJEXT) \
- gmapl-filestring.$(OBJEXT) gmapl-iit-read-univ.$(OBJEXT) \
- gmapl-iit-read.$(OBJEXT) gmapl-md5.$(OBJEXT) \
- gmapl-bzip2.$(OBJEXT) gmapl-sequence.$(OBJEXT) \
- gmapl-reader.$(OBJEXT) gmapl-genomicpos.$(OBJEXT) \
- gmapl-compress.$(OBJEXT) gmapl-compress-write.$(OBJEXT) \
- gmapl-gbuffer.$(OBJEXT) gmapl-genome.$(OBJEXT) \
- gmapl-popcount.$(OBJEXT) gmapl-genome128_hr.$(OBJEXT) \
- gmapl-genome_sites.$(OBJEXT) gmapl-genome-write.$(OBJEXT) \
- gmapl-bitpack64-read.$(OBJEXT) \
- gmapl-bitpack64-readtwo.$(OBJEXT) gmapl-indexdb.$(OBJEXT) \
- gmapl-indexdb_hr.$(OBJEXT) gmapl-oligo.$(OBJEXT) \
- gmapl-block.$(OBJEXT) gmapl-chrom.$(OBJEXT) \
- gmapl-segmentpos.$(OBJEXT) gmapl-chrnum.$(OBJEXT) \
- gmapl-uinttable.$(OBJEXT) gmapl-gregion.$(OBJEXT) \
- gmapl-match.$(OBJEXT) gmapl-matchpool.$(OBJEXT) \
- gmapl-diagnostic.$(OBJEXT) gmapl-stage1.$(OBJEXT) \
- gmapl-diag.$(OBJEXT) gmapl-diagpool.$(OBJEXT) \
- gmapl-cmet.$(OBJEXT) gmapl-atoi.$(OBJEXT) \
- gmapl-orderstat.$(OBJEXT) gmapl-oligoindex_hr.$(OBJEXT) \
- gmapl-intron.$(OBJEXT) gmapl-maxent.$(OBJEXT) \
- gmapl-maxent_hr.$(OBJEXT) gmapl-pair.$(OBJEXT) \
- gmapl-pairpool.$(OBJEXT) gmapl-cellpool.$(OBJEXT) \
- gmapl-stage2.$(OBJEXT) gmapl-doublelist.$(OBJEXT) \
- gmapl-smooth.$(OBJEXT) gmapl-splicestringpool.$(OBJEXT) \
- gmapl-splicetrie_build.$(OBJEXT) gmapl-splicetrie.$(OBJEXT) \
- gmapl-boyer-moore.$(OBJEXT) gmapl-dynprog.$(OBJEXT) \
- gmapl-dynprog_simd.$(OBJEXT) gmapl-dynprog_single.$(OBJEXT) \
- gmapl-dynprog_genome.$(OBJEXT) gmapl-dynprog_cdna.$(OBJEXT) \
- gmapl-dynprog_end.$(OBJEXT) gmapl-translation.$(OBJEXT) \
- gmapl-pbinom.$(OBJEXT) gmapl-changepoint.$(OBJEXT) \
- gmapl-stage3.$(OBJEXT) gmapl-request.$(OBJEXT) \
- gmapl-result.$(OBJEXT) gmapl-output.$(OBJEXT) \
- gmapl-inbuffer.$(OBJEXT) gmapl-samheader.$(OBJEXT) \
- gmapl-outbuffer.$(OBJEXT) gmapl-chimera.$(OBJEXT) \
- gmapl-datadir.$(OBJEXT) gmapl-getopt.$(OBJEXT) \
- gmapl-getopt1.$(OBJEXT) gmapl-gmap.$(OBJEXT)
-dist_gmapl_OBJECTS = $(am__objects_6)
+am__objects_12 = gmapl-cpuid.$(OBJEXT) gmapl-gmapl_select.$(OBJEXT)
+dist_gmapl_OBJECTS = $(am__objects_12)
gmapl_OBJECTS = $(dist_gmapl_OBJECTS)
-gmapl_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
- $(am__DEPENDENCIES_1)
+gmapl_DEPENDENCIES =
gmapl_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(gmapl_CFLAGS) $(CFLAGS) $(gmapl_LDFLAGS) \
$(LDFLAGS) -o $@
-am__objects_7 = gsnap-except.$(OBJEXT) gsnap-assert.$(OBJEXT) \
- gsnap-mem.$(OBJEXT) gsnap-intlist.$(OBJEXT) \
- gsnap-list.$(OBJEXT) gsnap-littleendian.$(OBJEXT) \
- gsnap-bigendian.$(OBJEXT) gsnap-univinterval.$(OBJEXT) \
- gsnap-interval.$(OBJEXT) gsnap-uintlist.$(OBJEXT) \
- gsnap-stopwatch.$(OBJEXT) gsnap-access.$(OBJEXT) \
- gsnap-filestring.$(OBJEXT) gsnap-iit-read-univ.$(OBJEXT) \
- gsnap-iit-read.$(OBJEXT) gsnap-md5.$(OBJEXT) \
- gsnap-bzip2.$(OBJEXT) gsnap-sequence.$(OBJEXT) \
- gsnap-reader.$(OBJEXT) gsnap-genomicpos.$(OBJEXT) \
- gsnap-compress.$(OBJEXT) gsnap-genome.$(OBJEXT) \
- gsnap-popcount.$(OBJEXT) gsnap-genome128_hr.$(OBJEXT) \
- gsnap-genome_sites.$(OBJEXT) gsnap-bitpack64-read.$(OBJEXT) \
- gsnap-bitpack64-readtwo.$(OBJEXT) gsnap-indexdb.$(OBJEXT) \
- gsnap-indexdb_hr.$(OBJEXT) gsnap-oligo.$(OBJEXT) \
- gsnap-chrom.$(OBJEXT) gsnap-segmentpos.$(OBJEXT) \
- gsnap-chrnum.$(OBJEXT) gsnap-maxent_hr.$(OBJEXT) \
- gsnap-samprint.$(OBJEXT) gsnap-mapq.$(OBJEXT) \
- gsnap-shortread.$(OBJEXT) gsnap-substring.$(OBJEXT) \
- gsnap-junction.$(OBJEXT) gsnap-stage3hr.$(OBJEXT) \
- gsnap-spanningelt.$(OBJEXT) gsnap-cmet.$(OBJEXT) \
- gsnap-atoi.$(OBJEXT) gsnap-maxent.$(OBJEXT) \
- gsnap-pair.$(OBJEXT) gsnap-pairpool.$(OBJEXT) \
- gsnap-diag.$(OBJEXT) gsnap-diagpool.$(OBJEXT) \
- gsnap-orderstat.$(OBJEXT) gsnap-oligoindex_hr.$(OBJEXT) \
- gsnap-cellpool.$(OBJEXT) gsnap-stage2.$(OBJEXT) \
- gsnap-intron.$(OBJEXT) gsnap-boyer-moore.$(OBJEXT) \
- gsnap-changepoint.$(OBJEXT) gsnap-pbinom.$(OBJEXT) \
- gsnap-dynprog.$(OBJEXT) gsnap-dynprog_simd.$(OBJEXT) \
- gsnap-dynprog_single.$(OBJEXT) gsnap-dynprog_genome.$(OBJEXT) \
- gsnap-dynprog_cdna.$(OBJEXT) gsnap-dynprog_end.$(OBJEXT) \
- gsnap-gbuffer.$(OBJEXT) gsnap-translation.$(OBJEXT) \
- gsnap-doublelist.$(OBJEXT) gsnap-smooth.$(OBJEXT) \
- gsnap-chimera.$(OBJEXT) gsnap-stage3.$(OBJEXT) \
- gsnap-splicestringpool.$(OBJEXT) \
- gsnap-splicetrie_build.$(OBJEXT) gsnap-splicetrie.$(OBJEXT) \
- gsnap-splice.$(OBJEXT) gsnap-indel.$(OBJEXT) \
- gsnap-bitpack64-access.$(OBJEXT) gsnap-bytecoding.$(OBJEXT) \
- gsnap-univdiag.$(OBJEXT) gsnap-sarray-read.$(OBJEXT) \
- gsnap-stage1hr.$(OBJEXT) gsnap-request.$(OBJEXT) \
- gsnap-resulthr.$(OBJEXT) gsnap-output.$(OBJEXT) \
- gsnap-inbuffer.$(OBJEXT) gsnap-samheader.$(OBJEXT) \
- gsnap-outbuffer.$(OBJEXT) gsnap-datadir.$(OBJEXT) \
- gsnap-getopt.$(OBJEXT) gsnap-getopt1.$(OBJEXT) \
- gsnap-gsnap.$(OBJEXT)
-dist_gsnap_OBJECTS = $(am__objects_7)
-gsnap_OBJECTS = $(dist_gsnap_OBJECTS)
-gsnap_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+am__objects_13 = gmapl_avx2-except.$(OBJEXT) \
+ gmapl_avx2-assert.$(OBJEXT) gmapl_avx2-mem.$(OBJEXT) \
+ gmapl_avx2-intlist.$(OBJEXT) gmapl_avx2-list.$(OBJEXT) \
+ gmapl_avx2-littleendian.$(OBJEXT) \
+ gmapl_avx2-bigendian.$(OBJEXT) \
+ gmapl_avx2-univinterval.$(OBJEXT) \
+ gmapl_avx2-interval.$(OBJEXT) gmapl_avx2-uintlist.$(OBJEXT) \
+ gmapl_avx2-stopwatch.$(OBJEXT) gmapl_avx2-semaphore.$(OBJEXT) \
+ gmapl_avx2-access.$(OBJEXT) gmapl_avx2-filestring.$(OBJEXT) \
+ gmapl_avx2-iit-read-univ.$(OBJEXT) \
+ gmapl_avx2-iit-read.$(OBJEXT) gmapl_avx2-md5.$(OBJEXT) \
+ gmapl_avx2-bzip2.$(OBJEXT) gmapl_avx2-sequence.$(OBJEXT) \
+ gmapl_avx2-reader.$(OBJEXT) gmapl_avx2-genomicpos.$(OBJEXT) \
+ gmapl_avx2-compress.$(OBJEXT) \
+ gmapl_avx2-compress-write.$(OBJEXT) \
+ gmapl_avx2-gbuffer.$(OBJEXT) gmapl_avx2-genome.$(OBJEXT) \
+ gmapl_avx2-popcount.$(OBJEXT) \
+ gmapl_avx2-genome128_hr.$(OBJEXT) \
+ gmapl_avx2-genome_sites.$(OBJEXT) \
+ gmapl_avx2-genome-write.$(OBJEXT) \
+ gmapl_avx2-bitpack64-read.$(OBJEXT) \
+ gmapl_avx2-bitpack64-readtwo.$(OBJEXT) \
+ gmapl_avx2-indexdb.$(OBJEXT) gmapl_avx2-indexdb_hr.$(OBJEXT) \
+ gmapl_avx2-oligo.$(OBJEXT) gmapl_avx2-block.$(OBJEXT) \
+ gmapl_avx2-chrom.$(OBJEXT) gmapl_avx2-segmentpos.$(OBJEXT) \
+ gmapl_avx2-chrnum.$(OBJEXT) gmapl_avx2-uinttable.$(OBJEXT) \
+ gmapl_avx2-gregion.$(OBJEXT) gmapl_avx2-match.$(OBJEXT) \
+ gmapl_avx2-matchpool.$(OBJEXT) gmapl_avx2-diagnostic.$(OBJEXT) \
+ gmapl_avx2-stage1.$(OBJEXT) gmapl_avx2-diag.$(OBJEXT) \
+ gmapl_avx2-diagpool.$(OBJEXT) gmapl_avx2-cmet.$(OBJEXT) \
+ gmapl_avx2-atoi.$(OBJEXT) gmapl_avx2-orderstat.$(OBJEXT) \
+ gmapl_avx2-oligoindex_hr.$(OBJEXT) gmapl_avx2-intron.$(OBJEXT) \
+ gmapl_avx2-maxent.$(OBJEXT) gmapl_avx2-maxent_hr.$(OBJEXT) \
+ gmapl_avx2-pair.$(OBJEXT) gmapl_avx2-pairpool.$(OBJEXT) \
+ gmapl_avx2-cellpool.$(OBJEXT) gmapl_avx2-stage2.$(OBJEXT) \
+ gmapl_avx2-doublelist.$(OBJEXT) gmapl_avx2-smooth.$(OBJEXT) \
+ gmapl_avx2-splicestringpool.$(OBJEXT) \
+ gmapl_avx2-splicetrie_build.$(OBJEXT) \
+ gmapl_avx2-splicetrie.$(OBJEXT) \
+ gmapl_avx2-boyer-moore.$(OBJEXT) gmapl_avx2-dynprog.$(OBJEXT) \
+ gmapl_avx2-dynprog_simd.$(OBJEXT) \
+ gmapl_avx2-dynprog_single.$(OBJEXT) \
+ gmapl_avx2-dynprog_genome.$(OBJEXT) \
+ gmapl_avx2-dynprog_cdna.$(OBJEXT) \
+ gmapl_avx2-dynprog_end.$(OBJEXT) \
+ gmapl_avx2-translation.$(OBJEXT) gmapl_avx2-pbinom.$(OBJEXT) \
+ gmapl_avx2-changepoint.$(OBJEXT) gmapl_avx2-stage3.$(OBJEXT) \
+ gmapl_avx2-request.$(OBJEXT) gmapl_avx2-result.$(OBJEXT) \
+ gmapl_avx2-output.$(OBJEXT) gmapl_avx2-inbuffer.$(OBJEXT) \
+ gmapl_avx2-samheader.$(OBJEXT) gmapl_avx2-outbuffer.$(OBJEXT) \
+ gmapl_avx2-chimera.$(OBJEXT) gmapl_avx2-datadir.$(OBJEXT) \
+ gmapl_avx2-parserange.$(OBJEXT) gmapl_avx2-getopt.$(OBJEXT) \
+ gmapl_avx2-getopt1.$(OBJEXT) gmapl_avx2-gmap.$(OBJEXT)
+dist_gmapl_avx2_OBJECTS = $(am__objects_13)
+gmapl_avx2_OBJECTS = $(dist_gmapl_avx2_OBJECTS)
+gmapl_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmapl_avx2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_avx2_CFLAGS) \
+ $(CFLAGS) $(gmapl_avx2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_14 = gmapl_nosimd-except.$(OBJEXT) \
+ gmapl_nosimd-assert.$(OBJEXT) gmapl_nosimd-mem.$(OBJEXT) \
+ gmapl_nosimd-intlist.$(OBJEXT) gmapl_nosimd-list.$(OBJEXT) \
+ gmapl_nosimd-littleendian.$(OBJEXT) \
+ gmapl_nosimd-bigendian.$(OBJEXT) \
+ gmapl_nosimd-univinterval.$(OBJEXT) \
+ gmapl_nosimd-interval.$(OBJEXT) \
+ gmapl_nosimd-uintlist.$(OBJEXT) \
+ gmapl_nosimd-stopwatch.$(OBJEXT) \
+ gmapl_nosimd-semaphore.$(OBJEXT) gmapl_nosimd-access.$(OBJEXT) \
+ gmapl_nosimd-filestring.$(OBJEXT) \
+ gmapl_nosimd-iit-read-univ.$(OBJEXT) \
+ gmapl_nosimd-iit-read.$(OBJEXT) gmapl_nosimd-md5.$(OBJEXT) \
+ gmapl_nosimd-bzip2.$(OBJEXT) gmapl_nosimd-sequence.$(OBJEXT) \
+ gmapl_nosimd-reader.$(OBJEXT) \
+ gmapl_nosimd-genomicpos.$(OBJEXT) \
+ gmapl_nosimd-compress.$(OBJEXT) \
+ gmapl_nosimd-compress-write.$(OBJEXT) \
+ gmapl_nosimd-gbuffer.$(OBJEXT) gmapl_nosimd-genome.$(OBJEXT) \
+ gmapl_nosimd-popcount.$(OBJEXT) \
+ gmapl_nosimd-genome128_hr.$(OBJEXT) \
+ gmapl_nosimd-genome_sites.$(OBJEXT) \
+ gmapl_nosimd-genome-write.$(OBJEXT) \
+ gmapl_nosimd-bitpack64-read.$(OBJEXT) \
+ gmapl_nosimd-bitpack64-readtwo.$(OBJEXT) \
+ gmapl_nosimd-indexdb.$(OBJEXT) \
+ gmapl_nosimd-indexdb_hr.$(OBJEXT) gmapl_nosimd-oligo.$(OBJEXT) \
+ gmapl_nosimd-block.$(OBJEXT) gmapl_nosimd-chrom.$(OBJEXT) \
+ gmapl_nosimd-segmentpos.$(OBJEXT) \
+ gmapl_nosimd-chrnum.$(OBJEXT) gmapl_nosimd-uinttable.$(OBJEXT) \
+ gmapl_nosimd-gregion.$(OBJEXT) gmapl_nosimd-match.$(OBJEXT) \
+ gmapl_nosimd-matchpool.$(OBJEXT) \
+ gmapl_nosimd-diagnostic.$(OBJEXT) \
+ gmapl_nosimd-stage1.$(OBJEXT) gmapl_nosimd-diag.$(OBJEXT) \
+ gmapl_nosimd-diagpool.$(OBJEXT) gmapl_nosimd-cmet.$(OBJEXT) \
+ gmapl_nosimd-atoi.$(OBJEXT) gmapl_nosimd-orderstat.$(OBJEXT) \
+ gmapl_nosimd-oligoindex_hr.$(OBJEXT) \
+ gmapl_nosimd-intron.$(OBJEXT) gmapl_nosimd-maxent.$(OBJEXT) \
+ gmapl_nosimd-maxent_hr.$(OBJEXT) gmapl_nosimd-pair.$(OBJEXT) \
+ gmapl_nosimd-pairpool.$(OBJEXT) \
+ gmapl_nosimd-cellpool.$(OBJEXT) gmapl_nosimd-stage2.$(OBJEXT) \
+ gmapl_nosimd-doublelist.$(OBJEXT) \
+ gmapl_nosimd-smooth.$(OBJEXT) \
+ gmapl_nosimd-splicestringpool.$(OBJEXT) \
+ gmapl_nosimd-splicetrie_build.$(OBJEXT) \
+ gmapl_nosimd-splicetrie.$(OBJEXT) \
+ gmapl_nosimd-boyer-moore.$(OBJEXT) \
+ gmapl_nosimd-dynprog.$(OBJEXT) \
+ gmapl_nosimd-dynprog_simd.$(OBJEXT) \
+ gmapl_nosimd-dynprog_single.$(OBJEXT) \
+ gmapl_nosimd-dynprog_genome.$(OBJEXT) \
+ gmapl_nosimd-dynprog_cdna.$(OBJEXT) \
+ gmapl_nosimd-dynprog_end.$(OBJEXT) \
+ gmapl_nosimd-translation.$(OBJEXT) \
+ gmapl_nosimd-pbinom.$(OBJEXT) \
+ gmapl_nosimd-changepoint.$(OBJEXT) \
+ gmapl_nosimd-stage3.$(OBJEXT) gmapl_nosimd-request.$(OBJEXT) \
+ gmapl_nosimd-result.$(OBJEXT) gmapl_nosimd-output.$(OBJEXT) \
+ gmapl_nosimd-inbuffer.$(OBJEXT) \
+ gmapl_nosimd-samheader.$(OBJEXT) \
+ gmapl_nosimd-outbuffer.$(OBJEXT) \
+ gmapl_nosimd-chimera.$(OBJEXT) gmapl_nosimd-datadir.$(OBJEXT) \
+ gmapl_nosimd-parserange.$(OBJEXT) \
+ gmapl_nosimd-getopt.$(OBJEXT) gmapl_nosimd-getopt1.$(OBJEXT) \
+ gmapl_nosimd-gmap.$(OBJEXT)
+dist_gmapl_nosimd_OBJECTS = $(am__objects_14)
+gmapl_nosimd_OBJECTS = $(dist_gmapl_nosimd_OBJECTS)
+gmapl_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+gmapl_nosimd_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_nosimd_CFLAGS) \
+ $(CFLAGS) $(gmapl_nosimd_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_15 = gmapl_sse2-except.$(OBJEXT) \
+ gmapl_sse2-assert.$(OBJEXT) gmapl_sse2-mem.$(OBJEXT) \
+ gmapl_sse2-intlist.$(OBJEXT) gmapl_sse2-list.$(OBJEXT) \
+ gmapl_sse2-littleendian.$(OBJEXT) \
+ gmapl_sse2-bigendian.$(OBJEXT) \
+ gmapl_sse2-univinterval.$(OBJEXT) \
+ gmapl_sse2-interval.$(OBJEXT) gmapl_sse2-uintlist.$(OBJEXT) \
+ gmapl_sse2-stopwatch.$(OBJEXT) gmapl_sse2-semaphore.$(OBJEXT) \
+ gmapl_sse2-access.$(OBJEXT) gmapl_sse2-filestring.$(OBJEXT) \
+ gmapl_sse2-iit-read-univ.$(OBJEXT) \
+ gmapl_sse2-iit-read.$(OBJEXT) gmapl_sse2-md5.$(OBJEXT) \
+ gmapl_sse2-bzip2.$(OBJEXT) gmapl_sse2-sequence.$(OBJEXT) \
+ gmapl_sse2-reader.$(OBJEXT) gmapl_sse2-genomicpos.$(OBJEXT) \
+ gmapl_sse2-compress.$(OBJEXT) \
+ gmapl_sse2-compress-write.$(OBJEXT) \
+ gmapl_sse2-gbuffer.$(OBJEXT) gmapl_sse2-genome.$(OBJEXT) \
+ gmapl_sse2-popcount.$(OBJEXT) \
+ gmapl_sse2-genome128_hr.$(OBJEXT) \
+ gmapl_sse2-genome_sites.$(OBJEXT) \
+ gmapl_sse2-genome-write.$(OBJEXT) \
+ gmapl_sse2-bitpack64-read.$(OBJEXT) \
+ gmapl_sse2-bitpack64-readtwo.$(OBJEXT) \
+ gmapl_sse2-indexdb.$(OBJEXT) gmapl_sse2-indexdb_hr.$(OBJEXT) \
+ gmapl_sse2-oligo.$(OBJEXT) gmapl_sse2-block.$(OBJEXT) \
+ gmapl_sse2-chrom.$(OBJEXT) gmapl_sse2-segmentpos.$(OBJEXT) \
+ gmapl_sse2-chrnum.$(OBJEXT) gmapl_sse2-uinttable.$(OBJEXT) \
+ gmapl_sse2-gregion.$(OBJEXT) gmapl_sse2-match.$(OBJEXT) \
+ gmapl_sse2-matchpool.$(OBJEXT) gmapl_sse2-diagnostic.$(OBJEXT) \
+ gmapl_sse2-stage1.$(OBJEXT) gmapl_sse2-diag.$(OBJEXT) \
+ gmapl_sse2-diagpool.$(OBJEXT) gmapl_sse2-cmet.$(OBJEXT) \
+ gmapl_sse2-atoi.$(OBJEXT) gmapl_sse2-orderstat.$(OBJEXT) \
+ gmapl_sse2-oligoindex_hr.$(OBJEXT) gmapl_sse2-intron.$(OBJEXT) \
+ gmapl_sse2-maxent.$(OBJEXT) gmapl_sse2-maxent_hr.$(OBJEXT) \
+ gmapl_sse2-pair.$(OBJEXT) gmapl_sse2-pairpool.$(OBJEXT) \
+ gmapl_sse2-cellpool.$(OBJEXT) gmapl_sse2-stage2.$(OBJEXT) \
+ gmapl_sse2-doublelist.$(OBJEXT) gmapl_sse2-smooth.$(OBJEXT) \
+ gmapl_sse2-splicestringpool.$(OBJEXT) \
+ gmapl_sse2-splicetrie_build.$(OBJEXT) \
+ gmapl_sse2-splicetrie.$(OBJEXT) \
+ gmapl_sse2-boyer-moore.$(OBJEXT) gmapl_sse2-dynprog.$(OBJEXT) \
+ gmapl_sse2-dynprog_simd.$(OBJEXT) \
+ gmapl_sse2-dynprog_single.$(OBJEXT) \
+ gmapl_sse2-dynprog_genome.$(OBJEXT) \
+ gmapl_sse2-dynprog_cdna.$(OBJEXT) \
+ gmapl_sse2-dynprog_end.$(OBJEXT) \
+ gmapl_sse2-translation.$(OBJEXT) gmapl_sse2-pbinom.$(OBJEXT) \
+ gmapl_sse2-changepoint.$(OBJEXT) gmapl_sse2-stage3.$(OBJEXT) \
+ gmapl_sse2-request.$(OBJEXT) gmapl_sse2-result.$(OBJEXT) \
+ gmapl_sse2-output.$(OBJEXT) gmapl_sse2-inbuffer.$(OBJEXT) \
+ gmapl_sse2-samheader.$(OBJEXT) gmapl_sse2-outbuffer.$(OBJEXT) \
+ gmapl_sse2-chimera.$(OBJEXT) gmapl_sse2-datadir.$(OBJEXT) \
+ gmapl_sse2-parserange.$(OBJEXT) gmapl_sse2-getopt.$(OBJEXT) \
+ gmapl_sse2-getopt1.$(OBJEXT) gmapl_sse2-gmap.$(OBJEXT)
+dist_gmapl_sse2_OBJECTS = $(am__objects_15)
+gmapl_sse2_OBJECTS = $(dist_gmapl_sse2_OBJECTS)
+gmapl_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmapl_sse2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse2_CFLAGS) \
+ $(CFLAGS) $(gmapl_sse2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_16 = gmapl_sse41-except.$(OBJEXT) \
+ gmapl_sse41-assert.$(OBJEXT) gmapl_sse41-mem.$(OBJEXT) \
+ gmapl_sse41-intlist.$(OBJEXT) gmapl_sse41-list.$(OBJEXT) \
+ gmapl_sse41-littleendian.$(OBJEXT) \
+ gmapl_sse41-bigendian.$(OBJEXT) \
+ gmapl_sse41-univinterval.$(OBJEXT) \
+ gmapl_sse41-interval.$(OBJEXT) gmapl_sse41-uintlist.$(OBJEXT) \
+ gmapl_sse41-stopwatch.$(OBJEXT) \
+ gmapl_sse41-semaphore.$(OBJEXT) gmapl_sse41-access.$(OBJEXT) \
+ gmapl_sse41-filestring.$(OBJEXT) \
+ gmapl_sse41-iit-read-univ.$(OBJEXT) \
+ gmapl_sse41-iit-read.$(OBJEXT) gmapl_sse41-md5.$(OBJEXT) \
+ gmapl_sse41-bzip2.$(OBJEXT) gmapl_sse41-sequence.$(OBJEXT) \
+ gmapl_sse41-reader.$(OBJEXT) gmapl_sse41-genomicpos.$(OBJEXT) \
+ gmapl_sse41-compress.$(OBJEXT) \
+ gmapl_sse41-compress-write.$(OBJEXT) \
+ gmapl_sse41-gbuffer.$(OBJEXT) gmapl_sse41-genome.$(OBJEXT) \
+ gmapl_sse41-popcount.$(OBJEXT) \
+ gmapl_sse41-genome128_hr.$(OBJEXT) \
+ gmapl_sse41-genome_sites.$(OBJEXT) \
+ gmapl_sse41-genome-write.$(OBJEXT) \
+ gmapl_sse41-bitpack64-read.$(OBJEXT) \
+ gmapl_sse41-bitpack64-readtwo.$(OBJEXT) \
+ gmapl_sse41-indexdb.$(OBJEXT) gmapl_sse41-indexdb_hr.$(OBJEXT) \
+ gmapl_sse41-oligo.$(OBJEXT) gmapl_sse41-block.$(OBJEXT) \
+ gmapl_sse41-chrom.$(OBJEXT) gmapl_sse41-segmentpos.$(OBJEXT) \
+ gmapl_sse41-chrnum.$(OBJEXT) gmapl_sse41-uinttable.$(OBJEXT) \
+ gmapl_sse41-gregion.$(OBJEXT) gmapl_sse41-match.$(OBJEXT) \
+ gmapl_sse41-matchpool.$(OBJEXT) \
+ gmapl_sse41-diagnostic.$(OBJEXT) gmapl_sse41-stage1.$(OBJEXT) \
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+ gmapl_sse41-orderstat.$(OBJEXT) \
+ gmapl_sse41-oligoindex_hr.$(OBJEXT) \
+ gmapl_sse41-intron.$(OBJEXT) gmapl_sse41-maxent.$(OBJEXT) \
+ gmapl_sse41-maxent_hr.$(OBJEXT) gmapl_sse41-pair.$(OBJEXT) \
+ gmapl_sse41-pairpool.$(OBJEXT) gmapl_sse41-cellpool.$(OBJEXT) \
+ gmapl_sse41-stage2.$(OBJEXT) gmapl_sse41-doublelist.$(OBJEXT) \
+ gmapl_sse41-smooth.$(OBJEXT) \
+ gmapl_sse41-splicestringpool.$(OBJEXT) \
+ gmapl_sse41-splicetrie_build.$(OBJEXT) \
+ gmapl_sse41-splicetrie.$(OBJEXT) \
+ gmapl_sse41-boyer-moore.$(OBJEXT) \
+ gmapl_sse41-dynprog.$(OBJEXT) \
+ gmapl_sse41-dynprog_simd.$(OBJEXT) \
+ gmapl_sse41-dynprog_single.$(OBJEXT) \
+ gmapl_sse41-dynprog_genome.$(OBJEXT) \
+ gmapl_sse41-dynprog_cdna.$(OBJEXT) \
+ gmapl_sse41-dynprog_end.$(OBJEXT) \
+ gmapl_sse41-translation.$(OBJEXT) gmapl_sse41-pbinom.$(OBJEXT) \
+ gmapl_sse41-changepoint.$(OBJEXT) gmapl_sse41-stage3.$(OBJEXT) \
+ gmapl_sse41-request.$(OBJEXT) gmapl_sse41-result.$(OBJEXT) \
+ gmapl_sse41-output.$(OBJEXT) gmapl_sse41-inbuffer.$(OBJEXT) \
+ gmapl_sse41-samheader.$(OBJEXT) \
+ gmapl_sse41-outbuffer.$(OBJEXT) gmapl_sse41-chimera.$(OBJEXT) \
+ gmapl_sse41-datadir.$(OBJEXT) gmapl_sse41-parserange.$(OBJEXT) \
+ gmapl_sse41-getopt.$(OBJEXT) gmapl_sse41-getopt1.$(OBJEXT) \
+ gmapl_sse41-gmap.$(OBJEXT)
+dist_gmapl_sse41_OBJECTS = $(am__objects_16)
+gmapl_sse41_OBJECTS = $(dist_gmapl_sse41_OBJECTS)
+gmapl_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmapl_sse41_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse41_CFLAGS) \
+ $(CFLAGS) $(gmapl_sse41_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_17 = gmapl_sse42-except.$(OBJEXT) \
+ gmapl_sse42-assert.$(OBJEXT) gmapl_sse42-mem.$(OBJEXT) \
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+ gmapl_sse42-littleendian.$(OBJEXT) \
+ gmapl_sse42-bigendian.$(OBJEXT) \
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+ gmapl_sse42-interval.$(OBJEXT) gmapl_sse42-uintlist.$(OBJEXT) \
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+ gmapl_sse42-filestring.$(OBJEXT) \
+ gmapl_sse42-iit-read-univ.$(OBJEXT) \
+ gmapl_sse42-iit-read.$(OBJEXT) gmapl_sse42-md5.$(OBJEXT) \
+ gmapl_sse42-bzip2.$(OBJEXT) gmapl_sse42-sequence.$(OBJEXT) \
+ gmapl_sse42-reader.$(OBJEXT) gmapl_sse42-genomicpos.$(OBJEXT) \
+ gmapl_sse42-compress.$(OBJEXT) \
+ gmapl_sse42-compress-write.$(OBJEXT) \
+ gmapl_sse42-gbuffer.$(OBJEXT) gmapl_sse42-genome.$(OBJEXT) \
+ gmapl_sse42-popcount.$(OBJEXT) \
+ gmapl_sse42-genome128_hr.$(OBJEXT) \
+ gmapl_sse42-genome_sites.$(OBJEXT) \
+ gmapl_sse42-genome-write.$(OBJEXT) \
+ gmapl_sse42-bitpack64-read.$(OBJEXT) \
+ gmapl_sse42-bitpack64-readtwo.$(OBJEXT) \
+ gmapl_sse42-indexdb.$(OBJEXT) gmapl_sse42-indexdb_hr.$(OBJEXT) \
+ gmapl_sse42-oligo.$(OBJEXT) gmapl_sse42-block.$(OBJEXT) \
+ gmapl_sse42-chrom.$(OBJEXT) gmapl_sse42-segmentpos.$(OBJEXT) \
+ gmapl_sse42-chrnum.$(OBJEXT) gmapl_sse42-uinttable.$(OBJEXT) \
+ gmapl_sse42-gregion.$(OBJEXT) gmapl_sse42-match.$(OBJEXT) \
+ gmapl_sse42-matchpool.$(OBJEXT) \
+ gmapl_sse42-diagnostic.$(OBJEXT) gmapl_sse42-stage1.$(OBJEXT) \
+ gmapl_sse42-diag.$(OBJEXT) gmapl_sse42-diagpool.$(OBJEXT) \
+ gmapl_sse42-cmet.$(OBJEXT) gmapl_sse42-atoi.$(OBJEXT) \
+ gmapl_sse42-orderstat.$(OBJEXT) \
+ gmapl_sse42-oligoindex_hr.$(OBJEXT) \
+ gmapl_sse42-intron.$(OBJEXT) gmapl_sse42-maxent.$(OBJEXT) \
+ gmapl_sse42-maxent_hr.$(OBJEXT) gmapl_sse42-pair.$(OBJEXT) \
+ gmapl_sse42-pairpool.$(OBJEXT) gmapl_sse42-cellpool.$(OBJEXT) \
+ gmapl_sse42-stage2.$(OBJEXT) gmapl_sse42-doublelist.$(OBJEXT) \
+ gmapl_sse42-smooth.$(OBJEXT) \
+ gmapl_sse42-splicestringpool.$(OBJEXT) \
+ gmapl_sse42-splicetrie_build.$(OBJEXT) \
+ gmapl_sse42-splicetrie.$(OBJEXT) \
+ gmapl_sse42-boyer-moore.$(OBJEXT) \
+ gmapl_sse42-dynprog.$(OBJEXT) \
+ gmapl_sse42-dynprog_simd.$(OBJEXT) \
+ gmapl_sse42-dynprog_single.$(OBJEXT) \
+ gmapl_sse42-dynprog_genome.$(OBJEXT) \
+ gmapl_sse42-dynprog_cdna.$(OBJEXT) \
+ gmapl_sse42-dynprog_end.$(OBJEXT) \
+ gmapl_sse42-translation.$(OBJEXT) gmapl_sse42-pbinom.$(OBJEXT) \
+ gmapl_sse42-changepoint.$(OBJEXT) gmapl_sse42-stage3.$(OBJEXT) \
+ gmapl_sse42-request.$(OBJEXT) gmapl_sse42-result.$(OBJEXT) \
+ gmapl_sse42-output.$(OBJEXT) gmapl_sse42-inbuffer.$(OBJEXT) \
+ gmapl_sse42-samheader.$(OBJEXT) \
+ gmapl_sse42-outbuffer.$(OBJEXT) gmapl_sse42-chimera.$(OBJEXT) \
+ gmapl_sse42-datadir.$(OBJEXT) gmapl_sse42-parserange.$(OBJEXT) \
+ gmapl_sse42-getopt.$(OBJEXT) gmapl_sse42-getopt1.$(OBJEXT) \
+ gmapl_sse42-gmap.$(OBJEXT)
+dist_gmapl_sse42_OBJECTS = $(am__objects_17)
+gmapl_sse42_OBJECTS = $(dist_gmapl_sse42_OBJECTS)
+gmapl_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
+gmapl_sse42_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_sse42_CFLAGS) \
+ $(CFLAGS) $(gmapl_sse42_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_18 = gmapl_ssse3-except.$(OBJEXT) \
+ gmapl_ssse3-assert.$(OBJEXT) gmapl_ssse3-mem.$(OBJEXT) \
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+ gmapl_ssse3-littleendian.$(OBJEXT) \
+ gmapl_ssse3-bigendian.$(OBJEXT) \
+ gmapl_ssse3-univinterval.$(OBJEXT) \
+ gmapl_ssse3-interval.$(OBJEXT) gmapl_ssse3-uintlist.$(OBJEXT) \
+ gmapl_ssse3-stopwatch.$(OBJEXT) \
+ gmapl_ssse3-semaphore.$(OBJEXT) gmapl_ssse3-access.$(OBJEXT) \
+ gmapl_ssse3-filestring.$(OBJEXT) \
+ gmapl_ssse3-iit-read-univ.$(OBJEXT) \
+ gmapl_ssse3-iit-read.$(OBJEXT) gmapl_ssse3-md5.$(OBJEXT) \
+ gmapl_ssse3-bzip2.$(OBJEXT) gmapl_ssse3-sequence.$(OBJEXT) \
+ gmapl_ssse3-reader.$(OBJEXT) gmapl_ssse3-genomicpos.$(OBJEXT) \
+ gmapl_ssse3-compress.$(OBJEXT) \
+ gmapl_ssse3-compress-write.$(OBJEXT) \
+ gmapl_ssse3-gbuffer.$(OBJEXT) gmapl_ssse3-genome.$(OBJEXT) \
+ gmapl_ssse3-popcount.$(OBJEXT) \
+ gmapl_ssse3-genome128_hr.$(OBJEXT) \
+ gmapl_ssse3-genome_sites.$(OBJEXT) \
+ gmapl_ssse3-genome-write.$(OBJEXT) \
+ gmapl_ssse3-bitpack64-read.$(OBJEXT) \
+ gmapl_ssse3-bitpack64-readtwo.$(OBJEXT) \
+ gmapl_ssse3-indexdb.$(OBJEXT) gmapl_ssse3-indexdb_hr.$(OBJEXT) \
+ gmapl_ssse3-oligo.$(OBJEXT) gmapl_ssse3-block.$(OBJEXT) \
+ gmapl_ssse3-chrom.$(OBJEXT) gmapl_ssse3-segmentpos.$(OBJEXT) \
+ gmapl_ssse3-chrnum.$(OBJEXT) gmapl_ssse3-uinttable.$(OBJEXT) \
+ gmapl_ssse3-gregion.$(OBJEXT) gmapl_ssse3-match.$(OBJEXT) \
+ gmapl_ssse3-matchpool.$(OBJEXT) \
+ gmapl_ssse3-diagnostic.$(OBJEXT) gmapl_ssse3-stage1.$(OBJEXT) \
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+ gmapl_ssse3-cmet.$(OBJEXT) gmapl_ssse3-atoi.$(OBJEXT) \
+ gmapl_ssse3-orderstat.$(OBJEXT) \
+ gmapl_ssse3-oligoindex_hr.$(OBJEXT) \
+ gmapl_ssse3-intron.$(OBJEXT) gmapl_ssse3-maxent.$(OBJEXT) \
+ gmapl_ssse3-maxent_hr.$(OBJEXT) gmapl_ssse3-pair.$(OBJEXT) \
+ gmapl_ssse3-pairpool.$(OBJEXT) gmapl_ssse3-cellpool.$(OBJEXT) \
+ gmapl_ssse3-stage2.$(OBJEXT) gmapl_ssse3-doublelist.$(OBJEXT) \
+ gmapl_ssse3-smooth.$(OBJEXT) \
+ gmapl_ssse3-splicestringpool.$(OBJEXT) \
+ gmapl_ssse3-splicetrie_build.$(OBJEXT) \
+ gmapl_ssse3-splicetrie.$(OBJEXT) \
+ gmapl_ssse3-boyer-moore.$(OBJEXT) \
+ gmapl_ssse3-dynprog.$(OBJEXT) \
+ gmapl_ssse3-dynprog_simd.$(OBJEXT) \
+ gmapl_ssse3-dynprog_single.$(OBJEXT) \
+ gmapl_ssse3-dynprog_genome.$(OBJEXT) \
+ gmapl_ssse3-dynprog_cdna.$(OBJEXT) \
+ gmapl_ssse3-dynprog_end.$(OBJEXT) \
+ gmapl_ssse3-translation.$(OBJEXT) gmapl_ssse3-pbinom.$(OBJEXT) \
+ gmapl_ssse3-changepoint.$(OBJEXT) gmapl_ssse3-stage3.$(OBJEXT) \
+ gmapl_ssse3-request.$(OBJEXT) gmapl_ssse3-result.$(OBJEXT) \
+ gmapl_ssse3-output.$(OBJEXT) gmapl_ssse3-inbuffer.$(OBJEXT) \
+ gmapl_ssse3-samheader.$(OBJEXT) \
+ gmapl_ssse3-outbuffer.$(OBJEXT) gmapl_ssse3-chimera.$(OBJEXT) \
+ gmapl_ssse3-datadir.$(OBJEXT) gmapl_ssse3-parserange.$(OBJEXT) \
+ gmapl_ssse3-getopt.$(OBJEXT) gmapl_ssse3-getopt1.$(OBJEXT) \
+ gmapl_ssse3-gmap.$(OBJEXT)
+dist_gmapl_ssse3_OBJECTS = $(am__objects_18)
+gmapl_ssse3_OBJECTS = $(dist_gmapl_ssse3_OBJECTS)
+gmapl_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gmapl_ssse3_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gmapl_ssse3_CFLAGS) \
+ $(CFLAGS) $(gmapl_ssse3_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_19 = gsnap-cpuid.$(OBJEXT) gsnap-gsnap_select.$(OBJEXT)
+dist_gsnap_OBJECTS = $(am__objects_19)
+gsnap_OBJECTS = $(dist_gsnap_OBJECTS)
+gsnap_DEPENDENCIES =
gsnap_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(gsnap_CFLAGS) $(CFLAGS) $(gsnap_LDFLAGS) \
$(LDFLAGS) -o $@
-am__objects_8 = gsnapl-except.$(OBJEXT) gsnapl-assert.$(OBJEXT) \
- gsnapl-mem.$(OBJEXT) gsnapl-intlist.$(OBJEXT) \
- gsnapl-list.$(OBJEXT) gsnapl-littleendian.$(OBJEXT) \
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- gsnapl-md5.$(OBJEXT) gsnapl-bzip2.$(OBJEXT) \
- gsnapl-sequence.$(OBJEXT) gsnapl-reader.$(OBJEXT) \
- gsnapl-genomicpos.$(OBJEXT) gsnapl-compress.$(OBJEXT) \
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- gsnapl-genome128_hr.$(OBJEXT) gsnapl-genome_sites.$(OBJEXT) \
- gsnapl-bitpack64-read.$(OBJEXT) \
- gsnapl-bitpack64-readtwo.$(OBJEXT) gsnapl-indexdb.$(OBJEXT) \
- gsnapl-indexdb_hr.$(OBJEXT) gsnapl-oligo.$(OBJEXT) \
- gsnapl-chrom.$(OBJEXT) gsnapl-segmentpos.$(OBJEXT) \
- gsnapl-chrnum.$(OBJEXT) gsnapl-maxent_hr.$(OBJEXT) \
- gsnapl-samprint.$(OBJEXT) gsnapl-mapq.$(OBJEXT) \
- gsnapl-shortread.$(OBJEXT) gsnapl-substring.$(OBJEXT) \
- gsnapl-junction.$(OBJEXT) gsnapl-stage3hr.$(OBJEXT) \
- gsnapl-spanningelt.$(OBJEXT) gsnapl-cmet.$(OBJEXT) \
- gsnapl-atoi.$(OBJEXT) gsnapl-maxent.$(OBJEXT) \
- gsnapl-pair.$(OBJEXT) gsnapl-pairpool.$(OBJEXT) \
- gsnapl-diag.$(OBJEXT) gsnapl-diagpool.$(OBJEXT) \
- gsnapl-orderstat.$(OBJEXT) gsnapl-oligoindex_hr.$(OBJEXT) \
- gsnapl-cellpool.$(OBJEXT) gsnapl-stage2.$(OBJEXT) \
- gsnapl-intron.$(OBJEXT) gsnapl-boyer-moore.$(OBJEXT) \
- gsnapl-changepoint.$(OBJEXT) gsnapl-pbinom.$(OBJEXT) \
- gsnapl-dynprog.$(OBJEXT) gsnapl-dynprog_simd.$(OBJEXT) \
- gsnapl-dynprog_single.$(OBJEXT) \
- gsnapl-dynprog_genome.$(OBJEXT) gsnapl-dynprog_cdna.$(OBJEXT) \
- gsnapl-dynprog_end.$(OBJEXT) gsnapl-gbuffer.$(OBJEXT) \
- gsnapl-translation.$(OBJEXT) gsnapl-doublelist.$(OBJEXT) \
- gsnapl-smooth.$(OBJEXT) gsnapl-chimera.$(OBJEXT) \
- gsnapl-stage3.$(OBJEXT) gsnapl-splicestringpool.$(OBJEXT) \
- gsnapl-splicetrie_build.$(OBJEXT) gsnapl-splicetrie.$(OBJEXT) \
- gsnapl-splice.$(OBJEXT) gsnapl-indel.$(OBJEXT) \
- gsnapl-bitpack64-access.$(OBJEXT) gsnapl-stage1hr.$(OBJEXT) \
- gsnapl-request.$(OBJEXT) gsnapl-resulthr.$(OBJEXT) \
- gsnapl-output.$(OBJEXT) gsnapl-inbuffer.$(OBJEXT) \
- gsnapl-samheader.$(OBJEXT) gsnapl-outbuffer.$(OBJEXT) \
- gsnapl-datadir.$(OBJEXT) gsnapl-getopt.$(OBJEXT) \
- gsnapl-getopt1.$(OBJEXT) gsnapl-gsnap.$(OBJEXT)
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-gsnapl_OBJECTS = $(dist_gsnapl_OBJECTS)
-gsnapl_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+am__objects_20 = gsnap_avx2-except.$(OBJEXT) \
+ gsnap_avx2-assert.$(OBJEXT) gsnap_avx2-mem.$(OBJEXT) \
+ gsnap_avx2-intlist.$(OBJEXT) gsnap_avx2-list.$(OBJEXT) \
+ gsnap_avx2-littleendian.$(OBJEXT) \
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+ gsnap_avx2-interval.$(OBJEXT) gsnap_avx2-uintlist.$(OBJEXT) \
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+ gsnap_avx2-access.$(OBJEXT) gsnap_avx2-filestring.$(OBJEXT) \
+ gsnap_avx2-iit-read-univ.$(OBJEXT) \
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+ gsnap_avx2-bzip2.$(OBJEXT) gsnap_avx2-sequence.$(OBJEXT) \
+ gsnap_avx2-reader.$(OBJEXT) gsnap_avx2-genomicpos.$(OBJEXT) \
+ gsnap_avx2-compress.$(OBJEXT) gsnap_avx2-genome.$(OBJEXT) \
+ gsnap_avx2-popcount.$(OBJEXT) \
+ gsnap_avx2-genome128_hr.$(OBJEXT) \
+ gsnap_avx2-genome_sites.$(OBJEXT) \
+ gsnap_avx2-bitpack64-read.$(OBJEXT) \
+ gsnap_avx2-bitpack64-readtwo.$(OBJEXT) \
+ gsnap_avx2-indexdb.$(OBJEXT) gsnap_avx2-indexdb_hr.$(OBJEXT) \
+ gsnap_avx2-oligo.$(OBJEXT) gsnap_avx2-chrom.$(OBJEXT) \
+ gsnap_avx2-segmentpos.$(OBJEXT) gsnap_avx2-chrnum.$(OBJEXT) \
+ gsnap_avx2-maxent_hr.$(OBJEXT) gsnap_avx2-samprint.$(OBJEXT) \
+ gsnap_avx2-mapq.$(OBJEXT) gsnap_avx2-shortread.$(OBJEXT) \
+ gsnap_avx2-substring.$(OBJEXT) gsnap_avx2-junction.$(OBJEXT) \
+ gsnap_avx2-stage3hr.$(OBJEXT) gsnap_avx2-spanningelt.$(OBJEXT) \
+ gsnap_avx2-cmet.$(OBJEXT) gsnap_avx2-atoi.$(OBJEXT) \
+ gsnap_avx2-maxent.$(OBJEXT) gsnap_avx2-pair.$(OBJEXT) \
+ gsnap_avx2-pairpool.$(OBJEXT) gsnap_avx2-diag.$(OBJEXT) \
+ gsnap_avx2-diagpool.$(OBJEXT) gsnap_avx2-orderstat.$(OBJEXT) \
+ gsnap_avx2-oligoindex_hr.$(OBJEXT) \
+ gsnap_avx2-cellpool.$(OBJEXT) gsnap_avx2-stage2.$(OBJEXT) \
+ gsnap_avx2-intron.$(OBJEXT) gsnap_avx2-boyer-moore.$(OBJEXT) \
+ gsnap_avx2-changepoint.$(OBJEXT) gsnap_avx2-pbinom.$(OBJEXT) \
+ gsnap_avx2-dynprog.$(OBJEXT) gsnap_avx2-dynprog_simd.$(OBJEXT) \
+ gsnap_avx2-dynprog_single.$(OBJEXT) \
+ gsnap_avx2-dynprog_genome.$(OBJEXT) \
+ gsnap_avx2-dynprog_cdna.$(OBJEXT) \
+ gsnap_avx2-dynprog_end.$(OBJEXT) gsnap_avx2-gbuffer.$(OBJEXT) \
+ gsnap_avx2-translation.$(OBJEXT) \
+ gsnap_avx2-doublelist.$(OBJEXT) gsnap_avx2-smooth.$(OBJEXT) \
+ gsnap_avx2-chimera.$(OBJEXT) gsnap_avx2-stage3.$(OBJEXT) \
+ gsnap_avx2-splicestringpool.$(OBJEXT) \
+ gsnap_avx2-splicetrie_build.$(OBJEXT) \
+ gsnap_avx2-splicetrie.$(OBJEXT) gsnap_avx2-splice.$(OBJEXT) \
+ gsnap_avx2-indel.$(OBJEXT) \
+ gsnap_avx2-bitpack64-access.$(OBJEXT) \
+ gsnap_avx2-bytecoding.$(OBJEXT) gsnap_avx2-univdiag.$(OBJEXT) \
+ gsnap_avx2-sarray-read.$(OBJEXT) gsnap_avx2-stage1hr.$(OBJEXT) \
+ gsnap_avx2-request.$(OBJEXT) gsnap_avx2-resulthr.$(OBJEXT) \
+ gsnap_avx2-output.$(OBJEXT) gsnap_avx2-inbuffer.$(OBJEXT) \
+ gsnap_avx2-samheader.$(OBJEXT) gsnap_avx2-outbuffer.$(OBJEXT) \
+ gsnap_avx2-datadir.$(OBJEXT) gsnap_avx2-parserange.$(OBJEXT) \
+ gsnap_avx2-getopt.$(OBJEXT) gsnap_avx2-getopt1.$(OBJEXT) \
+ gsnap_avx2-gsnap.$(OBJEXT)
+dist_gsnap_avx2_OBJECTS = $(am__objects_20)
+gsnap_avx2_OBJECTS = $(dist_gsnap_avx2_OBJECTS)
+gsnap_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gsnap_avx2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_avx2_CFLAGS) \
+ $(CFLAGS) $(gsnap_avx2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_21 = gsnap_nosimd-except.$(OBJEXT) \
+ gsnap_nosimd-assert.$(OBJEXT) gsnap_nosimd-mem.$(OBJEXT) \
+ gsnap_nosimd-intlist.$(OBJEXT) gsnap_nosimd-list.$(OBJEXT) \
+ gsnap_nosimd-littleendian.$(OBJEXT) \
+ gsnap_nosimd-bigendian.$(OBJEXT) \
+ gsnap_nosimd-univinterval.$(OBJEXT) \
+ gsnap_nosimd-interval.$(OBJEXT) \
+ gsnap_nosimd-uintlist.$(OBJEXT) \
+ gsnap_nosimd-stopwatch.$(OBJEXT) \
+ gsnap_nosimd-semaphore.$(OBJEXT) gsnap_nosimd-access.$(OBJEXT) \
+ gsnap_nosimd-filestring.$(OBJEXT) \
+ gsnap_nosimd-iit-read-univ.$(OBJEXT) \
+ gsnap_nosimd-iit-read.$(OBJEXT) gsnap_nosimd-md5.$(OBJEXT) \
+ gsnap_nosimd-bzip2.$(OBJEXT) gsnap_nosimd-sequence.$(OBJEXT) \
+ gsnap_nosimd-reader.$(OBJEXT) \
+ gsnap_nosimd-genomicpos.$(OBJEXT) \
+ gsnap_nosimd-compress.$(OBJEXT) gsnap_nosimd-genome.$(OBJEXT) \
+ gsnap_nosimd-popcount.$(OBJEXT) \
+ gsnap_nosimd-genome128_hr.$(OBJEXT) \
+ gsnap_nosimd-genome_sites.$(OBJEXT) \
+ gsnap_nosimd-bitpack64-read.$(OBJEXT) \
+ gsnap_nosimd-bitpack64-readtwo.$(OBJEXT) \
+ gsnap_nosimd-indexdb.$(OBJEXT) \
+ gsnap_nosimd-indexdb_hr.$(OBJEXT) gsnap_nosimd-oligo.$(OBJEXT) \
+ gsnap_nosimd-chrom.$(OBJEXT) gsnap_nosimd-segmentpos.$(OBJEXT) \
+ gsnap_nosimd-chrnum.$(OBJEXT) gsnap_nosimd-maxent_hr.$(OBJEXT) \
+ gsnap_nosimd-samprint.$(OBJEXT) gsnap_nosimd-mapq.$(OBJEXT) \
+ gsnap_nosimd-shortread.$(OBJEXT) \
+ gsnap_nosimd-substring.$(OBJEXT) \
+ gsnap_nosimd-junction.$(OBJEXT) \
+ gsnap_nosimd-stage3hr.$(OBJEXT) \
+ gsnap_nosimd-spanningelt.$(OBJEXT) gsnap_nosimd-cmet.$(OBJEXT) \
+ gsnap_nosimd-atoi.$(OBJEXT) gsnap_nosimd-maxent.$(OBJEXT) \
+ gsnap_nosimd-pair.$(OBJEXT) gsnap_nosimd-pairpool.$(OBJEXT) \
+ gsnap_nosimd-diag.$(OBJEXT) gsnap_nosimd-diagpool.$(OBJEXT) \
+ gsnap_nosimd-orderstat.$(OBJEXT) \
+ gsnap_nosimd-oligoindex_hr.$(OBJEXT) \
+ gsnap_nosimd-cellpool.$(OBJEXT) gsnap_nosimd-stage2.$(OBJEXT) \
+ gsnap_nosimd-intron.$(OBJEXT) \
+ gsnap_nosimd-boyer-moore.$(OBJEXT) \
+ gsnap_nosimd-changepoint.$(OBJEXT) \
+ gsnap_nosimd-pbinom.$(OBJEXT) gsnap_nosimd-dynprog.$(OBJEXT) \
+ gsnap_nosimd-dynprog_simd.$(OBJEXT) \
+ gsnap_nosimd-dynprog_single.$(OBJEXT) \
+ gsnap_nosimd-dynprog_genome.$(OBJEXT) \
+ gsnap_nosimd-dynprog_cdna.$(OBJEXT) \
+ gsnap_nosimd-dynprog_end.$(OBJEXT) \
+ gsnap_nosimd-gbuffer.$(OBJEXT) \
+ gsnap_nosimd-translation.$(OBJEXT) \
+ gsnap_nosimd-doublelist.$(OBJEXT) \
+ gsnap_nosimd-smooth.$(OBJEXT) gsnap_nosimd-chimera.$(OBJEXT) \
+ gsnap_nosimd-stage3.$(OBJEXT) \
+ gsnap_nosimd-splicestringpool.$(OBJEXT) \
+ gsnap_nosimd-splicetrie_build.$(OBJEXT) \
+ gsnap_nosimd-splicetrie.$(OBJEXT) \
+ gsnap_nosimd-splice.$(OBJEXT) gsnap_nosimd-indel.$(OBJEXT) \
+ gsnap_nosimd-bitpack64-access.$(OBJEXT) \
+ gsnap_nosimd-bytecoding.$(OBJEXT) \
+ gsnap_nosimd-univdiag.$(OBJEXT) \
+ gsnap_nosimd-sarray-read.$(OBJEXT) \
+ gsnap_nosimd-stage1hr.$(OBJEXT) gsnap_nosimd-request.$(OBJEXT) \
+ gsnap_nosimd-resulthr.$(OBJEXT) gsnap_nosimd-output.$(OBJEXT) \
+ gsnap_nosimd-inbuffer.$(OBJEXT) \
+ gsnap_nosimd-samheader.$(OBJEXT) \
+ gsnap_nosimd-outbuffer.$(OBJEXT) \
+ gsnap_nosimd-datadir.$(OBJEXT) \
+ gsnap_nosimd-parserange.$(OBJEXT) \
+ gsnap_nosimd-getopt.$(OBJEXT) gsnap_nosimd-getopt1.$(OBJEXT) \
+ gsnap_nosimd-gsnap.$(OBJEXT)
+dist_gsnap_nosimd_OBJECTS = $(am__objects_21)
+gsnap_nosimd_OBJECTS = $(dist_gsnap_nosimd_OBJECTS)
+gsnap_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+gsnap_nosimd_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_nosimd_CFLAGS) \
+ $(CFLAGS) $(gsnap_nosimd_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_22 = gsnap_sse2-except.$(OBJEXT) \
+ gsnap_sse2-assert.$(OBJEXT) gsnap_sse2-mem.$(OBJEXT) \
+ gsnap_sse2-intlist.$(OBJEXT) gsnap_sse2-list.$(OBJEXT) \
+ gsnap_sse2-littleendian.$(OBJEXT) \
+ gsnap_sse2-bigendian.$(OBJEXT) \
+ gsnap_sse2-univinterval.$(OBJEXT) \
+ gsnap_sse2-interval.$(OBJEXT) gsnap_sse2-uintlist.$(OBJEXT) \
+ gsnap_sse2-stopwatch.$(OBJEXT) gsnap_sse2-semaphore.$(OBJEXT) \
+ gsnap_sse2-access.$(OBJEXT) gsnap_sse2-filestring.$(OBJEXT) \
+ gsnap_sse2-iit-read-univ.$(OBJEXT) \
+ gsnap_sse2-iit-read.$(OBJEXT) gsnap_sse2-md5.$(OBJEXT) \
+ gsnap_sse2-bzip2.$(OBJEXT) gsnap_sse2-sequence.$(OBJEXT) \
+ gsnap_sse2-reader.$(OBJEXT) gsnap_sse2-genomicpos.$(OBJEXT) \
+ gsnap_sse2-compress.$(OBJEXT) gsnap_sse2-genome.$(OBJEXT) \
+ gsnap_sse2-popcount.$(OBJEXT) \
+ gsnap_sse2-genome128_hr.$(OBJEXT) \
+ gsnap_sse2-genome_sites.$(OBJEXT) \
+ gsnap_sse2-bitpack64-read.$(OBJEXT) \
+ gsnap_sse2-bitpack64-readtwo.$(OBJEXT) \
+ gsnap_sse2-indexdb.$(OBJEXT) gsnap_sse2-indexdb_hr.$(OBJEXT) \
+ gsnap_sse2-oligo.$(OBJEXT) gsnap_sse2-chrom.$(OBJEXT) \
+ gsnap_sse2-segmentpos.$(OBJEXT) gsnap_sse2-chrnum.$(OBJEXT) \
+ gsnap_sse2-maxent_hr.$(OBJEXT) gsnap_sse2-samprint.$(OBJEXT) \
+ gsnap_sse2-mapq.$(OBJEXT) gsnap_sse2-shortread.$(OBJEXT) \
+ gsnap_sse2-substring.$(OBJEXT) gsnap_sse2-junction.$(OBJEXT) \
+ gsnap_sse2-stage3hr.$(OBJEXT) gsnap_sse2-spanningelt.$(OBJEXT) \
+ gsnap_sse2-cmet.$(OBJEXT) gsnap_sse2-atoi.$(OBJEXT) \
+ gsnap_sse2-maxent.$(OBJEXT) gsnap_sse2-pair.$(OBJEXT) \
+ gsnap_sse2-pairpool.$(OBJEXT) gsnap_sse2-diag.$(OBJEXT) \
+ gsnap_sse2-diagpool.$(OBJEXT) gsnap_sse2-orderstat.$(OBJEXT) \
+ gsnap_sse2-oligoindex_hr.$(OBJEXT) \
+ gsnap_sse2-cellpool.$(OBJEXT) gsnap_sse2-stage2.$(OBJEXT) \
+ gsnap_sse2-intron.$(OBJEXT) gsnap_sse2-boyer-moore.$(OBJEXT) \
+ gsnap_sse2-changepoint.$(OBJEXT) gsnap_sse2-pbinom.$(OBJEXT) \
+ gsnap_sse2-dynprog.$(OBJEXT) gsnap_sse2-dynprog_simd.$(OBJEXT) \
+ gsnap_sse2-dynprog_single.$(OBJEXT) \
+ gsnap_sse2-dynprog_genome.$(OBJEXT) \
+ gsnap_sse2-dynprog_cdna.$(OBJEXT) \
+ gsnap_sse2-dynprog_end.$(OBJEXT) gsnap_sse2-gbuffer.$(OBJEXT) \
+ gsnap_sse2-translation.$(OBJEXT) \
+ gsnap_sse2-doublelist.$(OBJEXT) gsnap_sse2-smooth.$(OBJEXT) \
+ gsnap_sse2-chimera.$(OBJEXT) gsnap_sse2-stage3.$(OBJEXT) \
+ gsnap_sse2-splicestringpool.$(OBJEXT) \
+ gsnap_sse2-splicetrie_build.$(OBJEXT) \
+ gsnap_sse2-splicetrie.$(OBJEXT) gsnap_sse2-splice.$(OBJEXT) \
+ gsnap_sse2-indel.$(OBJEXT) \
+ gsnap_sse2-bitpack64-access.$(OBJEXT) \
+ gsnap_sse2-bytecoding.$(OBJEXT) gsnap_sse2-univdiag.$(OBJEXT) \
+ gsnap_sse2-sarray-read.$(OBJEXT) gsnap_sse2-stage1hr.$(OBJEXT) \
+ gsnap_sse2-request.$(OBJEXT) gsnap_sse2-resulthr.$(OBJEXT) \
+ gsnap_sse2-output.$(OBJEXT) gsnap_sse2-inbuffer.$(OBJEXT) \
+ gsnap_sse2-samheader.$(OBJEXT) gsnap_sse2-outbuffer.$(OBJEXT) \
+ gsnap_sse2-datadir.$(OBJEXT) gsnap_sse2-parserange.$(OBJEXT) \
+ gsnap_sse2-getopt.$(OBJEXT) gsnap_sse2-getopt1.$(OBJEXT) \
+ gsnap_sse2-gsnap.$(OBJEXT)
+dist_gsnap_sse2_OBJECTS = $(am__objects_22)
+gsnap_sse2_OBJECTS = $(dist_gsnap_sse2_OBJECTS)
+gsnap_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
+gsnap_sse2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse2_CFLAGS) \
+ $(CFLAGS) $(gsnap_sse2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_23 = gsnap_sse41-except.$(OBJEXT) \
+ gsnap_sse41-assert.$(OBJEXT) gsnap_sse41-mem.$(OBJEXT) \
+ gsnap_sse41-intlist.$(OBJEXT) gsnap_sse41-list.$(OBJEXT) \
+ gsnap_sse41-littleendian.$(OBJEXT) \
+ gsnap_sse41-bigendian.$(OBJEXT) \
+ gsnap_sse41-univinterval.$(OBJEXT) \
+ gsnap_sse41-interval.$(OBJEXT) gsnap_sse41-uintlist.$(OBJEXT) \
+ gsnap_sse41-stopwatch.$(OBJEXT) \
+ gsnap_sse41-semaphore.$(OBJEXT) gsnap_sse41-access.$(OBJEXT) \
+ gsnap_sse41-filestring.$(OBJEXT) \
+ gsnap_sse41-iit-read-univ.$(OBJEXT) \
+ gsnap_sse41-iit-read.$(OBJEXT) gsnap_sse41-md5.$(OBJEXT) \
+ gsnap_sse41-bzip2.$(OBJEXT) gsnap_sse41-sequence.$(OBJEXT) \
+ gsnap_sse41-reader.$(OBJEXT) gsnap_sse41-genomicpos.$(OBJEXT) \
+ gsnap_sse41-compress.$(OBJEXT) gsnap_sse41-genome.$(OBJEXT) \
+ gsnap_sse41-popcount.$(OBJEXT) \
+ gsnap_sse41-genome128_hr.$(OBJEXT) \
+ gsnap_sse41-genome_sites.$(OBJEXT) \
+ gsnap_sse41-bitpack64-read.$(OBJEXT) \
+ gsnap_sse41-bitpack64-readtwo.$(OBJEXT) \
+ gsnap_sse41-indexdb.$(OBJEXT) gsnap_sse41-indexdb_hr.$(OBJEXT) \
+ gsnap_sse41-oligo.$(OBJEXT) gsnap_sse41-chrom.$(OBJEXT) \
+ gsnap_sse41-segmentpos.$(OBJEXT) gsnap_sse41-chrnum.$(OBJEXT) \
+ gsnap_sse41-maxent_hr.$(OBJEXT) gsnap_sse41-samprint.$(OBJEXT) \
+ gsnap_sse41-mapq.$(OBJEXT) gsnap_sse41-shortread.$(OBJEXT) \
+ gsnap_sse41-substring.$(OBJEXT) gsnap_sse41-junction.$(OBJEXT) \
+ gsnap_sse41-stage3hr.$(OBJEXT) \
+ gsnap_sse41-spanningelt.$(OBJEXT) gsnap_sse41-cmet.$(OBJEXT) \
+ gsnap_sse41-atoi.$(OBJEXT) gsnap_sse41-maxent.$(OBJEXT) \
+ gsnap_sse41-pair.$(OBJEXT) gsnap_sse41-pairpool.$(OBJEXT) \
+ gsnap_sse41-diag.$(OBJEXT) gsnap_sse41-diagpool.$(OBJEXT) \
+ gsnap_sse41-orderstat.$(OBJEXT) \
+ gsnap_sse41-oligoindex_hr.$(OBJEXT) \
+ gsnap_sse41-cellpool.$(OBJEXT) gsnap_sse41-stage2.$(OBJEXT) \
+ gsnap_sse41-intron.$(OBJEXT) gsnap_sse41-boyer-moore.$(OBJEXT) \
+ gsnap_sse41-changepoint.$(OBJEXT) gsnap_sse41-pbinom.$(OBJEXT) \
+ gsnap_sse41-dynprog.$(OBJEXT) \
+ gsnap_sse41-dynprog_simd.$(OBJEXT) \
+ gsnap_sse41-dynprog_single.$(OBJEXT) \
+ gsnap_sse41-dynprog_genome.$(OBJEXT) \
+ gsnap_sse41-dynprog_cdna.$(OBJEXT) \
+ gsnap_sse41-dynprog_end.$(OBJEXT) \
+ gsnap_sse41-gbuffer.$(OBJEXT) \
+ gsnap_sse41-translation.$(OBJEXT) \
+ gsnap_sse41-doublelist.$(OBJEXT) gsnap_sse41-smooth.$(OBJEXT) \
+ gsnap_sse41-chimera.$(OBJEXT) gsnap_sse41-stage3.$(OBJEXT) \
+ gsnap_sse41-splicestringpool.$(OBJEXT) \
+ gsnap_sse41-splicetrie_build.$(OBJEXT) \
+ gsnap_sse41-splicetrie.$(OBJEXT) gsnap_sse41-splice.$(OBJEXT) \
+ gsnap_sse41-indel.$(OBJEXT) \
+ gsnap_sse41-bitpack64-access.$(OBJEXT) \
+ gsnap_sse41-bytecoding.$(OBJEXT) \
+ gsnap_sse41-univdiag.$(OBJEXT) \
+ gsnap_sse41-sarray-read.$(OBJEXT) \
+ gsnap_sse41-stage1hr.$(OBJEXT) gsnap_sse41-request.$(OBJEXT) \
+ gsnap_sse41-resulthr.$(OBJEXT) gsnap_sse41-output.$(OBJEXT) \
+ gsnap_sse41-inbuffer.$(OBJEXT) gsnap_sse41-samheader.$(OBJEXT) \
+ gsnap_sse41-outbuffer.$(OBJEXT) gsnap_sse41-datadir.$(OBJEXT) \
+ gsnap_sse41-parserange.$(OBJEXT) gsnap_sse41-getopt.$(OBJEXT) \
+ gsnap_sse41-getopt1.$(OBJEXT) gsnap_sse41-gsnap.$(OBJEXT)
+dist_gsnap_sse41_OBJECTS = $(am__objects_23)
+gsnap_sse41_OBJECTS = $(dist_gsnap_sse41_OBJECTS)
+gsnap_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gsnap_sse41_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse41_CFLAGS) \
+ $(CFLAGS) $(gsnap_sse41_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_24 = gsnap_sse42-except.$(OBJEXT) \
+ gsnap_sse42-assert.$(OBJEXT) gsnap_sse42-mem.$(OBJEXT) \
+ gsnap_sse42-intlist.$(OBJEXT) gsnap_sse42-list.$(OBJEXT) \
+ gsnap_sse42-littleendian.$(OBJEXT) \
+ gsnap_sse42-bigendian.$(OBJEXT) \
+ gsnap_sse42-univinterval.$(OBJEXT) \
+ gsnap_sse42-interval.$(OBJEXT) gsnap_sse42-uintlist.$(OBJEXT) \
+ gsnap_sse42-stopwatch.$(OBJEXT) \
+ gsnap_sse42-semaphore.$(OBJEXT) gsnap_sse42-access.$(OBJEXT) \
+ gsnap_sse42-filestring.$(OBJEXT) \
+ gsnap_sse42-iit-read-univ.$(OBJEXT) \
+ gsnap_sse42-iit-read.$(OBJEXT) gsnap_sse42-md5.$(OBJEXT) \
+ gsnap_sse42-bzip2.$(OBJEXT) gsnap_sse42-sequence.$(OBJEXT) \
+ gsnap_sse42-reader.$(OBJEXT) gsnap_sse42-genomicpos.$(OBJEXT) \
+ gsnap_sse42-compress.$(OBJEXT) gsnap_sse42-genome.$(OBJEXT) \
+ gsnap_sse42-popcount.$(OBJEXT) \
+ gsnap_sse42-genome128_hr.$(OBJEXT) \
+ gsnap_sse42-genome_sites.$(OBJEXT) \
+ gsnap_sse42-bitpack64-read.$(OBJEXT) \
+ gsnap_sse42-bitpack64-readtwo.$(OBJEXT) \
+ gsnap_sse42-indexdb.$(OBJEXT) gsnap_sse42-indexdb_hr.$(OBJEXT) \
+ gsnap_sse42-oligo.$(OBJEXT) gsnap_sse42-chrom.$(OBJEXT) \
+ gsnap_sse42-segmentpos.$(OBJEXT) gsnap_sse42-chrnum.$(OBJEXT) \
+ gsnap_sse42-maxent_hr.$(OBJEXT) gsnap_sse42-samprint.$(OBJEXT) \
+ gsnap_sse42-mapq.$(OBJEXT) gsnap_sse42-shortread.$(OBJEXT) \
+ gsnap_sse42-substring.$(OBJEXT) gsnap_sse42-junction.$(OBJEXT) \
+ gsnap_sse42-stage3hr.$(OBJEXT) \
+ gsnap_sse42-spanningelt.$(OBJEXT) gsnap_sse42-cmet.$(OBJEXT) \
+ gsnap_sse42-atoi.$(OBJEXT) gsnap_sse42-maxent.$(OBJEXT) \
+ gsnap_sse42-pair.$(OBJEXT) gsnap_sse42-pairpool.$(OBJEXT) \
+ gsnap_sse42-diag.$(OBJEXT) gsnap_sse42-diagpool.$(OBJEXT) \
+ gsnap_sse42-orderstat.$(OBJEXT) \
+ gsnap_sse42-oligoindex_hr.$(OBJEXT) \
+ gsnap_sse42-cellpool.$(OBJEXT) gsnap_sse42-stage2.$(OBJEXT) \
+ gsnap_sse42-intron.$(OBJEXT) gsnap_sse42-boyer-moore.$(OBJEXT) \
+ gsnap_sse42-changepoint.$(OBJEXT) gsnap_sse42-pbinom.$(OBJEXT) \
+ gsnap_sse42-dynprog.$(OBJEXT) \
+ gsnap_sse42-dynprog_simd.$(OBJEXT) \
+ gsnap_sse42-dynprog_single.$(OBJEXT) \
+ gsnap_sse42-dynprog_genome.$(OBJEXT) \
+ gsnap_sse42-dynprog_cdna.$(OBJEXT) \
+ gsnap_sse42-dynprog_end.$(OBJEXT) \
+ gsnap_sse42-gbuffer.$(OBJEXT) \
+ gsnap_sse42-translation.$(OBJEXT) \
+ gsnap_sse42-doublelist.$(OBJEXT) gsnap_sse42-smooth.$(OBJEXT) \
+ gsnap_sse42-chimera.$(OBJEXT) gsnap_sse42-stage3.$(OBJEXT) \
+ gsnap_sse42-splicestringpool.$(OBJEXT) \
+ gsnap_sse42-splicetrie_build.$(OBJEXT) \
+ gsnap_sse42-splicetrie.$(OBJEXT) gsnap_sse42-splice.$(OBJEXT) \
+ gsnap_sse42-indel.$(OBJEXT) \
+ gsnap_sse42-bitpack64-access.$(OBJEXT) \
+ gsnap_sse42-bytecoding.$(OBJEXT) \
+ gsnap_sse42-univdiag.$(OBJEXT) \
+ gsnap_sse42-sarray-read.$(OBJEXT) \
+ gsnap_sse42-stage1hr.$(OBJEXT) gsnap_sse42-request.$(OBJEXT) \
+ gsnap_sse42-resulthr.$(OBJEXT) gsnap_sse42-output.$(OBJEXT) \
+ gsnap_sse42-inbuffer.$(OBJEXT) gsnap_sse42-samheader.$(OBJEXT) \
+ gsnap_sse42-outbuffer.$(OBJEXT) gsnap_sse42-datadir.$(OBJEXT) \
+ gsnap_sse42-parserange.$(OBJEXT) gsnap_sse42-getopt.$(OBJEXT) \
+ gsnap_sse42-getopt1.$(OBJEXT) gsnap_sse42-gsnap.$(OBJEXT)
+dist_gsnap_sse42_OBJECTS = $(am__objects_24)
+gsnap_sse42_OBJECTS = $(dist_gsnap_sse42_OBJECTS)
+gsnap_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gsnap_sse42_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_sse42_CFLAGS) \
+ $(CFLAGS) $(gsnap_sse42_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_25 = gsnap_ssse3-except.$(OBJEXT) \
+ gsnap_ssse3-assert.$(OBJEXT) gsnap_ssse3-mem.$(OBJEXT) \
+ gsnap_ssse3-intlist.$(OBJEXT) gsnap_ssse3-list.$(OBJEXT) \
+ gsnap_ssse3-littleendian.$(OBJEXT) \
+ gsnap_ssse3-bigendian.$(OBJEXT) \
+ gsnap_ssse3-univinterval.$(OBJEXT) \
+ gsnap_ssse3-interval.$(OBJEXT) gsnap_ssse3-uintlist.$(OBJEXT) \
+ gsnap_ssse3-stopwatch.$(OBJEXT) \
+ gsnap_ssse3-semaphore.$(OBJEXT) gsnap_ssse3-access.$(OBJEXT) \
+ gsnap_ssse3-filestring.$(OBJEXT) \
+ gsnap_ssse3-iit-read-univ.$(OBJEXT) \
+ gsnap_ssse3-iit-read.$(OBJEXT) gsnap_ssse3-md5.$(OBJEXT) \
+ gsnap_ssse3-bzip2.$(OBJEXT) gsnap_ssse3-sequence.$(OBJEXT) \
+ gsnap_ssse3-reader.$(OBJEXT) gsnap_ssse3-genomicpos.$(OBJEXT) \
+ gsnap_ssse3-compress.$(OBJEXT) gsnap_ssse3-genome.$(OBJEXT) \
+ gsnap_ssse3-popcount.$(OBJEXT) \
+ gsnap_ssse3-genome128_hr.$(OBJEXT) \
+ gsnap_ssse3-genome_sites.$(OBJEXT) \
+ gsnap_ssse3-bitpack64-read.$(OBJEXT) \
+ gsnap_ssse3-bitpack64-readtwo.$(OBJEXT) \
+ gsnap_ssse3-indexdb.$(OBJEXT) gsnap_ssse3-indexdb_hr.$(OBJEXT) \
+ gsnap_ssse3-oligo.$(OBJEXT) gsnap_ssse3-chrom.$(OBJEXT) \
+ gsnap_ssse3-segmentpos.$(OBJEXT) gsnap_ssse3-chrnum.$(OBJEXT) \
+ gsnap_ssse3-maxent_hr.$(OBJEXT) gsnap_ssse3-samprint.$(OBJEXT) \
+ gsnap_ssse3-mapq.$(OBJEXT) gsnap_ssse3-shortread.$(OBJEXT) \
+ gsnap_ssse3-substring.$(OBJEXT) gsnap_ssse3-junction.$(OBJEXT) \
+ gsnap_ssse3-stage3hr.$(OBJEXT) \
+ gsnap_ssse3-spanningelt.$(OBJEXT) gsnap_ssse3-cmet.$(OBJEXT) \
+ gsnap_ssse3-atoi.$(OBJEXT) gsnap_ssse3-maxent.$(OBJEXT) \
+ gsnap_ssse3-pair.$(OBJEXT) gsnap_ssse3-pairpool.$(OBJEXT) \
+ gsnap_ssse3-diag.$(OBJEXT) gsnap_ssse3-diagpool.$(OBJEXT) \
+ gsnap_ssse3-orderstat.$(OBJEXT) \
+ gsnap_ssse3-oligoindex_hr.$(OBJEXT) \
+ gsnap_ssse3-cellpool.$(OBJEXT) gsnap_ssse3-stage2.$(OBJEXT) \
+ gsnap_ssse3-intron.$(OBJEXT) gsnap_ssse3-boyer-moore.$(OBJEXT) \
+ gsnap_ssse3-changepoint.$(OBJEXT) gsnap_ssse3-pbinom.$(OBJEXT) \
+ gsnap_ssse3-dynprog.$(OBJEXT) \
+ gsnap_ssse3-dynprog_simd.$(OBJEXT) \
+ gsnap_ssse3-dynprog_single.$(OBJEXT) \
+ gsnap_ssse3-dynprog_genome.$(OBJEXT) \
+ gsnap_ssse3-dynprog_cdna.$(OBJEXT) \
+ gsnap_ssse3-dynprog_end.$(OBJEXT) \
+ gsnap_ssse3-gbuffer.$(OBJEXT) \
+ gsnap_ssse3-translation.$(OBJEXT) \
+ gsnap_ssse3-doublelist.$(OBJEXT) gsnap_ssse3-smooth.$(OBJEXT) \
+ gsnap_ssse3-chimera.$(OBJEXT) gsnap_ssse3-stage3.$(OBJEXT) \
+ gsnap_ssse3-splicestringpool.$(OBJEXT) \
+ gsnap_ssse3-splicetrie_build.$(OBJEXT) \
+ gsnap_ssse3-splicetrie.$(OBJEXT) gsnap_ssse3-splice.$(OBJEXT) \
+ gsnap_ssse3-indel.$(OBJEXT) \
+ gsnap_ssse3-bitpack64-access.$(OBJEXT) \
+ gsnap_ssse3-bytecoding.$(OBJEXT) \
+ gsnap_ssse3-univdiag.$(OBJEXT) \
+ gsnap_ssse3-sarray-read.$(OBJEXT) \
+ gsnap_ssse3-stage1hr.$(OBJEXT) gsnap_ssse3-request.$(OBJEXT) \
+ gsnap_ssse3-resulthr.$(OBJEXT) gsnap_ssse3-output.$(OBJEXT) \
+ gsnap_ssse3-inbuffer.$(OBJEXT) gsnap_ssse3-samheader.$(OBJEXT) \
+ gsnap_ssse3-outbuffer.$(OBJEXT) gsnap_ssse3-datadir.$(OBJEXT) \
+ gsnap_ssse3-parserange.$(OBJEXT) gsnap_ssse3-getopt.$(OBJEXT) \
+ gsnap_ssse3-getopt1.$(OBJEXT) gsnap_ssse3-gsnap.$(OBJEXT)
+dist_gsnap_ssse3_OBJECTS = $(am__objects_25)
+gsnap_ssse3_OBJECTS = $(dist_gsnap_ssse3_OBJECTS)
+gsnap_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gsnap_ssse3_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnap_ssse3_CFLAGS) \
+ $(CFLAGS) $(gsnap_ssse3_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_26 = gsnapl-cpuid.$(OBJEXT) gsnapl-gsnapl_select.$(OBJEXT)
+dist_gsnapl_OBJECTS = $(am__objects_26)
+gsnapl_OBJECTS = $(dist_gsnapl_OBJECTS)
+gsnapl_DEPENDENCIES =
gsnapl_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(gsnapl_CFLAGS) $(CFLAGS) \
$(gsnapl_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_9 = iit_dump-except.$(OBJEXT) iit_dump-assert.$(OBJEXT) \
+am__objects_27 = gsnapl_avx2-except.$(OBJEXT) \
+ gsnapl_avx2-assert.$(OBJEXT) gsnapl_avx2-mem.$(OBJEXT) \
+ gsnapl_avx2-intlist.$(OBJEXT) gsnapl_avx2-list.$(OBJEXT) \
+ gsnapl_avx2-littleendian.$(OBJEXT) \
+ gsnapl_avx2-bigendian.$(OBJEXT) \
+ gsnapl_avx2-univinterval.$(OBJEXT) \
+ gsnapl_avx2-interval.$(OBJEXT) gsnapl_avx2-uintlist.$(OBJEXT) \
+ gsnapl_avx2-uint8list.$(OBJEXT) \
+ gsnapl_avx2-stopwatch.$(OBJEXT) \
+ gsnapl_avx2-semaphore.$(OBJEXT) gsnapl_avx2-access.$(OBJEXT) \
+ gsnapl_avx2-filestring.$(OBJEXT) \
+ gsnapl_avx2-iit-read-univ.$(OBJEXT) \
+ gsnapl_avx2-iit-read.$(OBJEXT) gsnapl_avx2-md5.$(OBJEXT) \
+ gsnapl_avx2-bzip2.$(OBJEXT) gsnapl_avx2-sequence.$(OBJEXT) \
+ gsnapl_avx2-reader.$(OBJEXT) gsnapl_avx2-genomicpos.$(OBJEXT) \
+ gsnapl_avx2-compress.$(OBJEXT) gsnapl_avx2-genome.$(OBJEXT) \
+ gsnapl_avx2-popcount.$(OBJEXT) \
+ gsnapl_avx2-genome128_hr.$(OBJEXT) \
+ gsnapl_avx2-genome_sites.$(OBJEXT) \
+ gsnapl_avx2-bitpack64-read.$(OBJEXT) \
+ gsnapl_avx2-bitpack64-readtwo.$(OBJEXT) \
+ gsnapl_avx2-indexdb.$(OBJEXT) gsnapl_avx2-indexdb_hr.$(OBJEXT) \
+ gsnapl_avx2-oligo.$(OBJEXT) gsnapl_avx2-chrom.$(OBJEXT) \
+ gsnapl_avx2-segmentpos.$(OBJEXT) gsnapl_avx2-chrnum.$(OBJEXT) \
+ gsnapl_avx2-maxent_hr.$(OBJEXT) gsnapl_avx2-samprint.$(OBJEXT) \
+ gsnapl_avx2-mapq.$(OBJEXT) gsnapl_avx2-shortread.$(OBJEXT) \
+ gsnapl_avx2-substring.$(OBJEXT) gsnapl_avx2-junction.$(OBJEXT) \
+ gsnapl_avx2-stage3hr.$(OBJEXT) \
+ gsnapl_avx2-spanningelt.$(OBJEXT) gsnapl_avx2-cmet.$(OBJEXT) \
+ gsnapl_avx2-atoi.$(OBJEXT) gsnapl_avx2-maxent.$(OBJEXT) \
+ gsnapl_avx2-pair.$(OBJEXT) gsnapl_avx2-pairpool.$(OBJEXT) \
+ gsnapl_avx2-diag.$(OBJEXT) gsnapl_avx2-diagpool.$(OBJEXT) \
+ gsnapl_avx2-orderstat.$(OBJEXT) \
+ gsnapl_avx2-oligoindex_hr.$(OBJEXT) \
+ gsnapl_avx2-cellpool.$(OBJEXT) gsnapl_avx2-stage2.$(OBJEXT) \
+ gsnapl_avx2-intron.$(OBJEXT) gsnapl_avx2-boyer-moore.$(OBJEXT) \
+ gsnapl_avx2-changepoint.$(OBJEXT) gsnapl_avx2-pbinom.$(OBJEXT) \
+ gsnapl_avx2-dynprog.$(OBJEXT) \
+ gsnapl_avx2-dynprog_simd.$(OBJEXT) \
+ gsnapl_avx2-dynprog_single.$(OBJEXT) \
+ gsnapl_avx2-dynprog_genome.$(OBJEXT) \
+ gsnapl_avx2-dynprog_cdna.$(OBJEXT) \
+ gsnapl_avx2-dynprog_end.$(OBJEXT) \
+ gsnapl_avx2-gbuffer.$(OBJEXT) \
+ gsnapl_avx2-translation.$(OBJEXT) \
+ gsnapl_avx2-doublelist.$(OBJEXT) gsnapl_avx2-smooth.$(OBJEXT) \
+ gsnapl_avx2-chimera.$(OBJEXT) gsnapl_avx2-stage3.$(OBJEXT) \
+ gsnapl_avx2-splicestringpool.$(OBJEXT) \
+ gsnapl_avx2-splicetrie_build.$(OBJEXT) \
+ gsnapl_avx2-splicetrie.$(OBJEXT) gsnapl_avx2-splice.$(OBJEXT) \
+ gsnapl_avx2-indel.$(OBJEXT) \
+ gsnapl_avx2-bitpack64-access.$(OBJEXT) \
+ gsnapl_avx2-stage1hr.$(OBJEXT) gsnapl_avx2-request.$(OBJEXT) \
+ gsnapl_avx2-resulthr.$(OBJEXT) gsnapl_avx2-output.$(OBJEXT) \
+ gsnapl_avx2-inbuffer.$(OBJEXT) gsnapl_avx2-samheader.$(OBJEXT) \
+ gsnapl_avx2-outbuffer.$(OBJEXT) gsnapl_avx2-datadir.$(OBJEXT) \
+ gsnapl_avx2-parserange.$(OBJEXT) gsnapl_avx2-getopt.$(OBJEXT) \
+ gsnapl_avx2-getopt1.$(OBJEXT) gsnapl_avx2-gsnap.$(OBJEXT)
+dist_gsnapl_avx2_OBJECTS = $(am__objects_27)
+gsnapl_avx2_OBJECTS = $(dist_gsnapl_avx2_OBJECTS)
+gsnapl_avx2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gsnapl_avx2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_avx2_CFLAGS) \
+ $(CFLAGS) $(gsnapl_avx2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_28 = gsnapl_nosimd-except.$(OBJEXT) \
+ gsnapl_nosimd-assert.$(OBJEXT) gsnapl_nosimd-mem.$(OBJEXT) \
+ gsnapl_nosimd-intlist.$(OBJEXT) gsnapl_nosimd-list.$(OBJEXT) \
+ gsnapl_nosimd-littleendian.$(OBJEXT) \
+ gsnapl_nosimd-bigendian.$(OBJEXT) \
+ gsnapl_nosimd-univinterval.$(OBJEXT) \
+ gsnapl_nosimd-interval.$(OBJEXT) \
+ gsnapl_nosimd-uintlist.$(OBJEXT) \
+ gsnapl_nosimd-uint8list.$(OBJEXT) \
+ gsnapl_nosimd-stopwatch.$(OBJEXT) \
+ gsnapl_nosimd-semaphore.$(OBJEXT) \
+ gsnapl_nosimd-access.$(OBJEXT) \
+ gsnapl_nosimd-filestring.$(OBJEXT) \
+ gsnapl_nosimd-iit-read-univ.$(OBJEXT) \
+ gsnapl_nosimd-iit-read.$(OBJEXT) gsnapl_nosimd-md5.$(OBJEXT) \
+ gsnapl_nosimd-bzip2.$(OBJEXT) gsnapl_nosimd-sequence.$(OBJEXT) \
+ gsnapl_nosimd-reader.$(OBJEXT) \
+ gsnapl_nosimd-genomicpos.$(OBJEXT) \
+ gsnapl_nosimd-compress.$(OBJEXT) \
+ gsnapl_nosimd-genome.$(OBJEXT) \
+ gsnapl_nosimd-popcount.$(OBJEXT) \
+ gsnapl_nosimd-genome128_hr.$(OBJEXT) \
+ gsnapl_nosimd-genome_sites.$(OBJEXT) \
+ gsnapl_nosimd-bitpack64-read.$(OBJEXT) \
+ gsnapl_nosimd-bitpack64-readtwo.$(OBJEXT) \
+ gsnapl_nosimd-indexdb.$(OBJEXT) \
+ gsnapl_nosimd-indexdb_hr.$(OBJEXT) \
+ gsnapl_nosimd-oligo.$(OBJEXT) gsnapl_nosimd-chrom.$(OBJEXT) \
+ gsnapl_nosimd-segmentpos.$(OBJEXT) \
+ gsnapl_nosimd-chrnum.$(OBJEXT) \
+ gsnapl_nosimd-maxent_hr.$(OBJEXT) \
+ gsnapl_nosimd-samprint.$(OBJEXT) gsnapl_nosimd-mapq.$(OBJEXT) \
+ gsnapl_nosimd-shortread.$(OBJEXT) \
+ gsnapl_nosimd-substring.$(OBJEXT) \
+ gsnapl_nosimd-junction.$(OBJEXT) \
+ gsnapl_nosimd-stage3hr.$(OBJEXT) \
+ gsnapl_nosimd-spanningelt.$(OBJEXT) \
+ gsnapl_nosimd-cmet.$(OBJEXT) gsnapl_nosimd-atoi.$(OBJEXT) \
+ gsnapl_nosimd-maxent.$(OBJEXT) gsnapl_nosimd-pair.$(OBJEXT) \
+ gsnapl_nosimd-pairpool.$(OBJEXT) gsnapl_nosimd-diag.$(OBJEXT) \
+ gsnapl_nosimd-diagpool.$(OBJEXT) \
+ gsnapl_nosimd-orderstat.$(OBJEXT) \
+ gsnapl_nosimd-oligoindex_hr.$(OBJEXT) \
+ gsnapl_nosimd-cellpool.$(OBJEXT) \
+ gsnapl_nosimd-stage2.$(OBJEXT) gsnapl_nosimd-intron.$(OBJEXT) \
+ gsnapl_nosimd-boyer-moore.$(OBJEXT) \
+ gsnapl_nosimd-changepoint.$(OBJEXT) \
+ gsnapl_nosimd-pbinom.$(OBJEXT) gsnapl_nosimd-dynprog.$(OBJEXT) \
+ gsnapl_nosimd-dynprog_simd.$(OBJEXT) \
+ gsnapl_nosimd-dynprog_single.$(OBJEXT) \
+ gsnapl_nosimd-dynprog_genome.$(OBJEXT) \
+ gsnapl_nosimd-dynprog_cdna.$(OBJEXT) \
+ gsnapl_nosimd-dynprog_end.$(OBJEXT) \
+ gsnapl_nosimd-gbuffer.$(OBJEXT) \
+ gsnapl_nosimd-translation.$(OBJEXT) \
+ gsnapl_nosimd-doublelist.$(OBJEXT) \
+ gsnapl_nosimd-smooth.$(OBJEXT) gsnapl_nosimd-chimera.$(OBJEXT) \
+ gsnapl_nosimd-stage3.$(OBJEXT) \
+ gsnapl_nosimd-splicestringpool.$(OBJEXT) \
+ gsnapl_nosimd-splicetrie_build.$(OBJEXT) \
+ gsnapl_nosimd-splicetrie.$(OBJEXT) \
+ gsnapl_nosimd-splice.$(OBJEXT) gsnapl_nosimd-indel.$(OBJEXT) \
+ gsnapl_nosimd-bitpack64-access.$(OBJEXT) \
+ gsnapl_nosimd-stage1hr.$(OBJEXT) \
+ gsnapl_nosimd-request.$(OBJEXT) \
+ gsnapl_nosimd-resulthr.$(OBJEXT) \
+ gsnapl_nosimd-output.$(OBJEXT) \
+ gsnapl_nosimd-inbuffer.$(OBJEXT) \
+ gsnapl_nosimd-samheader.$(OBJEXT) \
+ gsnapl_nosimd-outbuffer.$(OBJEXT) \
+ gsnapl_nosimd-datadir.$(OBJEXT) \
+ gsnapl_nosimd-parserange.$(OBJEXT) \
+ gsnapl_nosimd-getopt.$(OBJEXT) gsnapl_nosimd-getopt1.$(OBJEXT) \
+ gsnapl_nosimd-gsnap.$(OBJEXT)
+dist_gsnapl_nosimd_OBJECTS = $(am__objects_28)
+gsnapl_nosimd_OBJECTS = $(dist_gsnapl_nosimd_OBJECTS)
+gsnapl_nosimd_DEPENDENCIES = $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+gsnapl_nosimd_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_nosimd_CFLAGS) \
+ $(CFLAGS) $(gsnapl_nosimd_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_29 = gsnapl_sse2-except.$(OBJEXT) \
+ gsnapl_sse2-assert.$(OBJEXT) gsnapl_sse2-mem.$(OBJEXT) \
+ gsnapl_sse2-intlist.$(OBJEXT) gsnapl_sse2-list.$(OBJEXT) \
+ gsnapl_sse2-littleendian.$(OBJEXT) \
+ gsnapl_sse2-bigendian.$(OBJEXT) \
+ gsnapl_sse2-univinterval.$(OBJEXT) \
+ gsnapl_sse2-interval.$(OBJEXT) gsnapl_sse2-uintlist.$(OBJEXT) \
+ gsnapl_sse2-uint8list.$(OBJEXT) \
+ gsnapl_sse2-stopwatch.$(OBJEXT) \
+ gsnapl_sse2-semaphore.$(OBJEXT) gsnapl_sse2-access.$(OBJEXT) \
+ gsnapl_sse2-filestring.$(OBJEXT) \
+ gsnapl_sse2-iit-read-univ.$(OBJEXT) \
+ gsnapl_sse2-iit-read.$(OBJEXT) gsnapl_sse2-md5.$(OBJEXT) \
+ gsnapl_sse2-bzip2.$(OBJEXT) gsnapl_sse2-sequence.$(OBJEXT) \
+ gsnapl_sse2-reader.$(OBJEXT) gsnapl_sse2-genomicpos.$(OBJEXT) \
+ gsnapl_sse2-compress.$(OBJEXT) gsnapl_sse2-genome.$(OBJEXT) \
+ gsnapl_sse2-popcount.$(OBJEXT) \
+ gsnapl_sse2-genome128_hr.$(OBJEXT) \
+ gsnapl_sse2-genome_sites.$(OBJEXT) \
+ gsnapl_sse2-bitpack64-read.$(OBJEXT) \
+ gsnapl_sse2-bitpack64-readtwo.$(OBJEXT) \
+ gsnapl_sse2-indexdb.$(OBJEXT) gsnapl_sse2-indexdb_hr.$(OBJEXT) \
+ gsnapl_sse2-oligo.$(OBJEXT) gsnapl_sse2-chrom.$(OBJEXT) \
+ gsnapl_sse2-segmentpos.$(OBJEXT) gsnapl_sse2-chrnum.$(OBJEXT) \
+ gsnapl_sse2-maxent_hr.$(OBJEXT) gsnapl_sse2-samprint.$(OBJEXT) \
+ gsnapl_sse2-mapq.$(OBJEXT) gsnapl_sse2-shortread.$(OBJEXT) \
+ gsnapl_sse2-substring.$(OBJEXT) gsnapl_sse2-junction.$(OBJEXT) \
+ gsnapl_sse2-stage3hr.$(OBJEXT) \
+ gsnapl_sse2-spanningelt.$(OBJEXT) gsnapl_sse2-cmet.$(OBJEXT) \
+ gsnapl_sse2-atoi.$(OBJEXT) gsnapl_sse2-maxent.$(OBJEXT) \
+ gsnapl_sse2-pair.$(OBJEXT) gsnapl_sse2-pairpool.$(OBJEXT) \
+ gsnapl_sse2-diag.$(OBJEXT) gsnapl_sse2-diagpool.$(OBJEXT) \
+ gsnapl_sse2-orderstat.$(OBJEXT) \
+ gsnapl_sse2-oligoindex_hr.$(OBJEXT) \
+ gsnapl_sse2-cellpool.$(OBJEXT) gsnapl_sse2-stage2.$(OBJEXT) \
+ gsnapl_sse2-intron.$(OBJEXT) gsnapl_sse2-boyer-moore.$(OBJEXT) \
+ gsnapl_sse2-changepoint.$(OBJEXT) gsnapl_sse2-pbinom.$(OBJEXT) \
+ gsnapl_sse2-dynprog.$(OBJEXT) \
+ gsnapl_sse2-dynprog_simd.$(OBJEXT) \
+ gsnapl_sse2-dynprog_single.$(OBJEXT) \
+ gsnapl_sse2-dynprog_genome.$(OBJEXT) \
+ gsnapl_sse2-dynprog_cdna.$(OBJEXT) \
+ gsnapl_sse2-dynprog_end.$(OBJEXT) \
+ gsnapl_sse2-gbuffer.$(OBJEXT) \
+ gsnapl_sse2-translation.$(OBJEXT) \
+ gsnapl_sse2-doublelist.$(OBJEXT) gsnapl_sse2-smooth.$(OBJEXT) \
+ gsnapl_sse2-chimera.$(OBJEXT) gsnapl_sse2-stage3.$(OBJEXT) \
+ gsnapl_sse2-splicestringpool.$(OBJEXT) \
+ gsnapl_sse2-splicetrie_build.$(OBJEXT) \
+ gsnapl_sse2-splicetrie.$(OBJEXT) gsnapl_sse2-splice.$(OBJEXT) \
+ gsnapl_sse2-indel.$(OBJEXT) \
+ gsnapl_sse2-bitpack64-access.$(OBJEXT) \
+ gsnapl_sse2-stage1hr.$(OBJEXT) gsnapl_sse2-request.$(OBJEXT) \
+ gsnapl_sse2-resulthr.$(OBJEXT) gsnapl_sse2-output.$(OBJEXT) \
+ gsnapl_sse2-inbuffer.$(OBJEXT) gsnapl_sse2-samheader.$(OBJEXT) \
+ gsnapl_sse2-outbuffer.$(OBJEXT) gsnapl_sse2-datadir.$(OBJEXT) \
+ gsnapl_sse2-parserange.$(OBJEXT) gsnapl_sse2-getopt.$(OBJEXT) \
+ gsnapl_sse2-getopt1.$(OBJEXT) gsnapl_sse2-gsnap.$(OBJEXT)
+dist_gsnapl_sse2_OBJECTS = $(am__objects_29)
+gsnapl_sse2_OBJECTS = $(dist_gsnapl_sse2_OBJECTS)
+gsnapl_sse2_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1)
+gsnapl_sse2_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse2_CFLAGS) \
+ $(CFLAGS) $(gsnapl_sse2_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_30 = gsnapl_sse41-except.$(OBJEXT) \
+ gsnapl_sse41-assert.$(OBJEXT) gsnapl_sse41-mem.$(OBJEXT) \
+ gsnapl_sse41-intlist.$(OBJEXT) gsnapl_sse41-list.$(OBJEXT) \
+ gsnapl_sse41-littleendian.$(OBJEXT) \
+ gsnapl_sse41-bigendian.$(OBJEXT) \
+ gsnapl_sse41-univinterval.$(OBJEXT) \
+ gsnapl_sse41-interval.$(OBJEXT) \
+ gsnapl_sse41-uintlist.$(OBJEXT) \
+ gsnapl_sse41-uint8list.$(OBJEXT) \
+ gsnapl_sse41-stopwatch.$(OBJEXT) \
+ gsnapl_sse41-semaphore.$(OBJEXT) gsnapl_sse41-access.$(OBJEXT) \
+ gsnapl_sse41-filestring.$(OBJEXT) \
+ gsnapl_sse41-iit-read-univ.$(OBJEXT) \
+ gsnapl_sse41-iit-read.$(OBJEXT) gsnapl_sse41-md5.$(OBJEXT) \
+ gsnapl_sse41-bzip2.$(OBJEXT) gsnapl_sse41-sequence.$(OBJEXT) \
+ gsnapl_sse41-reader.$(OBJEXT) \
+ gsnapl_sse41-genomicpos.$(OBJEXT) \
+ gsnapl_sse41-compress.$(OBJEXT) gsnapl_sse41-genome.$(OBJEXT) \
+ gsnapl_sse41-popcount.$(OBJEXT) \
+ gsnapl_sse41-genome128_hr.$(OBJEXT) \
+ gsnapl_sse41-genome_sites.$(OBJEXT) \
+ gsnapl_sse41-bitpack64-read.$(OBJEXT) \
+ gsnapl_sse41-bitpack64-readtwo.$(OBJEXT) \
+ gsnapl_sse41-indexdb.$(OBJEXT) \
+ gsnapl_sse41-indexdb_hr.$(OBJEXT) gsnapl_sse41-oligo.$(OBJEXT) \
+ gsnapl_sse41-chrom.$(OBJEXT) gsnapl_sse41-segmentpos.$(OBJEXT) \
+ gsnapl_sse41-chrnum.$(OBJEXT) gsnapl_sse41-maxent_hr.$(OBJEXT) \
+ gsnapl_sse41-samprint.$(OBJEXT) gsnapl_sse41-mapq.$(OBJEXT) \
+ gsnapl_sse41-shortread.$(OBJEXT) \
+ gsnapl_sse41-substring.$(OBJEXT) \
+ gsnapl_sse41-junction.$(OBJEXT) \
+ gsnapl_sse41-stage3hr.$(OBJEXT) \
+ gsnapl_sse41-spanningelt.$(OBJEXT) gsnapl_sse41-cmet.$(OBJEXT) \
+ gsnapl_sse41-atoi.$(OBJEXT) gsnapl_sse41-maxent.$(OBJEXT) \
+ gsnapl_sse41-pair.$(OBJEXT) gsnapl_sse41-pairpool.$(OBJEXT) \
+ gsnapl_sse41-diag.$(OBJEXT) gsnapl_sse41-diagpool.$(OBJEXT) \
+ gsnapl_sse41-orderstat.$(OBJEXT) \
+ gsnapl_sse41-oligoindex_hr.$(OBJEXT) \
+ gsnapl_sse41-cellpool.$(OBJEXT) gsnapl_sse41-stage2.$(OBJEXT) \
+ gsnapl_sse41-intron.$(OBJEXT) \
+ gsnapl_sse41-boyer-moore.$(OBJEXT) \
+ gsnapl_sse41-changepoint.$(OBJEXT) \
+ gsnapl_sse41-pbinom.$(OBJEXT) gsnapl_sse41-dynprog.$(OBJEXT) \
+ gsnapl_sse41-dynprog_simd.$(OBJEXT) \
+ gsnapl_sse41-dynprog_single.$(OBJEXT) \
+ gsnapl_sse41-dynprog_genome.$(OBJEXT) \
+ gsnapl_sse41-dynprog_cdna.$(OBJEXT) \
+ gsnapl_sse41-dynprog_end.$(OBJEXT) \
+ gsnapl_sse41-gbuffer.$(OBJEXT) \
+ gsnapl_sse41-translation.$(OBJEXT) \
+ gsnapl_sse41-doublelist.$(OBJEXT) \
+ gsnapl_sse41-smooth.$(OBJEXT) gsnapl_sse41-chimera.$(OBJEXT) \
+ gsnapl_sse41-stage3.$(OBJEXT) \
+ gsnapl_sse41-splicestringpool.$(OBJEXT) \
+ gsnapl_sse41-splicetrie_build.$(OBJEXT) \
+ gsnapl_sse41-splicetrie.$(OBJEXT) \
+ gsnapl_sse41-splice.$(OBJEXT) gsnapl_sse41-indel.$(OBJEXT) \
+ gsnapl_sse41-bitpack64-access.$(OBJEXT) \
+ gsnapl_sse41-stage1hr.$(OBJEXT) gsnapl_sse41-request.$(OBJEXT) \
+ gsnapl_sse41-resulthr.$(OBJEXT) gsnapl_sse41-output.$(OBJEXT) \
+ gsnapl_sse41-inbuffer.$(OBJEXT) \
+ gsnapl_sse41-samheader.$(OBJEXT) \
+ gsnapl_sse41-outbuffer.$(OBJEXT) \
+ gsnapl_sse41-datadir.$(OBJEXT) \
+ gsnapl_sse41-parserange.$(OBJEXT) \
+ gsnapl_sse41-getopt.$(OBJEXT) gsnapl_sse41-getopt1.$(OBJEXT) \
+ gsnapl_sse41-gsnap.$(OBJEXT)
+dist_gsnapl_sse41_OBJECTS = $(am__objects_30)
+gsnapl_sse41_OBJECTS = $(dist_gsnapl_sse41_OBJECTS)
+gsnapl_sse41_DEPENDENCIES = $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+gsnapl_sse41_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse41_CFLAGS) \
+ $(CFLAGS) $(gsnapl_sse41_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_31 = gsnapl_sse42-except.$(OBJEXT) \
+ gsnapl_sse42-assert.$(OBJEXT) gsnapl_sse42-mem.$(OBJEXT) \
+ gsnapl_sse42-intlist.$(OBJEXT) gsnapl_sse42-list.$(OBJEXT) \
+ gsnapl_sse42-littleendian.$(OBJEXT) \
+ gsnapl_sse42-bigendian.$(OBJEXT) \
+ gsnapl_sse42-univinterval.$(OBJEXT) \
+ gsnapl_sse42-interval.$(OBJEXT) \
+ gsnapl_sse42-uintlist.$(OBJEXT) \
+ gsnapl_sse42-uint8list.$(OBJEXT) \
+ gsnapl_sse42-stopwatch.$(OBJEXT) \
+ gsnapl_sse42-semaphore.$(OBJEXT) gsnapl_sse42-access.$(OBJEXT) \
+ gsnapl_sse42-filestring.$(OBJEXT) \
+ gsnapl_sse42-iit-read-univ.$(OBJEXT) \
+ gsnapl_sse42-iit-read.$(OBJEXT) gsnapl_sse42-md5.$(OBJEXT) \
+ gsnapl_sse42-bzip2.$(OBJEXT) gsnapl_sse42-sequence.$(OBJEXT) \
+ gsnapl_sse42-reader.$(OBJEXT) \
+ gsnapl_sse42-genomicpos.$(OBJEXT) \
+ gsnapl_sse42-compress.$(OBJEXT) gsnapl_sse42-genome.$(OBJEXT) \
+ gsnapl_sse42-popcount.$(OBJEXT) \
+ gsnapl_sse42-genome128_hr.$(OBJEXT) \
+ gsnapl_sse42-genome_sites.$(OBJEXT) \
+ gsnapl_sse42-bitpack64-read.$(OBJEXT) \
+ gsnapl_sse42-bitpack64-readtwo.$(OBJEXT) \
+ gsnapl_sse42-indexdb.$(OBJEXT) \
+ gsnapl_sse42-indexdb_hr.$(OBJEXT) gsnapl_sse42-oligo.$(OBJEXT) \
+ gsnapl_sse42-chrom.$(OBJEXT) gsnapl_sse42-segmentpos.$(OBJEXT) \
+ gsnapl_sse42-chrnum.$(OBJEXT) gsnapl_sse42-maxent_hr.$(OBJEXT) \
+ gsnapl_sse42-samprint.$(OBJEXT) gsnapl_sse42-mapq.$(OBJEXT) \
+ gsnapl_sse42-shortread.$(OBJEXT) \
+ gsnapl_sse42-substring.$(OBJEXT) \
+ gsnapl_sse42-junction.$(OBJEXT) \
+ gsnapl_sse42-stage3hr.$(OBJEXT) \
+ gsnapl_sse42-spanningelt.$(OBJEXT) gsnapl_sse42-cmet.$(OBJEXT) \
+ gsnapl_sse42-atoi.$(OBJEXT) gsnapl_sse42-maxent.$(OBJEXT) \
+ gsnapl_sse42-pair.$(OBJEXT) gsnapl_sse42-pairpool.$(OBJEXT) \
+ gsnapl_sse42-diag.$(OBJEXT) gsnapl_sse42-diagpool.$(OBJEXT) \
+ gsnapl_sse42-orderstat.$(OBJEXT) \
+ gsnapl_sse42-oligoindex_hr.$(OBJEXT) \
+ gsnapl_sse42-cellpool.$(OBJEXT) gsnapl_sse42-stage2.$(OBJEXT) \
+ gsnapl_sse42-intron.$(OBJEXT) \
+ gsnapl_sse42-boyer-moore.$(OBJEXT) \
+ gsnapl_sse42-changepoint.$(OBJEXT) \
+ gsnapl_sse42-pbinom.$(OBJEXT) gsnapl_sse42-dynprog.$(OBJEXT) \
+ gsnapl_sse42-dynprog_simd.$(OBJEXT) \
+ gsnapl_sse42-dynprog_single.$(OBJEXT) \
+ gsnapl_sse42-dynprog_genome.$(OBJEXT) \
+ gsnapl_sse42-dynprog_cdna.$(OBJEXT) \
+ gsnapl_sse42-dynprog_end.$(OBJEXT) \
+ gsnapl_sse42-gbuffer.$(OBJEXT) \
+ gsnapl_sse42-translation.$(OBJEXT) \
+ gsnapl_sse42-doublelist.$(OBJEXT) \
+ gsnapl_sse42-smooth.$(OBJEXT) gsnapl_sse42-chimera.$(OBJEXT) \
+ gsnapl_sse42-stage3.$(OBJEXT) \
+ gsnapl_sse42-splicestringpool.$(OBJEXT) \
+ gsnapl_sse42-splicetrie_build.$(OBJEXT) \
+ gsnapl_sse42-splicetrie.$(OBJEXT) \
+ gsnapl_sse42-splice.$(OBJEXT) gsnapl_sse42-indel.$(OBJEXT) \
+ gsnapl_sse42-bitpack64-access.$(OBJEXT) \
+ gsnapl_sse42-stage1hr.$(OBJEXT) gsnapl_sse42-request.$(OBJEXT) \
+ gsnapl_sse42-resulthr.$(OBJEXT) gsnapl_sse42-output.$(OBJEXT) \
+ gsnapl_sse42-inbuffer.$(OBJEXT) \
+ gsnapl_sse42-samheader.$(OBJEXT) \
+ gsnapl_sse42-outbuffer.$(OBJEXT) \
+ gsnapl_sse42-datadir.$(OBJEXT) \
+ gsnapl_sse42-parserange.$(OBJEXT) \
+ gsnapl_sse42-getopt.$(OBJEXT) gsnapl_sse42-getopt1.$(OBJEXT) \
+ gsnapl_sse42-gsnap.$(OBJEXT)
+dist_gsnapl_sse42_OBJECTS = $(am__objects_31)
+gsnapl_sse42_OBJECTS = $(dist_gsnapl_sse42_OBJECTS)
+gsnapl_sse42_DEPENDENCIES = $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+gsnapl_sse42_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_sse42_CFLAGS) \
+ $(CFLAGS) $(gsnapl_sse42_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_32 = gsnapl_ssse3-except.$(OBJEXT) \
+ gsnapl_ssse3-assert.$(OBJEXT) gsnapl_ssse3-mem.$(OBJEXT) \
+ gsnapl_ssse3-intlist.$(OBJEXT) gsnapl_ssse3-list.$(OBJEXT) \
+ gsnapl_ssse3-littleendian.$(OBJEXT) \
+ gsnapl_ssse3-bigendian.$(OBJEXT) \
+ gsnapl_ssse3-univinterval.$(OBJEXT) \
+ gsnapl_ssse3-interval.$(OBJEXT) \
+ gsnapl_ssse3-uintlist.$(OBJEXT) \
+ gsnapl_ssse3-uint8list.$(OBJEXT) \
+ gsnapl_ssse3-stopwatch.$(OBJEXT) \
+ gsnapl_ssse3-semaphore.$(OBJEXT) gsnapl_ssse3-access.$(OBJEXT) \
+ gsnapl_ssse3-filestring.$(OBJEXT) \
+ gsnapl_ssse3-iit-read-univ.$(OBJEXT) \
+ gsnapl_ssse3-iit-read.$(OBJEXT) gsnapl_ssse3-md5.$(OBJEXT) \
+ gsnapl_ssse3-bzip2.$(OBJEXT) gsnapl_ssse3-sequence.$(OBJEXT) \
+ gsnapl_ssse3-reader.$(OBJEXT) \
+ gsnapl_ssse3-genomicpos.$(OBJEXT) \
+ gsnapl_ssse3-compress.$(OBJEXT) gsnapl_ssse3-genome.$(OBJEXT) \
+ gsnapl_ssse3-popcount.$(OBJEXT) \
+ gsnapl_ssse3-genome128_hr.$(OBJEXT) \
+ gsnapl_ssse3-genome_sites.$(OBJEXT) \
+ gsnapl_ssse3-bitpack64-read.$(OBJEXT) \
+ gsnapl_ssse3-bitpack64-readtwo.$(OBJEXT) \
+ gsnapl_ssse3-indexdb.$(OBJEXT) \
+ gsnapl_ssse3-indexdb_hr.$(OBJEXT) gsnapl_ssse3-oligo.$(OBJEXT) \
+ gsnapl_ssse3-chrom.$(OBJEXT) gsnapl_ssse3-segmentpos.$(OBJEXT) \
+ gsnapl_ssse3-chrnum.$(OBJEXT) gsnapl_ssse3-maxent_hr.$(OBJEXT) \
+ gsnapl_ssse3-samprint.$(OBJEXT) gsnapl_ssse3-mapq.$(OBJEXT) \
+ gsnapl_ssse3-shortread.$(OBJEXT) \
+ gsnapl_ssse3-substring.$(OBJEXT) \
+ gsnapl_ssse3-junction.$(OBJEXT) \
+ gsnapl_ssse3-stage3hr.$(OBJEXT) \
+ gsnapl_ssse3-spanningelt.$(OBJEXT) gsnapl_ssse3-cmet.$(OBJEXT) \
+ gsnapl_ssse3-atoi.$(OBJEXT) gsnapl_ssse3-maxent.$(OBJEXT) \
+ gsnapl_ssse3-pair.$(OBJEXT) gsnapl_ssse3-pairpool.$(OBJEXT) \
+ gsnapl_ssse3-diag.$(OBJEXT) gsnapl_ssse3-diagpool.$(OBJEXT) \
+ gsnapl_ssse3-orderstat.$(OBJEXT) \
+ gsnapl_ssse3-oligoindex_hr.$(OBJEXT) \
+ gsnapl_ssse3-cellpool.$(OBJEXT) gsnapl_ssse3-stage2.$(OBJEXT) \
+ gsnapl_ssse3-intron.$(OBJEXT) \
+ gsnapl_ssse3-boyer-moore.$(OBJEXT) \
+ gsnapl_ssse3-changepoint.$(OBJEXT) \
+ gsnapl_ssse3-pbinom.$(OBJEXT) gsnapl_ssse3-dynprog.$(OBJEXT) \
+ gsnapl_ssse3-dynprog_simd.$(OBJEXT) \
+ gsnapl_ssse3-dynprog_single.$(OBJEXT) \
+ gsnapl_ssse3-dynprog_genome.$(OBJEXT) \
+ gsnapl_ssse3-dynprog_cdna.$(OBJEXT) \
+ gsnapl_ssse3-dynprog_end.$(OBJEXT) \
+ gsnapl_ssse3-gbuffer.$(OBJEXT) \
+ gsnapl_ssse3-translation.$(OBJEXT) \
+ gsnapl_ssse3-doublelist.$(OBJEXT) \
+ gsnapl_ssse3-smooth.$(OBJEXT) gsnapl_ssse3-chimera.$(OBJEXT) \
+ gsnapl_ssse3-stage3.$(OBJEXT) \
+ gsnapl_ssse3-splicestringpool.$(OBJEXT) \
+ gsnapl_ssse3-splicetrie_build.$(OBJEXT) \
+ gsnapl_ssse3-splicetrie.$(OBJEXT) \
+ gsnapl_ssse3-splice.$(OBJEXT) gsnapl_ssse3-indel.$(OBJEXT) \
+ gsnapl_ssse3-bitpack64-access.$(OBJEXT) \
+ gsnapl_ssse3-stage1hr.$(OBJEXT) gsnapl_ssse3-request.$(OBJEXT) \
+ gsnapl_ssse3-resulthr.$(OBJEXT) gsnapl_ssse3-output.$(OBJEXT) \
+ gsnapl_ssse3-inbuffer.$(OBJEXT) \
+ gsnapl_ssse3-samheader.$(OBJEXT) \
+ gsnapl_ssse3-outbuffer.$(OBJEXT) \
+ gsnapl_ssse3-datadir.$(OBJEXT) \
+ gsnapl_ssse3-parserange.$(OBJEXT) \
+ gsnapl_ssse3-getopt.$(OBJEXT) gsnapl_ssse3-getopt1.$(OBJEXT) \
+ gsnapl_ssse3-gsnap.$(OBJEXT)
+dist_gsnapl_ssse3_OBJECTS = $(am__objects_32)
+gsnapl_ssse3_OBJECTS = $(dist_gsnapl_ssse3_OBJECTS)
+gsnapl_ssse3_DEPENDENCIES = $(am__DEPENDENCIES_1) \
+ $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+gsnapl_ssse3_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
+ $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gsnapl_ssse3_CFLAGS) \
+ $(CFLAGS) $(gsnapl_ssse3_LDFLAGS) $(LDFLAGS) -o $@
+am__objects_33 = iit_dump-except.$(OBJEXT) iit_dump-assert.$(OBJEXT) \
iit_dump-mem.$(OBJEXT) iit_dump-littleendian.$(OBJEXT) \
iit_dump-bigendian.$(OBJEXT) iit_dump-intlist.$(OBJEXT) \
iit_dump-list.$(OBJEXT) iit_dump-univinterval.$(OBJEXT) \
iit_dump-interval.$(OBJEXT) iit_dump-uintlist.$(OBJEXT) \
- iit_dump-stopwatch.$(OBJEXT) iit_dump-access.$(OBJEXT) \
- iit_dump-filestring.$(OBJEXT) iit_dump-iit-read-univ.$(OBJEXT) \
- iit_dump-iit-read.$(OBJEXT) iit_dump-getopt.$(OBJEXT) \
+ iit_dump-stopwatch.$(OBJEXT) iit_dump-semaphore.$(OBJEXT) \
+ iit_dump-access.$(OBJEXT) iit_dump-filestring.$(OBJEXT) \
+ iit_dump-iit-read-univ.$(OBJEXT) iit_dump-iit-read.$(OBJEXT) \
+ iit_dump-parserange.$(OBJEXT) iit_dump-getopt.$(OBJEXT) \
iit_dump-getopt1.$(OBJEXT) iit_dump-iit_dump.$(OBJEXT)
-dist_iit_dump_OBJECTS = $(am__objects_9)
+dist_iit_dump_OBJECTS = $(am__objects_33)
iit_dump_OBJECTS = $(dist_iit_dump_OBJECTS)
iit_dump_DEPENDENCIES = $(am__DEPENDENCIES_1)
iit_dump_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(iit_dump_CFLAGS) $(CFLAGS) \
$(iit_dump_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_10 = iit_get-except.$(OBJEXT) iit_get-assert.$(OBJEXT) \
+am__objects_34 = iit_get-except.$(OBJEXT) iit_get-assert.$(OBJEXT) \
iit_get-mem.$(OBJEXT) iit_get-intlist.$(OBJEXT) \
iit_get-list.$(OBJEXT) iit_get-littleendian.$(OBJEXT) \
iit_get-bigendian.$(OBJEXT) iit_get-univinterval.$(OBJEXT) \
iit_get-interval.$(OBJEXT) iit_get-uintlist.$(OBJEXT) \
- iit_get-stopwatch.$(OBJEXT) iit_get-access.$(OBJEXT) \
- iit_get-filestring.$(OBJEXT) iit_get-iit-read-univ.$(OBJEXT) \
- iit_get-iit-read.$(OBJEXT) iit_get-parserange.$(OBJEXT) \
- iit_get-getopt.$(OBJEXT) iit_get-getopt1.$(OBJEXT) \
- iit_get-iit_get.$(OBJEXT)
-dist_iit_get_OBJECTS = $(am__objects_10)
+ iit_get-stopwatch.$(OBJEXT) iit_get-semaphore.$(OBJEXT) \
+ iit_get-access.$(OBJEXT) iit_get-filestring.$(OBJEXT) \
+ iit_get-iit-read-univ.$(OBJEXT) iit_get-iit-read.$(OBJEXT) \
+ iit_get-parserange.$(OBJEXT) iit_get-getopt.$(OBJEXT) \
+ iit_get-getopt1.$(OBJEXT) iit_get-iit_get.$(OBJEXT)
+dist_iit_get_OBJECTS = $(am__objects_34)
iit_get_OBJECTS = $(dist_iit_get_OBJECTS)
iit_get_DEPENDENCIES = $(am__DEPENDENCIES_1)
iit_get_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(iit_get_CFLAGS) $(CFLAGS) \
$(iit_get_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_11 = iit_store-except.$(OBJEXT) iit_store-assert.$(OBJEXT) \
+am__objects_35 = iit_store-except.$(OBJEXT) iit_store-assert.$(OBJEXT) \
iit_store-mem.$(OBJEXT) iit_store-intlist.$(OBJEXT) \
iit_store-list.$(OBJEXT) iit_store-littleendian.$(OBJEXT) \
iit_store-bigendian.$(OBJEXT) iit_store-univinterval.$(OBJEXT) \
iit_store-interval.$(OBJEXT) iit_store-uintlist.$(OBJEXT) \
- iit_store-stopwatch.$(OBJEXT) iit_store-access.$(OBJEXT) \
- iit_store-doublelist.$(OBJEXT) \
+ iit_store-stopwatch.$(OBJEXT) iit_store-semaphore.$(OBJEXT) \
+ iit_store-access.$(OBJEXT) iit_store-doublelist.$(OBJEXT) \
iit_store-iit-write-univ.$(OBJEXT) \
iit_store-iit-write.$(OBJEXT) iit_store-tableint.$(OBJEXT) \
iit_store-table.$(OBJEXT) iit_store-chrom.$(OBJEXT) \
iit_store-getopt.$(OBJEXT) iit_store-getopt1.$(OBJEXT) \
iit_store-iit_store.$(OBJEXT)
-dist_iit_store_OBJECTS = $(am__objects_11)
+dist_iit_store_OBJECTS = $(am__objects_35)
iit_store_OBJECTS = $(dist_iit_store_OBJECTS)
iit_store_DEPENDENCIES = $(am__DEPENDENCIES_1)
iit_store_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \
$(LIBTOOLFLAGS) --mode=link $(CCLD) $(iit_store_CFLAGS) \
$(CFLAGS) $(iit_store_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_12 = sam_sort-except.$(OBJEXT) sam_sort-assert.$(OBJEXT) \
+am__objects_36 = sam_sort-except.$(OBJEXT) sam_sort-assert.$(OBJEXT) \
sam_sort-mem.$(OBJEXT) sam_sort-littleendian.$(OBJEXT) \
sam_sort-bigendian.$(OBJEXT) sam_sort-intlist.$(OBJEXT) \
sam_sort-list.$(OBJEXT) sam_sort-stopwatch.$(OBJEXT) \
- sam_sort-access.$(OBJEXT) sam_sort-univinterval.$(OBJEXT) \
- sam_sort-interval.$(OBJEXT) sam_sort-uintlist.$(OBJEXT) \
- sam_sort-filestring.$(OBJEXT) sam_sort-iit-read-univ.$(OBJEXT) \
+ sam_sort-semaphore.$(OBJEXT) sam_sort-access.$(OBJEXT) \
+ sam_sort-univinterval.$(OBJEXT) sam_sort-interval.$(OBJEXT) \
+ sam_sort-uintlist.$(OBJEXT) sam_sort-filestring.$(OBJEXT) \
+ sam_sort-parserange.$(OBJEXT) sam_sort-iit-read-univ.$(OBJEXT) \
sam_sort-iit-read.$(OBJEXT) sam_sort-samheader.$(OBJEXT) \
sam_sort-samread.$(OBJEXT) sam_sort-datadir.$(OBJEXT) \
sam_sort-getopt.$(OBJEXT) sam_sort-getopt1.$(OBJEXT) \
sam_sort-sam_sort.$(OBJEXT)
-dist_sam_sort_OBJECTS = $(am__objects_12)
+dist_sam_sort_OBJECTS = $(am__objects_36)
sam_sort_OBJECTS = $(dist_sam_sort_OBJECTS)
sam_sort_DEPENDENCIES = $(am__DEPENDENCIES_1)
sam_sort_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(sam_sort_CFLAGS) $(CFLAGS) \
$(sam_sort_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_13 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
+am__objects_37 = snpindex-except.$(OBJEXT) snpindex-assert.$(OBJEXT) \
snpindex-mem.$(OBJEXT) snpindex-intlist.$(OBJEXT) \
snpindex-list.$(OBJEXT) snpindex-littleendian.$(OBJEXT) \
snpindex-bigendian.$(OBJEXT) snpindex-univinterval.$(OBJEXT) \
snpindex-interval.$(OBJEXT) snpindex-uintlist.$(OBJEXT) \
- snpindex-stopwatch.$(OBJEXT) snpindex-access.$(OBJEXT) \
- snpindex-filestring.$(OBJEXT) snpindex-iit-read-univ.$(OBJEXT) \
- snpindex-iit-read.$(OBJEXT) snpindex-genomicpos.$(OBJEXT) \
- snpindex-compress.$(OBJEXT) snpindex-compress-write.$(OBJEXT) \
- snpindex-popcount.$(OBJEXT) snpindex-genome128_hr.$(OBJEXT) \
+ snpindex-stopwatch.$(OBJEXT) snpindex-semaphore.$(OBJEXT) \
+ snpindex-access.$(OBJEXT) snpindex-filestring.$(OBJEXT) \
+ snpindex-iit-read-univ.$(OBJEXT) snpindex-iit-read.$(OBJEXT) \
+ snpindex-genomicpos.$(OBJEXT) snpindex-compress.$(OBJEXT) \
+ snpindex-compress-write.$(OBJEXT) snpindex-popcount.$(OBJEXT) \
+ snpindex-genome128_hr.$(OBJEXT) \
snpindex-bitpack64-read.$(OBJEXT) \
snpindex-bitpack64-readtwo.$(OBJEXT) \
+ snpindex-bitpack64-access.$(OBJEXT) \
+ snpindex-bitpack64-incr.$(OBJEXT) \
snpindex-bitpack64-write.$(OBJEXT) snpindex-indexdb.$(OBJEXT) \
snpindex-indexdb-write.$(OBJEXT) snpindex-chrom.$(OBJEXT) \
snpindex-md5.$(OBJEXT) snpindex-bzip2.$(OBJEXT) \
snpindex-sequence.$(OBJEXT) snpindex-genome.$(OBJEXT) \
- snpindex-datadir.$(OBJEXT) snpindex-getopt.$(OBJEXT) \
- snpindex-getopt1.$(OBJEXT) snpindex-snpindex.$(OBJEXT)
-dist_snpindex_OBJECTS = $(am__objects_13)
+ snpindex-datadir.$(OBJEXT) snpindex-parserange.$(OBJEXT) \
+ snpindex-getopt.$(OBJEXT) snpindex-getopt1.$(OBJEXT) \
+ snpindex-snpindex.$(OBJEXT)
+dist_snpindex_OBJECTS = $(am__objects_37)
snpindex_OBJECTS = $(dist_snpindex_OBJECTS)
snpindex_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
snpindex_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(snpindex_CFLAGS) $(CFLAGS) \
$(snpindex_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_14 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
+am__objects_38 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
uniqscan-mem.$(OBJEXT) uniqscan-intlist.$(OBJEXT) \
uniqscan-list.$(OBJEXT) uniqscan-littleendian.$(OBJEXT) \
uniqscan-bigendian.$(OBJEXT) uniqscan-univinterval.$(OBJEXT) \
uniqscan-interval.$(OBJEXT) uniqscan-uintlist.$(OBJEXT) \
- uniqscan-stopwatch.$(OBJEXT) uniqscan-access.$(OBJEXT) \
- uniqscan-filestring.$(OBJEXT) uniqscan-iit-read-univ.$(OBJEXT) \
- uniqscan-iit-read.$(OBJEXT) uniqscan-md5.$(OBJEXT) \
- uniqscan-bzip2.$(OBJEXT) uniqscan-sequence.$(OBJEXT) \
- uniqscan-reader.$(OBJEXT) uniqscan-genomicpos.$(OBJEXT) \
- uniqscan-compress.$(OBJEXT) uniqscan-genome.$(OBJEXT) \
- uniqscan-popcount.$(OBJEXT) uniqscan-genome128_hr.$(OBJEXT) \
+ uniqscan-stopwatch.$(OBJEXT) uniqscan-semaphore.$(OBJEXT) \
+ uniqscan-access.$(OBJEXT) uniqscan-filestring.$(OBJEXT) \
+ uniqscan-iit-read-univ.$(OBJEXT) uniqscan-iit-read.$(OBJEXT) \
+ uniqscan-md5.$(OBJEXT) uniqscan-bzip2.$(OBJEXT) \
+ uniqscan-sequence.$(OBJEXT) uniqscan-reader.$(OBJEXT) \
+ uniqscan-genomicpos.$(OBJEXT) uniqscan-compress.$(OBJEXT) \
+ uniqscan-genome.$(OBJEXT) uniqscan-popcount.$(OBJEXT) \
+ uniqscan-genome128_hr.$(OBJEXT) \
uniqscan-genome_sites.$(OBJEXT) \
uniqscan-bitpack64-read.$(OBJEXT) \
uniqscan-bitpack64-readtwo.$(OBJEXT) \
@@ -522,22 +1969,23 @@ am__objects_14 = uniqscan-except.$(OBJEXT) uniqscan-assert.$(OBJEXT) \
uniqscan-bytecoding.$(OBJEXT) uniqscan-univdiag.$(OBJEXT) \
uniqscan-sarray-read.$(OBJEXT) uniqscan-stage1hr.$(OBJEXT) \
uniqscan-resulthr.$(OBJEXT) uniqscan-datadir.$(OBJEXT) \
- uniqscan-getopt.$(OBJEXT) uniqscan-getopt1.$(OBJEXT) \
- uniqscan-uniqscan.$(OBJEXT)
-dist_uniqscan_OBJECTS = $(am__objects_14)
+ uniqscan-parserange.$(OBJEXT) uniqscan-getopt.$(OBJEXT) \
+ uniqscan-getopt1.$(OBJEXT) uniqscan-uniqscan.$(OBJEXT)
+dist_uniqscan_OBJECTS = $(am__objects_38)
uniqscan_OBJECTS = $(dist_uniqscan_OBJECTS)
uniqscan_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
uniqscan_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
--mode=link $(CCLD) $(uniqscan_CFLAGS) $(CFLAGS) \
$(uniqscan_LDFLAGS) $(LDFLAGS) -o $@
-am__objects_15 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
+am__objects_39 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
uniqscanl-mem.$(OBJEXT) uniqscanl-intlist.$(OBJEXT) \
uniqscanl-list.$(OBJEXT) uniqscanl-littleendian.$(OBJEXT) \
uniqscanl-bigendian.$(OBJEXT) uniqscanl-univinterval.$(OBJEXT) \
uniqscanl-interval.$(OBJEXT) uniqscanl-uintlist.$(OBJEXT) \
uniqscanl-uint8list.$(OBJEXT) uniqscanl-stopwatch.$(OBJEXT) \
- uniqscanl-access.$(OBJEXT) uniqscanl-filestring.$(OBJEXT) \
+ uniqscanl-semaphore.$(OBJEXT) uniqscanl-access.$(OBJEXT) \
+ uniqscanl-filestring.$(OBJEXT) \
uniqscanl-iit-read-univ.$(OBJEXT) uniqscanl-iit-read.$(OBJEXT) \
uniqscanl-md5.$(OBJEXT) uniqscanl-bzip2.$(OBJEXT) \
uniqscanl-sequence.$(OBJEXT) uniqscanl-reader.$(OBJEXT) \
@@ -575,9 +2023,10 @@ am__objects_15 = uniqscanl-except.$(OBJEXT) uniqscanl-assert.$(OBJEXT) \
uniqscanl-splicetrie.$(OBJEXT) uniqscanl-splice.$(OBJEXT) \
uniqscanl-indel.$(OBJEXT) uniqscanl-bitpack64-access.$(OBJEXT) \
uniqscanl-stage1hr.$(OBJEXT) uniqscanl-resulthr.$(OBJEXT) \
- uniqscanl-datadir.$(OBJEXT) uniqscanl-getopt.$(OBJEXT) \
- uniqscanl-getopt1.$(OBJEXT) uniqscanl-uniqscan.$(OBJEXT)
-dist_uniqscanl_OBJECTS = $(am__objects_15)
+ uniqscanl-datadir.$(OBJEXT) uniqscanl-parserange.$(OBJEXT) \
+ uniqscanl-getopt.$(OBJEXT) uniqscanl-getopt1.$(OBJEXT) \
+ uniqscanl-uniqscan.$(OBJEXT)
+dist_uniqscanl_OBJECTS = $(am__objects_39)
uniqscanl_OBJECTS = $(dist_uniqscanl_OBJECTS)
uniqscanl_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
$(am__DEPENDENCIES_1)
@@ -599,16 +2048,40 @@ LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
$(LDFLAGS) -o $@
SOURCES = $(dist_atoiindex_SOURCES) $(dist_cmetindex_SOURCES) \
$(dist_get_genome_SOURCES) $(dist_gmap_SOURCES) \
+ $(dist_gmap_avx2_SOURCES) $(dist_gmap_nosimd_SOURCES) \
+ $(dist_gmap_sse2_SOURCES) $(dist_gmap_sse41_SOURCES) \
+ $(dist_gmap_sse42_SOURCES) $(dist_gmap_ssse3_SOURCES) \
$(dist_gmapindex_SOURCES) $(dist_gmapl_SOURCES) \
- $(dist_gsnap_SOURCES) $(dist_gsnapl_SOURCES) \
+ $(dist_gmapl_avx2_SOURCES) $(dist_gmapl_nosimd_SOURCES) \
+ $(dist_gmapl_sse2_SOURCES) $(dist_gmapl_sse41_SOURCES) \
+ $(dist_gmapl_sse42_SOURCES) $(dist_gmapl_ssse3_SOURCES) \
+ $(dist_gsnap_SOURCES) $(dist_gsnap_avx2_SOURCES) \
+ $(dist_gsnap_nosimd_SOURCES) $(dist_gsnap_sse2_SOURCES) \
+ $(dist_gsnap_sse41_SOURCES) $(dist_gsnap_sse42_SOURCES) \
+ $(dist_gsnap_ssse3_SOURCES) $(dist_gsnapl_SOURCES) \
+ $(dist_gsnapl_avx2_SOURCES) $(dist_gsnapl_nosimd_SOURCES) \
+ $(dist_gsnapl_sse2_SOURCES) $(dist_gsnapl_sse41_SOURCES) \
+ $(dist_gsnapl_sse42_SOURCES) $(dist_gsnapl_ssse3_SOURCES) \
$(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
$(dist_iit_store_SOURCES) $(dist_sam_sort_SOURCES) \
$(dist_snpindex_SOURCES) $(dist_uniqscan_SOURCES) \
$(dist_uniqscanl_SOURCES)
DIST_SOURCES = $(dist_atoiindex_SOURCES) $(dist_cmetindex_SOURCES) \
$(dist_get_genome_SOURCES) $(dist_gmap_SOURCES) \
+ $(dist_gmap_avx2_SOURCES) $(dist_gmap_nosimd_SOURCES) \
+ $(dist_gmap_sse2_SOURCES) $(dist_gmap_sse41_SOURCES) \
+ $(dist_gmap_sse42_SOURCES) $(dist_gmap_ssse3_SOURCES) \
$(dist_gmapindex_SOURCES) $(dist_gmapl_SOURCES) \
- $(dist_gsnap_SOURCES) $(dist_gsnapl_SOURCES) \
+ $(dist_gmapl_avx2_SOURCES) $(dist_gmapl_nosimd_SOURCES) \
+ $(dist_gmapl_sse2_SOURCES) $(dist_gmapl_sse41_SOURCES) \
+ $(dist_gmapl_sse42_SOURCES) $(dist_gmapl_ssse3_SOURCES) \
+ $(dist_gsnap_SOURCES) $(dist_gsnap_avx2_SOURCES) \
+ $(dist_gsnap_nosimd_SOURCES) $(dist_gsnap_sse2_SOURCES) \
+ $(dist_gsnap_sse41_SOURCES) $(dist_gsnap_sse42_SOURCES) \
+ $(dist_gsnap_ssse3_SOURCES) $(dist_gsnapl_SOURCES) \
+ $(dist_gsnapl_avx2_SOURCES) $(dist_gsnapl_nosimd_SOURCES) \
+ $(dist_gsnapl_sse2_SOURCES) $(dist_gsnapl_sse41_SOURCES) \
+ $(dist_gsnapl_sse42_SOURCES) $(dist_gsnapl_ssse3_SOURCES) \
$(dist_iit_dump_SOURCES) $(dist_iit_get_SOURCES) \
$(dist_iit_store_SOURCES) $(dist_sam_sort_SOURCES) \
$(dist_snpindex_SOURCES) $(dist_uniqscan_SOURCES) \
@@ -677,7 +2150,6 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
-POPCNT_CFLAGS = @POPCNT_CFLAGS@
PTHREAD_CC = @PTHREAD_CC@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
PTHREAD_LIBS = @PTHREAD_LIBS@
@@ -685,7 +2157,11 @@ RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
-SIMD_CFLAGS = @SIMD_CFLAGS@
+SIMD_AVX2_CFLAGS = @SIMD_AVX2_CFLAGS@
+SIMD_SSE2_CFLAGS = @SIMD_SSE2_CFLAGS@
+SIMD_SSE4_1_CFLAGS = @SIMD_SSE4_1_CFLAGS@
+SIMD_SSE4_2_CFLAGS = @SIMD_SSE4_2_CFLAGS@
+SIMD_SSSE3_CFLAGS = @SIMD_SSSE3_CFLAGS@
STRIP = @STRIP@
VERSION = @VERSION@
ZLIB_LIBS = @ZLIB_LIBS@
@@ -752,12 +2228,36 @@ CLEANFILES = fa_coords gmap_process
# Include master.c and master.h, so they get included in distribution
EXTRA_DIST = mpidebug.c mpidebug.h master.c master.h
+GMAP_SELECT_FILES = bool.h cpuid.c cpuid.h gmap_select.c
+gmap_CC = $(CC)
+gmap_CFLAGS = $(AM_CFLAGS)
+gmap_LDFLAGS = $(AM_LDFLAGS)
+gmap_LDADD =
+dist_gmap_SOURCES = $(GMAP_SELECT_FILES)
+GMAPL_SELECT_FILES = bool.h cpuid.c cpuid.h gmapl_select.c
+gmapl_CC = $(CC)
+gmapl_CFLAGS = $(AM_CFLAGS)
+gmapl_LDFLAGS = $(AM_LDFLAGS)
+gmapl_LDADD =
+dist_gmapl_SOURCES = $(GMAPL_SELECT_FILES)
+GSNAP_SELECT_FILES = bool.h cpuid.c cpuid.h gsnap_select.c
+gsnap_CC = $(CC)
+gsnap_CFLAGS = $(AM_CFLAGS)
+gsnap_LDFLAGS = $(AM_LDFLAGS)
+gsnap_LDADD =
+dist_gsnap_SOURCES = $(GSNAP_SELECT_FILES)
+GSNAPL_SELECT_FILES = bool.h cpuid.c cpuid.h gsnapl_select.c
+gsnapl_CC = $(CC)
+gsnapl_CFLAGS = $(AM_CFLAGS)
+gsnapl_LDFLAGS = $(AM_LDFLAGS)
+gsnapl_LDADD =
+dist_gsnapl_SOURCES = $(GSNAPL_SELECT_FILES)
GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -786,22 +2286,47 @@ GMAP_FILES = fopen.h bool.h types.h separator.h comp.h \
pbinom.c pbinom.h changepoint.c changepoint.h sense.h fastlog.h stage3.c stage3.h \
request.c request.h result.c result.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- chimera.c chimera.h datadir.c datadir.h \
+ chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gmap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-gmap_CC = $(PTHREAD_CC)
-gmap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
-gmap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gmap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
-dist_gmap_SOURCES = $(GMAP_FILES)
+gmap_nosimd_CC = $(PTHREAD_CC)
+gmap_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\"
+gmap_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_nosimd_SOURCES = $(GMAP_FILES)
+gmap_sse2_CC = $(PTHREAD_CC)
+gmap_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gmap_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_sse2_SOURCES = $(GMAP_FILES)
+gmap_ssse3_CC = $(PTHREAD_CC)
+gmap_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gmap_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_ssse3_SOURCES = $(GMAP_FILES)
+gmap_sse41_CC = $(PTHREAD_CC)
+gmap_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gmap_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_sse41_SOURCES = $(GMAP_FILES)
+gmap_sse42_CC = $(PTHREAD_CC)
+gmap_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gmap_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_sse42_SOURCES = $(GMAP_FILES)
+gmap_avx2_CC = $(PTHREAD_CC)
+gmap_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gmap_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmap_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmap_avx2_SOURCES = $(GMAP_FILES)
GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -830,23 +2355,48 @@ GMAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
pbinom.c pbinom.h changepoint.c changepoint.h sense.h fastlog.h stage3.c stage3.h \
request.c request.h result.c result.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- chimera.c chimera.h datadir.c datadir.h \
+ chimera.c chimera.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gmap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-gmapl_CC = $(PTHREAD_CC)
-gmapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
-gmapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gmapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
-dist_gmapl_SOURCES = $(GMAPL_FILES)
+gmapl_nosimd_CC = $(PTHREAD_CC)
+gmapl_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1
+gmapl_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_nosimd_SOURCES = $(GMAPL_FILES)
+gmapl_sse2_CC = $(PTHREAD_CC)
+gmapl_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gmapl_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_sse2_SOURCES = $(GMAPL_FILES)
+gmapl_ssse3_CC = $(PTHREAD_CC)
+gmapl_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gmapl_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_ssse3_SOURCES = $(GMAPL_FILES)
+gmapl_sse41_CC = $(PTHREAD_CC)
+gmapl_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gmapl_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_sse41_SOURCES = $(GMAPL_FILES)
+gmapl_sse42_CC = $(PTHREAD_CC)
+gmapl_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gmapl_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_sse42_SOURCES = $(GMAPL_FILES)
+gmapl_avx2_CC = $(PTHREAD_CC)
+gmapl_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gmapl_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gmapl_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gmapl_avx2_SOURCES = $(GMAPL_FILES)
GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -871,28 +2421,54 @@ GSNAP_FILES = fopen.h bool.h types.h separator.h comp.h \
chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
- bytecoding.c bytecoding.h univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
+ bytecoding.c bytecoding.h \
+ univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
stage1hr.c stage1hr.h \
request.c request.h resulthr.c resulthr.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gsnap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
# Previously included -lrt for shm_open, but we are not calling that
-gsnap_CC = $(PTHREAD_CC)
-gsnap_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
-gsnap_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gsnap_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
-dist_gsnap_SOURCES = $(GSNAP_FILES)
+gsnap_nosimd_CC = $(PTHREAD_CC)
+gsnap_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+gsnap_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_nosimd_SOURCES = $(GSNAP_FILES)
+gsnap_sse2_CC = $(PTHREAD_CC)
+gsnap_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gsnap_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_sse2_SOURCES = $(GSNAP_FILES)
+gsnap_ssse3_CC = $(PTHREAD_CC)
+gsnap_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gsnap_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_ssse3_SOURCES = $(GSNAP_FILES)
+gsnap_sse41_CC = $(PTHREAD_CC)
+gsnap_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gsnap_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_sse41_SOURCES = $(GSNAP_FILES)
+gsnap_sse42_CC = $(PTHREAD_CC)
+gsnap_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gsnap_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_sse42_SOURCES = $(GSNAP_FILES)
+gsnap_avx2_CC = $(PTHREAD_CC)
+gsnap_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gsnap_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnap_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnap_avx2_SOURCES = $(GSNAP_FILES)
GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h uint8list.c uint8list.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -920,22 +2496,49 @@ GSNAPL_FILES = fopen.h bool.h types.h separator.h comp.h \
stage1hr.c stage1hr.h \
request.c request.h resulthr.c resulthr.h output.c output.h \
inbuffer.c inbuffer.h samheader.c samheader.h outbuffer.c outbuffer.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h gsnap.c
# Note: dist_ commands get read by bootstrap, and don't follow the flags
-gsnapl_CC = $(PTHREAD_CC)
-gsnapl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
-gsnapl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
-gsnapl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
-dist_gsnapl_SOURCES = $(GSNAPL_FILES)
+gsnapl_nosimd_CC = $(PTHREAD_CC)
+gsnapl_nosimd_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+gsnapl_nosimd_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_nosimd_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_nosimd_SOURCES = $(GSNAPL_FILES)
+gsnapl_sse2_CC = $(PTHREAD_CC)
+gsnapl_sse2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 $(SIMD_SSE2_CFLAGS)
+gsnapl_sse2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_sse2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_sse2_SOURCES = $(GSNAPL_FILES)
+gsnapl_ssse3_CC = $(PTHREAD_CC)
+gsnapl_ssse3_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 $(SIMD_SSSE3_CFLAGS)
+gsnapl_ssse3_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_ssse3_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_ssse3_SOURCES = $(GSNAPL_FILES)
+gsnapl_sse41_CC = $(PTHREAD_CC)
+gsnapl_sse41_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 $(SIMD_SSE4_1_CFLAGS)
+gsnapl_sse41_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_sse41_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_sse41_SOURCES = $(GSNAPL_FILES)
+gsnapl_sse42_CC = $(PTHREAD_CC)
+gsnapl_sse42_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 $(SIMD_SSE4_2_CFLAGS)
+gsnapl_sse42_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_sse42_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_sse42_SOURCES = $(GSNAPL_FILES)
+gsnapl_avx2_CC = $(PTHREAD_CC)
+gsnapl_avx2_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 $(SIMD_AVX2_CFLAGS)
+gsnapl_avx2_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
+gsnapl_avx2_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+dist_gsnapl_avx2_SOURCES = $(GSNAPL_FILES)
+
+# Build as a non-SIMD program
UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -960,13 +2563,14 @@ UNIQSCAN_FILES = fopen.h bool.h types.h separator.h comp.h \
chimera.c chimera.h sense.h fastlog.h stage3.c stage3.h \
splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
- bytecoding.c bytecoding.h univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
+ bytecoding.c bytecoding.h \
+ univdiagdef.h univdiag.c univdiag.h sarray-read.c sarray-read.h \
stage1hr.c stage1hr.h resulthr.c resulthr.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscan_CC = $(PTHREAD_CC)
-uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
+uniqscan_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1
uniqscan_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscan_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_uniqscan_SOURCES = $(UNIQSCAN_FILES)
@@ -975,7 +2579,7 @@ UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h uint8list.c uint8list.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h reader.c reader.h \
@@ -1001,20 +2605,22 @@ UNIQSCANL_FILES = fopen.h bool.h types.h separator.h comp.h \
splicestringpool.c splicestringpool.h splicetrie_build.c splicetrie_build.h splicetrie.c splicetrie.h \
splice.c splice.h indel.c indel.h bitpack64-access.c bitpack64-access.h \
stage1hr.c stage1hr.h resulthr.c resulthr.h \
- datadir.c datadir.h mode.h \
+ datadir.c datadir.h mode.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h uniqscan.c
uniqscanl_CC = $(PTHREAD_CC)
-uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
+uniqscanl_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DTARGET=\"$(target)\" -DGMAPDB=\"$(GMAPDB)\" -DMAX_READLENGTH=$(MAX_READLENGTH) -DGSNAP=1 -DLARGE_GENOMES=1
uniqscanl_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
uniqscanl_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_uniqscanl_SOURCES = $(UNIQSCANL_FILES)
+
+# Build utility programs as non-SIMD programs
GMAPINDEX_FILES = fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iit-write-univ.c iit-write-univ.h \
iitdef.h iit-read.c iit-read.h \
@@ -1022,15 +2628,18 @@ GMAPINDEX_FILES = fopen.h bool.h types.h \
genomicpos.c genomicpos.h compress-write.c compress-write.h genome-write.c genome-write.h \
compress.c compress.h popcount.c popcount.h genome128_hr.c genome128_hr.h \
bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
- bitpack64-access.c bitpack64-access.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.c indexdb.h indexdb-write.c indexdb-write.h \
- table.c table.h tableuint.c tableuint.h tableuint8.c tableuint8.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.c indexdb.h \
+ indexdb-write.c indexdb-write.h \
+ table.c table.h tableuint.c tableuint.h tableuint8.c tableuint8.h tableint.c tableint.h \
chrom.c chrom.h segmentpos.c segmentpos.h \
- saca-k.c saca-k.h uint8list.c uint8list.h bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ saca-k.c saca-k.h uint8list.c uint8list.h \
+ bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ parserange.c parserange.h \
gmapindex.c
gmapindex_CC = $(PTHREAD_CC)
-gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DUTILITYP=1
+gmapindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DUTILITYP=1
gmapindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
gmapindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_gmapindex_SOURCES = $(GMAPINDEX_FILES)
@@ -1039,20 +2648,22 @@ SNPINDEX_FILES = fopen.h bool.h types.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
genomicpos.c genomicpos.h compress.c compress.h compress-write.c compress-write.h \
popcount.c popcount.h genome128_hr.c genome128_hr.h \
- bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.c indexdb.h indexdb-write.c indexdb-write.h \
+ bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.c indexdb.h \
+ indexdb-write.c indexdb-write.h \
chrom.c chrom.h \
complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
- datadir.c datadir.h \
+ datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h snpindex.c
snpindex_CC = $(PTHREAD_CC)
-snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+snpindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
snpindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
snpindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_snpindex_SOURCES = $(SNPINDEX_FILES)
@@ -1060,23 +2671,26 @@ CMETINDEX_FILES = fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
genomicpos.c genomicpos.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
univinterval.c univinterval.h interval.h interval.c \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.h iit-read.c \
complement.h compress.c compress.h compress-write.c compress-write.h \
popcount.c popcount.h genome128_hr.c genome128_hr.h \
- bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.h indexdb.c indexdb-write.c indexdb-write.h \
+ bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.h indexdb.c \
+ indexdb-write.c indexdb-write.h \
cmet.c cmet.h \
complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
uintlist.c uintlist.h intlist.c intlist.h \
- saca-k.c saca-k.h uint8list.c uint8list.h bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
- list.c list.h listdef.h datadir.c datadir.h \
+ saca-k.c saca-k.h uint8list.c uint8list.h \
+ bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ list.c list.h listdef.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h cmetindex.c
cmetindex_CC = $(PTHREAD_CC)
-cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+cmetindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
cmetindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
cmetindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_cmetindex_SOURCES = $(CMETINDEX_FILES)
@@ -1084,23 +2698,26 @@ ATOIINDEX_FILES = fopen.h bool.h types.h \
except.c except.h assert.c assert.h mem.c mem.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
genomicpos.c genomicpos.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
univinterval.c univinterval.h interval.h interval.c \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.h iit-read.c \
complement.h compress.c compress.h compress-write.c compress-write.h \
popcount.c popcount.h genome128_hr.c genome128_hr.h \
- bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h bitpack64-write.c bitpack64-write.h \
- indexdbdef.h indexdb.h indexdb.c indexdb-write.c indexdb-write.h \
+ bitpack64-read.c bitpack64-read.h bitpack64-readtwo.c bitpack64-readtwo.h \
+ bitpack64-access.c bitpack64-access.h bitpack64-incr.c bitpack64-incr.h bitpack64-write.c bitpack64-write.h \
+ indexdbdef.h indexdb.h indexdb.c \
+ indexdb-write.c indexdb-write.h \
atoi.c atoi.h \
complement.h md5.c md5.h bzip2.c bzip2.h sequence.c sequence.h genome.c genome.h \
uintlist.c uintlist.h intlist.c intlist.h \
- saca-k.c saca-k.h uint8list.c uint8list.h bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
- list.c list.h listdef.h datadir.c datadir.h \
+ saca-k.c saca-k.h uint8list.c uint8list.h \
+ bytecoding.c bytecoding.h sarray-write.c sarray-write.h \
+ list.c list.h listdef.h datadir.c datadir.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h atoiindex.c
atoiindex_CC = $(PTHREAD_CC)
-atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) $(POPCNT_CFLAGS) $(SIMD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
+atoiindex_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\" -DUTILITYP=1
atoiindex_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG)
atoiindex_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
dist_atoiindex_SOURCES = $(ATOIINDEX_FILES)
@@ -1109,7 +2726,7 @@ GET_GENOME_FILES = fopen.h bool.h types.h separator.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
@@ -1130,7 +2747,7 @@ IIT_STORE_FILES = fopen.h bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
doublelist.c doublelist.h \
iit-write-univ.c iit-write-univ.h iitdef.h iit-write.c iit-write.h \
tableint.c tableint.h table.c table.h chrom.c chrom.h \
@@ -1147,7 +2764,7 @@ IIT_GET_FILES = fopen.h bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
complement.h parserange.c parserange.h getopt.c getopt1.c getopt.h iit_get.c
@@ -1162,9 +2779,9 @@ IIT_DUMP_FILES = fopen.h bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
intlistdef.h intlist.c intlist.h list.c list.h \
univinterval.c univinterval.h interval.c interval.h uintlist.c uintlist.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
filestring.c filestring.h \
- iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
+ iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h parserange.c parserange.h \
getopt.c getopt1.c getopt.h iit_dump.c
iit_dump_CC = $(PTHREAD_CC)
@@ -1177,11 +2794,11 @@ SAM_SORT_FILES = bool.h types.h \
littleendian.c littleendian.h bigendian.c bigendian.h \
genomicpos.h chrnum.h \
intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
- stopwatch.c stopwatch.h access.c access.h \
+ stopwatch.c stopwatch.h semaphore.c semaphore.h access.c access.h \
univinterval.c univinterval.h interval.c interval.h \
uintlist.c uintlist.h \
filestring.c filestring.h \
- iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
+ parserange.c parserange.h iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
samflags.h samheader.c samheader.h samread.c samread.h \
datadir.c datadir.h \
getopt.c getopt1.c getopt.h sam_sort.c
@@ -1298,18 +2915,90 @@ get-genome$(EXEEXT): $(get_genome_OBJECTS) $(get_genome_DEPENDENCIES)
gmap$(EXEEXT): $(gmap_OBJECTS) $(gmap_DEPENDENCIES)
@rm -f gmap$(EXEEXT)
$(gmap_LINK) $(gmap_OBJECTS) $(gmap_LDADD) $(LIBS)
+gmap.avx2$(EXEEXT): $(gmap_avx2_OBJECTS) $(gmap_avx2_DEPENDENCIES)
+ @rm -f gmap.avx2$(EXEEXT)
+ $(gmap_avx2_LINK) $(gmap_avx2_OBJECTS) $(gmap_avx2_LDADD) $(LIBS)
+gmap.nosimd$(EXEEXT): $(gmap_nosimd_OBJECTS) $(gmap_nosimd_DEPENDENCIES)
+ @rm -f gmap.nosimd$(EXEEXT)
+ $(gmap_nosimd_LINK) $(gmap_nosimd_OBJECTS) $(gmap_nosimd_LDADD) $(LIBS)
+gmap.sse2$(EXEEXT): $(gmap_sse2_OBJECTS) $(gmap_sse2_DEPENDENCIES)
+ @rm -f gmap.sse2$(EXEEXT)
+ $(gmap_sse2_LINK) $(gmap_sse2_OBJECTS) $(gmap_sse2_LDADD) $(LIBS)
+gmap.sse41$(EXEEXT): $(gmap_sse41_OBJECTS) $(gmap_sse41_DEPENDENCIES)
+ @rm -f gmap.sse41$(EXEEXT)
+ $(gmap_sse41_LINK) $(gmap_sse41_OBJECTS) $(gmap_sse41_LDADD) $(LIBS)
+gmap.sse42$(EXEEXT): $(gmap_sse42_OBJECTS) $(gmap_sse42_DEPENDENCIES)
+ @rm -f gmap.sse42$(EXEEXT)
+ $(gmap_sse42_LINK) $(gmap_sse42_OBJECTS) $(gmap_sse42_LDADD) $(LIBS)
+gmap.ssse3$(EXEEXT): $(gmap_ssse3_OBJECTS) $(gmap_ssse3_DEPENDENCIES)
+ @rm -f gmap.ssse3$(EXEEXT)
+ $(gmap_ssse3_LINK) $(gmap_ssse3_OBJECTS) $(gmap_ssse3_LDADD) $(LIBS)
gmapindex$(EXEEXT): $(gmapindex_OBJECTS) $(gmapindex_DEPENDENCIES)
@rm -f gmapindex$(EXEEXT)
$(gmapindex_LINK) $(gmapindex_OBJECTS) $(gmapindex_LDADD) $(LIBS)
gmapl$(EXEEXT): $(gmapl_OBJECTS) $(gmapl_DEPENDENCIES)
@rm -f gmapl$(EXEEXT)
$(gmapl_LINK) $(gmapl_OBJECTS) $(gmapl_LDADD) $(LIBS)
+gmapl.avx2$(EXEEXT): $(gmapl_avx2_OBJECTS) $(gmapl_avx2_DEPENDENCIES)
+ @rm -f gmapl.avx2$(EXEEXT)
+ $(gmapl_avx2_LINK) $(gmapl_avx2_OBJECTS) $(gmapl_avx2_LDADD) $(LIBS)
+gmapl.nosimd$(EXEEXT): $(gmapl_nosimd_OBJECTS) $(gmapl_nosimd_DEPENDENCIES)
+ @rm -f gmapl.nosimd$(EXEEXT)
+ $(gmapl_nosimd_LINK) $(gmapl_nosimd_OBJECTS) $(gmapl_nosimd_LDADD) $(LIBS)
+gmapl.sse2$(EXEEXT): $(gmapl_sse2_OBJECTS) $(gmapl_sse2_DEPENDENCIES)
+ @rm -f gmapl.sse2$(EXEEXT)
+ $(gmapl_sse2_LINK) $(gmapl_sse2_OBJECTS) $(gmapl_sse2_LDADD) $(LIBS)
+gmapl.sse41$(EXEEXT): $(gmapl_sse41_OBJECTS) $(gmapl_sse41_DEPENDENCIES)
+ @rm -f gmapl.sse41$(EXEEXT)
+ $(gmapl_sse41_LINK) $(gmapl_sse41_OBJECTS) $(gmapl_sse41_LDADD) $(LIBS)
+gmapl.sse42$(EXEEXT): $(gmapl_sse42_OBJECTS) $(gmapl_sse42_DEPENDENCIES)
+ @rm -f gmapl.sse42$(EXEEXT)
+ $(gmapl_sse42_LINK) $(gmapl_sse42_OBJECTS) $(gmapl_sse42_LDADD) $(LIBS)
+gmapl.ssse3$(EXEEXT): $(gmapl_ssse3_OBJECTS) $(gmapl_ssse3_DEPENDENCIES)
+ @rm -f gmapl.ssse3$(EXEEXT)
+ $(gmapl_ssse3_LINK) $(gmapl_ssse3_OBJECTS) $(gmapl_ssse3_LDADD) $(LIBS)
gsnap$(EXEEXT): $(gsnap_OBJECTS) $(gsnap_DEPENDENCIES)
@rm -f gsnap$(EXEEXT)
$(gsnap_LINK) $(gsnap_OBJECTS) $(gsnap_LDADD) $(LIBS)
+gsnap.avx2$(EXEEXT): $(gsnap_avx2_OBJECTS) $(gsnap_avx2_DEPENDENCIES)
+ @rm -f gsnap.avx2$(EXEEXT)
+ $(gsnap_avx2_LINK) $(gsnap_avx2_OBJECTS) $(gsnap_avx2_LDADD) $(LIBS)
+gsnap.nosimd$(EXEEXT): $(gsnap_nosimd_OBJECTS) $(gsnap_nosimd_DEPENDENCIES)
+ @rm -f gsnap.nosimd$(EXEEXT)
+ $(gsnap_nosimd_LINK) $(gsnap_nosimd_OBJECTS) $(gsnap_nosimd_LDADD) $(LIBS)
+gsnap.sse2$(EXEEXT): $(gsnap_sse2_OBJECTS) $(gsnap_sse2_DEPENDENCIES)
+ @rm -f gsnap.sse2$(EXEEXT)
+ $(gsnap_sse2_LINK) $(gsnap_sse2_OBJECTS) $(gsnap_sse2_LDADD) $(LIBS)
+gsnap.sse41$(EXEEXT): $(gsnap_sse41_OBJECTS) $(gsnap_sse41_DEPENDENCIES)
+ @rm -f gsnap.sse41$(EXEEXT)
+ $(gsnap_sse41_LINK) $(gsnap_sse41_OBJECTS) $(gsnap_sse41_LDADD) $(LIBS)
+gsnap.sse42$(EXEEXT): $(gsnap_sse42_OBJECTS) $(gsnap_sse42_DEPENDENCIES)
+ @rm -f gsnap.sse42$(EXEEXT)
+ $(gsnap_sse42_LINK) $(gsnap_sse42_OBJECTS) $(gsnap_sse42_LDADD) $(LIBS)
+gsnap.ssse3$(EXEEXT): $(gsnap_ssse3_OBJECTS) $(gsnap_ssse3_DEPENDENCIES)
+ @rm -f gsnap.ssse3$(EXEEXT)
+ $(gsnap_ssse3_LINK) $(gsnap_ssse3_OBJECTS) $(gsnap_ssse3_LDADD) $(LIBS)
gsnapl$(EXEEXT): $(gsnapl_OBJECTS) $(gsnapl_DEPENDENCIES)
@rm -f gsnapl$(EXEEXT)
$(gsnapl_LINK) $(gsnapl_OBJECTS) $(gsnapl_LDADD) $(LIBS)
+gsnapl.avx2$(EXEEXT): $(gsnapl_avx2_OBJECTS) $(gsnapl_avx2_DEPENDENCIES)
+ @rm -f gsnapl.avx2$(EXEEXT)
+ $(gsnapl_avx2_LINK) $(gsnapl_avx2_OBJECTS) $(gsnapl_avx2_LDADD) $(LIBS)
+gsnapl.nosimd$(EXEEXT): $(gsnapl_nosimd_OBJECTS) $(gsnapl_nosimd_DEPENDENCIES)
+ @rm -f gsnapl.nosimd$(EXEEXT)
+ $(gsnapl_nosimd_LINK) $(gsnapl_nosimd_OBJECTS) $(gsnapl_nosimd_LDADD) $(LIBS)
+gsnapl.sse2$(EXEEXT): $(gsnapl_sse2_OBJECTS) $(gsnapl_sse2_DEPENDENCIES)
+ @rm -f gsnapl.sse2$(EXEEXT)
+ $(gsnapl_sse2_LINK) $(gsnapl_sse2_OBJECTS) $(gsnapl_sse2_LDADD) $(LIBS)
+gsnapl.sse41$(EXEEXT): $(gsnapl_sse41_OBJECTS) $(gsnapl_sse41_DEPENDENCIES)
+ @rm -f gsnapl.sse41$(EXEEXT)
+ $(gsnapl_sse41_LINK) $(gsnapl_sse41_OBJECTS) $(gsnapl_sse41_LDADD) $(LIBS)
+gsnapl.sse42$(EXEEXT): $(gsnapl_sse42_OBJECTS) $(gsnapl_sse42_DEPENDENCIES)
+ @rm -f gsnapl.sse42$(EXEEXT)
+ $(gsnapl_sse42_LINK) $(gsnapl_sse42_OBJECTS) $(gsnapl_sse42_LDADD) $(LIBS)
+gsnapl.ssse3$(EXEEXT): $(gsnapl_ssse3_OBJECTS) $(gsnapl_ssse3_DEPENDENCIES)
+ @rm -f gsnapl.ssse3$(EXEEXT)
+ $(gsnapl_ssse3_LINK) $(gsnapl_ssse3_OBJECTS) $(gsnapl_ssse3_LDADD) $(LIBS)
iit_dump$(EXEEXT): $(iit_dump_OBJECTS) $(iit_dump_DEPENDENCIES)
@rm -f iit_dump$(EXEEXT)
$(iit_dump_LINK) $(iit_dump_OBJECTS) $(iit_dump_LDADD) $(LIBS)
@@ -1343,6 +3032,8 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-atoi.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-atoiindex.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-bigendian.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-bitpack64-access.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-bitpack64-incr.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-bitpack64-read.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-bitpack64-readtwo.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-bitpack64-write.Po at am__quote@
@@ -1368,9 +3059,11 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-md5.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-mem.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-parserange.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-popcount.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-saca-k.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-sarray-write.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-sequence.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/atoiindex-uint8list.Po at am__quote@
@@ -1379,6 +3072,8 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-access.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-assert.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-bigendian.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-bitpack64-access.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-bitpack64-incr.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-bitpack64-read.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-bitpack64-readtwo.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-bitpack64-write.Po at am__quote@
@@ -1406,9 +3101,11 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-md5.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-mem.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-parserange.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-popcount.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-saca-k.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-sarray-write.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-sequence.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/cmetindex-uint8list.Po at am__quote@
@@ -1437,97 +3134,528 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-md5.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-mem.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-parserange.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-sequence.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-uintlist.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/get_genome-univinterval.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-access.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-assert.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-atoi.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-bigendian.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-bitpack64-read.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-bitpack64-readtwo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-block.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-boyer-moore.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-bzip2.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-cellpool.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-changepoint.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-chimera.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-chrnum.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-chrom.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-cmet.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-compress-write.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-compress.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-datadir.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-diag.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-diagnostic.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-diagpool.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-doublelist.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-dynprog.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-dynprog_cdna.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-dynprog_end.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-dynprog_genome.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-dynprog_simd.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-dynprog_single.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-except.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-filestring.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-gbuffer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-genome-write.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-genome.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-genome128_hr.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-genome_sites.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-genomicpos.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-getopt.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-getopt1.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-gmap.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-gregion.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-iit-read-univ.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-iit-read.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-inbuffer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-indexdb.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-indexdb_hr.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-interval.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-intlist.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-intron.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-list.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-littleendian.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-match.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-matchpool.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-maxent.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-maxent_hr.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-md5.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-mem.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-oligo.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-oligoindex_hr.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-orderstat.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-outbuffer.Po at am__quote@
- at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gmap-output.Po at am__quote@
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+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gsnapl_ssse3-translation.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gsnapl_ssse3-uint8list.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gsnapl_ssse3-uintlist.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/gsnapl_ssse3-univinterval.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-access.Po at am__quote@
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@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-bigendian.Po at am__quote@
@@ -1838,6 +5296,8 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-mem.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-parserange.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-uintlist.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_dump-univinterval.Po at am__quote@
@@ -1857,6 +5317,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-mem.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-parserange.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-uintlist.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_get-univinterval.Po at am__quote@
@@ -1876,6 +5337,7 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-list.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-mem.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-table.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/iit_store-tableint.Po at am__quote@
@@ -1896,15 +5358,19 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-mem.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-parserange.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-sam_sort.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-samheader.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-samread.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-stopwatch.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-uintlist.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/sam_sort-univinterval.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-access.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-assert.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-bigendian.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-bitpack64-access.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-bitpack64-incr.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-bitpack64-read.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-bitpack64-readtwo.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-bitpack64-write.Po at am__quote@
@@ -1930,7 +5396,9 @@ distclean-compile:
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-littleendian.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-md5.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-mem.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-parserange.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-popcount.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-sequence.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-snpindex.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/snpindex-stopwatch.Po at am__quote@
@@ -1992,12 +5460,14 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-pair.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-pairpool.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-parserange.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-pbinom.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-popcount.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-reader.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-resulthr.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-sarray-read.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-segmentpos.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-sequence.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-shortread.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscan-smooth.Po at am__quote@
@@ -2072,11 +5542,13 @@ distclean-compile:
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@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-pair.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-pairpool.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-parserange.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-pbinom.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-popcount.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-reader.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-resulthr.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-segmentpos.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-semaphore.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-sequence.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-shortread.Po at am__quote@
@AMDEP_TRUE@@am__include@ @am__quote at ./$(DEPDIR)/uniqscanl-smooth.Po at am__quote@
@@ -2216,6 +5688,20 @@ atoiindex-stopwatch.obj: stopwatch.c
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+atoiindex-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-semaphore.o -MD -MP -MF $(DEPDIR)/atoiindex-semaphore.Tpo -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-semaphore.Tpo $(DEPDIR)/atoiindex-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='atoiindex-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+atoiindex-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-semaphore.obj -MD -MP -MF $(DEPDIR)/atoiindex-semaphore.Tpo -c -o atoiindex-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-semaphore.Tpo $(DEPDIR)/atoiindex-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='atoiindex-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
atoiindex-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-access.o -MD -MP -MF $(DEPDIR)/atoiindex-access.Tpo -c -o atoiindex-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-access.Tpo $(DEPDIR)/atoiindex-access.Po
@@ -2384,6 +5870,34 @@ atoiindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+atoiindex-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-access.o -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-access.Tpo -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-access.Tpo $(DEPDIR)/atoiindex-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='atoiindex-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+atoiindex-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-access.Tpo -c -o atoiindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-access.Tpo $(DEPDIR)/atoiindex-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='atoiindex-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+
+atoiindex-bitpack64-incr.o: bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-incr.o -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-incr.Tpo -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '$(srcdir)/'`bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-incr.Tpo $(DEPDIR)/atoiindex-bitpack64-incr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-incr.c' object='atoiindex-bitpack64-incr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '$(srcdir)/'`bitpack64-incr.c
+
+atoiindex-bitpack64-incr.obj: bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-incr.obj -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-incr.Tpo -c -o atoiindex-bitpack64-incr.obj `if test -f 'bitpack64-incr.c'; then $(CYGPATH_W) 'bitpack64-incr.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-incr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-incr.Tpo $(DEPDIR)/atoiindex-bitpack64-incr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-incr.c' object='atoiindex-bitpack64-incr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-bitpack64-incr.obj `if test -f 'bitpack64-incr.c'; then $(CYGPATH_W) 'bitpack64-incr.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-incr.c'; fi`
+
atoiindex-bitpack64-write.o: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-bitpack64-write.o -MD -MP -MF $(DEPDIR)/atoiindex-bitpack64-write.Tpo -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-bitpack64-write.Tpo $(DEPDIR)/atoiindex-bitpack64-write.Po
@@ -2608,6 +6122,20 @@ atoiindex-datadir.obj: datadir.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+atoiindex-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-parserange.o -MD -MP -MF $(DEPDIR)/atoiindex-parserange.Tpo -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-parserange.Tpo $(DEPDIR)/atoiindex-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='atoiindex-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+atoiindex-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-parserange.obj -MD -MP -MF $(DEPDIR)/atoiindex-parserange.Tpo -c -o atoiindex-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-parserange.Tpo $(DEPDIR)/atoiindex-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='atoiindex-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -c -o atoiindex-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
atoiindex-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(atoiindex_CFLAGS) $(CFLAGS) -MT atoiindex-getopt.o -MD -MP -MF $(DEPDIR)/atoiindex-getopt.Tpo -c -o atoiindex-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/atoiindex-getopt.Tpo $(DEPDIR)/atoiindex-getopt.Po
@@ -2748,6 +6276,20 @@ cmetindex-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+cmetindex-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-semaphore.o -MD -MP -MF $(DEPDIR)/cmetindex-semaphore.Tpo -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-semaphore.Tpo $(DEPDIR)/cmetindex-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='cmetindex-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+cmetindex-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-semaphore.obj -MD -MP -MF $(DEPDIR)/cmetindex-semaphore.Tpo -c -o cmetindex-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-semaphore.Tpo $(DEPDIR)/cmetindex-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='cmetindex-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
cmetindex-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-access.o -MD -MP -MF $(DEPDIR)/cmetindex-access.Tpo -c -o cmetindex-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-access.Tpo $(DEPDIR)/cmetindex-access.Po
@@ -2916,6 +6458,34 @@ cmetindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+cmetindex-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-access.o -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-access.Tpo -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-access.Tpo $(DEPDIR)/cmetindex-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='cmetindex-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+cmetindex-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-access.Tpo -c -o cmetindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-access.Tpo $(DEPDIR)/cmetindex-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='cmetindex-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+
+cmetindex-bitpack64-incr.o: bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-incr.o -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-incr.Tpo -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '$(srcdir)/'`bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-incr.Tpo $(DEPDIR)/cmetindex-bitpack64-incr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-incr.c' object='cmetindex-bitpack64-incr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '$(srcdir)/'`bitpack64-incr.c
+
+cmetindex-bitpack64-incr.obj: bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-incr.obj -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-incr.Tpo -c -o cmetindex-bitpack64-incr.obj `if test -f 'bitpack64-incr.c'; then $(CYGPATH_W) 'bitpack64-incr.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-incr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-incr.Tpo $(DEPDIR)/cmetindex-bitpack64-incr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-incr.c' object='cmetindex-bitpack64-incr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-bitpack64-incr.obj `if test -f 'bitpack64-incr.c'; then $(CYGPATH_W) 'bitpack64-incr.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-incr.c'; fi`
+
cmetindex-bitpack64-write.o: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-bitpack64-write.o -MD -MP -MF $(DEPDIR)/cmetindex-bitpack64-write.Tpo -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-bitpack64-write.Tpo $(DEPDIR)/cmetindex-bitpack64-write.Po
@@ -3140,6 +6710,20 @@ cmetindex-datadir.obj: datadir.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+cmetindex-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-parserange.o -MD -MP -MF $(DEPDIR)/cmetindex-parserange.Tpo -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-parserange.Tpo $(DEPDIR)/cmetindex-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='cmetindex-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+cmetindex-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-parserange.obj -MD -MP -MF $(DEPDIR)/cmetindex-parserange.Tpo -c -o cmetindex-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-parserange.Tpo $(DEPDIR)/cmetindex-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='cmetindex-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -c -o cmetindex-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
cmetindex-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cmetindex_CFLAGS) $(CFLAGS) -MT cmetindex-getopt.o -MD -MP -MF $(DEPDIR)/cmetindex-getopt.Tpo -c -o cmetindex-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/cmetindex-getopt.Tpo $(DEPDIR)/cmetindex-getopt.Po
@@ -3336,6 +6920,20 @@ get_genome-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -c -o get_genome-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+get_genome-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-semaphore.o -MD -MP -MF $(DEPDIR)/get_genome-semaphore.Tpo -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-semaphore.Tpo $(DEPDIR)/get_genome-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='get_genome-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+get_genome-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-semaphore.obj -MD -MP -MF $(DEPDIR)/get_genome-semaphore.Tpo -c -o get_genome-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-semaphore.Tpo $(DEPDIR)/get_genome-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='get_genome-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -c -o get_genome-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
get_genome-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -MT get_genome-access.o -MD -MP -MF $(DEPDIR)/get_genome-access.Tpo -c -o get_genome-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/get_genome-access.Tpo $(DEPDIR)/get_genome-access.Po
@@ -3560,5353 +7158,29993 @@ get_genome-get-genome.obj: get-genome.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(get_genome_CFLAGS) $(CFLAGS) -c -o get_genome-get-genome.obj `if test -f 'get-genome.c'; then $(CYGPATH_W) 'get-genome.c'; else $(CYGPATH_W) '$(srcdir)/get-genome.c'; fi`
-gmap-except.o: except.c
- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-except.o -MD -MP -MF $(DEPDIR)/gmap-except.Tpo -c -o gmap-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
- at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-except.Tpo $(DEPDIR)/gmap-except.Po
- at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmap-except.o' libtool=no @AMDEPBACKSLASH@
+gmap-cpuid.o: cpuid.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-cpuid.o -MD -MP -MF $(DEPDIR)/gmap-cpuid.Tpo -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '$(srcdir)/'`cpuid.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-cpuid.Tpo $(DEPDIR)/gmap-cpuid.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cpuid.c' object='gmap-cpuid.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '$(srcdir)/'`cpuid.c
-gmap-except.obj: except.c
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- at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-except.Tpo $(DEPDIR)/gmap-except.Po
- at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='except.c' object='gmap-except.obj' libtool=no @AMDEPBACKSLASH@
+gmap-cpuid.obj: cpuid.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-cpuid.obj -MD -MP -MF $(DEPDIR)/gmap-cpuid.Tpo -c -o gmap-cpuid.obj `if test -f 'cpuid.c'; then $(CYGPATH_W) 'cpuid.c'; else $(CYGPATH_W) '$(srcdir)/cpuid.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-cpuid.Tpo $(DEPDIR)/gmap-cpuid.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cpuid.c' object='gmap-cpuid.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
- at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-cpuid.obj `if test -f 'cpuid.c'; then $(CYGPATH_W) 'cpuid.c'; else $(CYGPATH_W) '$(srcdir)/cpuid.c'; fi`
-gmap-assert.o: assert.c
- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-assert.o -MD -MP -MF $(DEPDIR)/gmap-assert.Tpo -c -o gmap-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
- at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-assert.Tpo $(DEPDIR)/gmap-assert.Po
- at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmap-assert.o' libtool=no @AMDEPBACKSLASH@
+gmap-gmap_select.o: gmap_select.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gmap_select.o -MD -MP -MF $(DEPDIR)/gmap-gmap_select.Tpo -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '$(srcdir)/'`gmap_select.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gmap_select.Tpo $(DEPDIR)/gmap-gmap_select.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap_select.c' object='gmap-gmap_select.o' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '$(srcdir)/'`gmap_select.c
-gmap-assert.obj: assert.c
- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-assert.obj -MD -MP -MF $(DEPDIR)/gmap-assert.Tpo -c -o gmap-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
- at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-assert.Tpo $(DEPDIR)/gmap-assert.Po
- at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='assert.c' object='gmap-assert.obj' libtool=no @AMDEPBACKSLASH@
+gmap-gmap_select.obj: gmap_select.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_CFLAGS) $(CFLAGS) -MT gmap-gmap_select.obj -MD -MP -MF $(DEPDIR)/gmap-gmap_select.Tpo -c -o gmap-gmap_select.obj `if test -f 'gmap_select.c'; then $(CYGPATH_W) 'gmap_select.c'; else $(CYGPATH_W) '$(srcdir)/gmap_select.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap-gmap_select.Tpo $(DEPDIR)/gmap-gmap_select.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap_select.c' object='gmap-gmap_select.obj' libtool=no @AMDEPBACKSLASH@
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+gmap_nosimd-genome_sites.obj: genome_sites.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-genome_sites.Tpo $(DEPDIR)/gmap_nosimd-genome_sites.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gmap_nosimd-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
+
+gmap_nosimd-genome-write.o: genome-write.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-genome-write.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-genome-write.Tpo -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-genome-write.Tpo $(DEPDIR)/gmap_nosimd-genome-write.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmap_nosimd-genome-write.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '$(srcdir)/'`genome-write.c
+
+gmap_nosimd-genome-write.obj: genome-write.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-genome-write.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-genome-write.Tpo -c -o gmap_nosimd-genome-write.obj `if test -f 'genome-write.c'; then $(CYGPATH_W) 'genome-write.c'; else $(CYGPATH_W) '$(srcdir)/genome-write.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-genome-write.Tpo $(DEPDIR)/gmap_nosimd-genome-write.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome-write.c' object='gmap_nosimd-genome-write.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-genome-write.obj `if test -f 'genome-write.c'; then $(CYGPATH_W) 'genome-write.c'; else $(CYGPATH_W) '$(srcdir)/genome-write.c'; fi`
+
+gmap_nosimd-bitpack64-read.o: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-bitpack64-read.Tpo -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-bitpack64-read.Tpo $(DEPDIR)/gmap_nosimd-bitpack64-read.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+
+gmap_nosimd-bitpack64-read.obj: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-bitpack64-read.Tpo -c -o gmap_nosimd-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-bitpack64-read.Tpo $(DEPDIR)/gmap_nosimd-bitpack64-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gmap_nosimd-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+
+gmap_nosimd-bitpack64-readtwo.o: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-bitpack64-readtwo.Tpo -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-bitpack64-readtwo.Tpo $(DEPDIR)/gmap_nosimd-bitpack64-readtwo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmap_nosimd-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+
+gmap_nosimd-bitpack64-readtwo.obj: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-bitpack64-readtwo.Tpo -c -o gmap_nosimd-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-bitpack64-readtwo.Tpo $(DEPDIR)/gmap_nosimd-bitpack64-readtwo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gmap_nosimd-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+
+gmap_nosimd-indexdb.o: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-indexdb.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-indexdb.Tpo -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-indexdb.Tpo $(DEPDIR)/gmap_nosimd-indexdb.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmap_nosimd-indexdb.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+
+gmap_nosimd-indexdb.obj: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-indexdb.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-indexdb.Tpo -c -o gmap_nosimd-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-indexdb.Tpo $(DEPDIR)/gmap_nosimd-indexdb.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gmap_nosimd-indexdb.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+
+gmap_nosimd-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-indexdb_hr.Tpo -c -o gmap_nosimd-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-indexdb_hr.Tpo $(DEPDIR)/gmap_nosimd-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gmap_nosimd-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+
+gmap_nosimd-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-indexdb_hr.Tpo -c -o gmap_nosimd-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-indexdb_hr.Tpo $(DEPDIR)/gmap_nosimd-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gmap_nosimd-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+
+gmap_nosimd-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-oligo.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-oligo.Tpo -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-oligo.Tpo $(DEPDIR)/gmap_nosimd-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gmap_nosimd-oligo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gmap_nosimd-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-oligo.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-oligo.Tpo -c -o gmap_nosimd-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-oligo.Tpo $(DEPDIR)/gmap_nosimd-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gmap_nosimd-oligo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+
+gmap_nosimd-block.o: block.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-block.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-block.Tpo -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '$(srcdir)/'`block.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-block.Tpo $(DEPDIR)/gmap_nosimd-block.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='block.c' object='gmap_nosimd-block.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '$(srcdir)/'`block.c
+
+gmap_nosimd-block.obj: block.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-block.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-block.Tpo -c -o gmap_nosimd-block.obj `if test -f 'block.c'; then $(CYGPATH_W) 'block.c'; else $(CYGPATH_W) '$(srcdir)/block.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-block.Tpo $(DEPDIR)/gmap_nosimd-block.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='block.c' object='gmap_nosimd-block.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-block.obj `if test -f 'block.c'; then $(CYGPATH_W) 'block.c'; else $(CYGPATH_W) '$(srcdir)/block.c'; fi`
+
+gmap_nosimd-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-chrom.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-chrom.Tpo -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-chrom.Tpo $(DEPDIR)/gmap_nosimd-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmap_nosimd-chrom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+
+gmap_nosimd-chrom.obj: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-chrom.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-chrom.Tpo -c -o gmap_nosimd-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-chrom.Tpo $(DEPDIR)/gmap_nosimd-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gmap_nosimd-chrom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+
+gmap_nosimd-segmentpos.o: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-segmentpos.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-segmentpos.Tpo -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-segmentpos.Tpo $(DEPDIR)/gmap_nosimd-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmap_nosimd-segmentpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+
+gmap_nosimd-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-segmentpos.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-segmentpos.Tpo -c -o gmap_nosimd-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-segmentpos.Tpo $(DEPDIR)/gmap_nosimd-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gmap_nosimd-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gmap_nosimd-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-chrnum.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-chrnum.Tpo -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-chrnum.Tpo $(DEPDIR)/gmap_nosimd-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gmap_nosimd-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gmap_nosimd-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-chrnum.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-chrnum.Tpo -c -o gmap_nosimd-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-chrnum.Tpo $(DEPDIR)/gmap_nosimd-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gmap_nosimd-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gmap_nosimd-uinttable.o: uinttable.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-uinttable.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-uinttable.Tpo -c -o gmap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-uinttable.Tpo $(DEPDIR)/gmap_nosimd-uinttable.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmap_nosimd-uinttable.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
+
+gmap_nosimd-uinttable.obj: uinttable.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-uinttable.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-uinttable.Tpo -c -o gmap_nosimd-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-uinttable.Tpo $(DEPDIR)/gmap_nosimd-uinttable.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmap_nosimd-uinttable.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
+
+gmap_nosimd-gregion.o: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-gregion.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-gregion.Tpo -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-gregion.Tpo $(DEPDIR)/gmap_nosimd-gregion.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmap_nosimd-gregion.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
+
+gmap_nosimd-gregion.obj: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-gregion.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-gregion.Tpo -c -o gmap_nosimd-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-gregion.Tpo $(DEPDIR)/gmap_nosimd-gregion.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmap_nosimd-gregion.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
+
+gmap_nosimd-match.o: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-match.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-match.Tpo -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-match.Tpo $(DEPDIR)/gmap_nosimd-match.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmap_nosimd-match.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
+
+gmap_nosimd-match.obj: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-match.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-match.Tpo -c -o gmap_nosimd-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-match.Tpo $(DEPDIR)/gmap_nosimd-match.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmap_nosimd-match.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
+
+gmap_nosimd-matchpool.o: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-matchpool.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-matchpool.Tpo -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-matchpool.Tpo $(DEPDIR)/gmap_nosimd-matchpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmap_nosimd-matchpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
+
+gmap_nosimd-matchpool.obj: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-matchpool.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-matchpool.Tpo -c -o gmap_nosimd-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-matchpool.Tpo $(DEPDIR)/gmap_nosimd-matchpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmap_nosimd-matchpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
+
+gmap_nosimd-diagnostic.o: diagnostic.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-diagnostic.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-diagnostic.Tpo -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-diagnostic.Tpo $(DEPDIR)/gmap_nosimd-diagnostic.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmap_nosimd-diagnostic.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
+
+gmap_nosimd-diagnostic.obj: diagnostic.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-diagnostic.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-diagnostic.Tpo -c -o gmap_nosimd-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-diagnostic.Tpo $(DEPDIR)/gmap_nosimd-diagnostic.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmap_nosimd-diagnostic.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
+
+gmap_nosimd-stage1.o: stage1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-stage1.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-stage1.Tpo -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-stage1.Tpo $(DEPDIR)/gmap_nosimd-stage1.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmap_nosimd-stage1.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
+
+gmap_nosimd-stage1.obj: stage1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-stage1.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-stage1.Tpo -c -o gmap_nosimd-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-stage1.Tpo $(DEPDIR)/gmap_nosimd-stage1.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmap_nosimd-stage1.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
+
+gmap_nosimd-diag.o: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-diag.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-diag.Tpo -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-diag.Tpo $(DEPDIR)/gmap_nosimd-diag.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmap_nosimd-diag.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+
+gmap_nosimd-diag.obj: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-diag.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-diag.Tpo -c -o gmap_nosimd-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-diag.Tpo $(DEPDIR)/gmap_nosimd-diag.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmap_nosimd-diag.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+
+gmap_nosimd-diagpool.o: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-diagpool.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-diagpool.Tpo -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-diagpool.Tpo $(DEPDIR)/gmap_nosimd-diagpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmap_nosimd-diagpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+
+gmap_nosimd-diagpool.obj: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-diagpool.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-diagpool.Tpo -c -o gmap_nosimd-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-diagpool.Tpo $(DEPDIR)/gmap_nosimd-diagpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmap_nosimd-diagpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+
+gmap_nosimd-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-cmet.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-cmet.Tpo -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-cmet.Tpo $(DEPDIR)/gmap_nosimd-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmap_nosimd-cmet.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gmap_nosimd-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-cmet.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-cmet.Tpo -c -o gmap_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-cmet.Tpo $(DEPDIR)/gmap_nosimd-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmap_nosimd-cmet.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+
+gmap_nosimd-atoi.o: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-atoi.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-atoi.Tpo -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-atoi.Tpo $(DEPDIR)/gmap_nosimd-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmap_nosimd-atoi.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+
+gmap_nosimd-atoi.obj: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-atoi.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-atoi.Tpo -c -o gmap_nosimd-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-atoi.Tpo $(DEPDIR)/gmap_nosimd-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmap_nosimd-atoi.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+
+gmap_nosimd-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-orderstat.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-orderstat.Tpo -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-orderstat.Tpo $(DEPDIR)/gmap_nosimd-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmap_nosimd-orderstat.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+
+gmap_nosimd-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-orderstat.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-orderstat.Tpo -c -o gmap_nosimd-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-orderstat.Tpo $(DEPDIR)/gmap_nosimd-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmap_nosimd-orderstat.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+
+gmap_nosimd-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-oligoindex_hr.Tpo -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-oligoindex_hr.Tpo $(DEPDIR)/gmap_nosimd-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmap_nosimd-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gmap_nosimd-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-oligoindex_hr.Tpo -c -o gmap_nosimd-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-oligoindex_hr.Tpo $(DEPDIR)/gmap_nosimd-oligoindex_hr.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gmap_nosimd-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-intron.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-intron.Tpo -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-intron.Tpo $(DEPDIR)/gmap_nosimd-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmap_nosimd-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gmap_nosimd-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-intron.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-intron.Tpo -c -o gmap_nosimd-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-intron.Tpo $(DEPDIR)/gmap_nosimd-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmap_nosimd-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gmap_nosimd-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-maxent.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-maxent.Tpo -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-maxent.Tpo $(DEPDIR)/gmap_nosimd-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmap_nosimd-maxent.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+
+gmap_nosimd-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-maxent.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-maxent.Tpo -c -o gmap_nosimd-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-maxent.Tpo $(DEPDIR)/gmap_nosimd-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmap_nosimd-maxent.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+
+gmap_nosimd-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-maxent_hr.Tpo -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-maxent_hr.Tpo $(DEPDIR)/gmap_nosimd-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap_nosimd-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gmap_nosimd-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-maxent_hr.Tpo -c -o gmap_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-maxent_hr.Tpo $(DEPDIR)/gmap_nosimd-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap_nosimd-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gmap_nosimd-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-pair.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-pair.Tpo -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-pair.Tpo $(DEPDIR)/gmap_nosimd-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap_nosimd-pair.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmap_nosimd-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-pair.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-pair.Tpo -c -o gmap_nosimd-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-pair.Tpo $(DEPDIR)/gmap_nosimd-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap_nosimd-pair.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+
+gmap_nosimd-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-pairpool.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-pairpool.Tpo -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-pairpool.Tpo $(DEPDIR)/gmap_nosimd-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap_nosimd-pairpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmap_nosimd-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-pairpool.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-pairpool.Tpo -c -o gmap_nosimd-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-pairpool.Tpo $(DEPDIR)/gmap_nosimd-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap_nosimd-pairpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gmap_nosimd-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-cellpool.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-cellpool.Tpo -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-cellpool.Tpo $(DEPDIR)/gmap_nosimd-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap_nosimd-cellpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gmap_nosimd-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-cellpool.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-cellpool.Tpo -c -o gmap_nosimd-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-cellpool.Tpo $(DEPDIR)/gmap_nosimd-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap_nosimd-cellpool.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+
+gmap_nosimd-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-stage2.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-stage2.Tpo -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-stage2.Tpo $(DEPDIR)/gmap_nosimd-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmap_nosimd-stage2.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gmap_nosimd-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-stage2.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-stage2.Tpo -c -o gmap_nosimd-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-stage2.Tpo $(DEPDIR)/gmap_nosimd-stage2.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gmap_nosimd-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-doublelist.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-doublelist.Tpo -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-doublelist.Tpo $(DEPDIR)/gmap_nosimd-doublelist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmap_nosimd-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-doublelist.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-doublelist.Tpo -c -o gmap_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-doublelist.Tpo $(DEPDIR)/gmap_nosimd-doublelist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmap_nosimd-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-smooth.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-smooth.Tpo -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-smooth.Tpo $(DEPDIR)/gmap_nosimd-smooth.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmap_nosimd-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-smooth.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-smooth.Tpo -c -o gmap_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-smooth.Tpo $(DEPDIR)/gmap_nosimd-smooth.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmap_nosimd-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-splicestringpool.Tpo -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-splicestringpool.Tpo $(DEPDIR)/gmap_nosimd-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmap_nosimd-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmap_nosimd-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-splicestringpool.Tpo -c -o gmap_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-splicestringpool.Tpo $(DEPDIR)/gmap_nosimd-splicestringpool.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmap_nosimd-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-splicetrie_build.Tpo -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-splicetrie_build.Tpo $(DEPDIR)/gmap_nosimd-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmap_nosimd-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmap_nosimd-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-splicetrie_build.Tpo -c -o gmap_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-splicetrie_build.Tpo $(DEPDIR)/gmap_nosimd-splicetrie_build.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gmap_nosimd-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-splicetrie.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-splicetrie.Tpo -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-splicetrie.Tpo $(DEPDIR)/gmap_nosimd-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmap_nosimd-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-splicetrie.Tpo -c -o gmap_nosimd-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-splicetrie.Tpo $(DEPDIR)/gmap_nosimd-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmap_nosimd-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-boyer-moore.Tpo -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-boyer-moore.Tpo $(DEPDIR)/gmap_nosimd-boyer-moore.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmap_nosimd-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-boyer-moore.Tpo -c -o gmap_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-boyer-moore.Tpo $(DEPDIR)/gmap_nosimd-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmap_nosimd-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog.Tpo -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog.Tpo $(DEPDIR)/gmap_nosimd-dynprog.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmap_nosimd-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog.Tpo -c -o gmap_nosimd-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog.Tpo $(DEPDIR)/gmap_nosimd-dynprog.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmap_nosimd-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_simd.Tpo -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_simd.Tpo $(DEPDIR)/gmap_nosimd-dynprog_simd.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmap_nosimd-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_simd.Tpo -c -o gmap_nosimd-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_simd.Tpo $(DEPDIR)/gmap_nosimd-dynprog_simd.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmap_nosimd-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_single.Tpo -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_single.Tpo $(DEPDIR)/gmap_nosimd-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmap_nosimd-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_single.Tpo -c -o gmap_nosimd-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_single.Tpo $(DEPDIR)/gmap_nosimd-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gmap_nosimd-dynprog_genome.o: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_genome.Tpo -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_genome.Tpo $(DEPDIR)/gmap_nosimd-dynprog_genome.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+
+gmap_nosimd-dynprog_genome.obj: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_genome.Tpo -c -o gmap_nosimd-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_genome.Tpo $(DEPDIR)/gmap_nosimd-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmap_nosimd-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+
+gmap_nosimd-dynprog_cdna.o: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_cdna.Tpo -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gmap_nosimd-dynprog_cdna.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+
+gmap_nosimd-dynprog_cdna.obj: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_cdna.Tpo -c -o gmap_nosimd-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gmap_nosimd-dynprog_cdna.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+
+gmap_nosimd-dynprog_end.o: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_end.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_end.Tpo -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_end.Tpo $(DEPDIR)/gmap_nosimd-dynprog_end.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+
+gmap_nosimd-dynprog_end.obj: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-dynprog_end.Tpo -c -o gmap_nosimd-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-dynprog_end.Tpo $(DEPDIR)/gmap_nosimd-dynprog_end.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+
+gmap_nosimd-translation.o: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-translation.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-translation.Tpo -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-translation.Tpo $(DEPDIR)/gmap_nosimd-translation.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+
+gmap_nosimd-translation.obj: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-translation.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-translation.Tpo -c -o gmap_nosimd-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-translation.Tpo $(DEPDIR)/gmap_nosimd-translation.Po
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+
+gmap_nosimd-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-pbinom.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-pbinom.Tpo -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-pbinom.Tpo $(DEPDIR)/gmap_nosimd-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmap_nosimd-pbinom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+
+gmap_nosimd-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-pbinom.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-pbinom.Tpo -c -o gmap_nosimd-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-pbinom.Tpo $(DEPDIR)/gmap_nosimd-pbinom.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+
+gmap_nosimd-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-changepoint.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-changepoint.Tpo -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-changepoint.Tpo $(DEPDIR)/gmap_nosimd-changepoint.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+
+gmap_nosimd-changepoint.obj: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-changepoint.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-changepoint.Tpo -c -o gmap_nosimd-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-changepoint.Tpo $(DEPDIR)/gmap_nosimd-changepoint.Po
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+
+gmap_nosimd-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-stage3.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-stage3.Tpo -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-stage3.Tpo $(DEPDIR)/gmap_nosimd-stage3.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
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+gmap_nosimd-stage3.obj: stage3.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-stage3.Tpo $(DEPDIR)/gmap_nosimd-stage3.Po
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+
+gmap_nosimd-request.o: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-request.o -MD -MP -MF $(DEPDIR)/gmap_nosimd-request.Tpo -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-request.Tpo $(DEPDIR)/gmap_nosimd-request.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
+
+gmap_nosimd-request.obj: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_nosimd_CFLAGS) $(CFLAGS) -MT gmap_nosimd-request.obj -MD -MP -MF $(DEPDIR)/gmap_nosimd-request.Tpo -c -o gmap_nosimd-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_nosimd-request.Tpo $(DEPDIR)/gmap_nosimd-request.Po
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+gmap_nosimd-result.o: result.c
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+gmap_nosimd-result.obj: result.c
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+gmap_nosimd-output.o: output.c
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+gmap_nosimd-output.obj: output.c
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+gmap_nosimd-datadir.o: datadir.c
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+gmap_nosimd-parserange.o: parserange.c
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+gmap_nosimd-getopt1.o: getopt1.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-except.Tpo $(DEPDIR)/gmap_sse2-except.Po
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+gmap_sse2-assert.obj: assert.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-assert.Tpo $(DEPDIR)/gmap_sse2-assert.Po
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+gmap_sse2-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-mem.o -MD -MP -MF $(DEPDIR)/gmap_sse2-mem.Tpo -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-mem.Tpo $(DEPDIR)/gmap_sse2-mem.Po
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+gmap_sse2-mem.obj: mem.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-intlist.o -MD -MP -MF $(DEPDIR)/gmap_sse2-intlist.Tpo -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
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+gmap_sse2-intlist.obj: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-intlist.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-intlist.Tpo -c -o gmap_sse2-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-list.Tpo $(DEPDIR)/gmap_sse2-list.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-littleendian.o -MD -MP -MF $(DEPDIR)/gmap_sse2-littleendian.Tpo -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
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+gmap_sse2-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-univinterval.o -MD -MP -MF $(DEPDIR)/gmap_sse2-univinterval.Tpo -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
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+gmap_sse2-univinterval.obj: univinterval.c
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+gmap_sse2-interval.o: interval.c
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+gmap_sse2-interval.obj: interval.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-stopwatch.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-stopwatch.Tpo -c -o gmap_sse2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-stopwatch.Tpo $(DEPDIR)/gmap_sse2-stopwatch.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gmap_sse2-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+
+gmap_sse2-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-semaphore.o -MD -MP -MF $(DEPDIR)/gmap_sse2-semaphore.Tpo -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-semaphore.Tpo $(DEPDIR)/gmap_sse2-semaphore.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+gmap_sse2-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-semaphore.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-semaphore.Tpo -c -o gmap_sse2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-semaphore.Tpo $(DEPDIR)/gmap_sse2-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='gmap_sse2-semaphore.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
+gmap_sse2-access.o: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-access.o -MD -MP -MF $(DEPDIR)/gmap_sse2-access.Tpo -c -o gmap_sse2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-access.Tpo $(DEPDIR)/gmap_sse2-access.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+
+gmap_sse2-access.obj: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-access.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-access.Tpo -c -o gmap_sse2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-access.Tpo $(DEPDIR)/gmap_sse2-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gmap_sse2-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+
+gmap_sse2-filestring.o: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-filestring.o -MD -MP -MF $(DEPDIR)/gmap_sse2-filestring.Tpo -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-filestring.Tpo $(DEPDIR)/gmap_sse2-filestring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='filestring.c' object='gmap_sse2-filestring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+
+gmap_sse2-filestring.obj: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-filestring.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-filestring.Tpo -c -o gmap_sse2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-filestring.Tpo $(DEPDIR)/gmap_sse2-filestring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='filestring.c' object='gmap_sse2-filestring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+
+gmap_sse2-iit-read-univ.o: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gmap_sse2-iit-read-univ.Tpo -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-iit-read-univ.Tpo $(DEPDIR)/gmap_sse2-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmap_sse2-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+
+gmap_sse2-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-iit-read-univ.Tpo -c -o gmap_sse2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-iit-read-univ.Tpo $(DEPDIR)/gmap_sse2-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gmap_sse2-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+
+gmap_sse2-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-iit-read.o -MD -MP -MF $(DEPDIR)/gmap_sse2-iit-read.Tpo -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-iit-read.Tpo $(DEPDIR)/gmap_sse2-iit-read.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+
+gmap_sse2-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-iit-read.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-iit-read.Tpo -c -o gmap_sse2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-iit-read.Tpo $(DEPDIR)/gmap_sse2-iit-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gmap_sse2-iit-read.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+
+gmap_sse2-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-md5.o -MD -MP -MF $(DEPDIR)/gmap_sse2-md5.Tpo -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-md5.Tpo $(DEPDIR)/gmap_sse2-md5.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gmap_sse2-md5.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+
+gmap_sse2-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-md5.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-md5.Tpo -c -o gmap_sse2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-md5.Tpo $(DEPDIR)/gmap_sse2-md5.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+
+gmap_sse2-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-bzip2.o -MD -MP -MF $(DEPDIR)/gmap_sse2-bzip2.Tpo -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-bzip2.Tpo $(DEPDIR)/gmap_sse2-bzip2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmap_sse2-bzip2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+
+gmap_sse2-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-bzip2.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-bzip2.Tpo -c -o gmap_sse2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-bzip2.Tpo $(DEPDIR)/gmap_sse2-bzip2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gmap_sse2-bzip2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+
+gmap_sse2-sequence.o: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-sequence.o -MD -MP -MF $(DEPDIR)/gmap_sse2-sequence.Tpo -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-sequence.Tpo $(DEPDIR)/gmap_sse2-sequence.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmap_sse2-sequence.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+
+gmap_sse2-sequence.obj: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-sequence.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-sequence.Tpo -c -o gmap_sse2-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-sequence.Tpo $(DEPDIR)/gmap_sse2-sequence.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gmap_sse2-sequence.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+
+gmap_sse2-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-reader.o -MD -MP -MF $(DEPDIR)/gmap_sse2-reader.Tpo -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-reader.Tpo $(DEPDIR)/gmap_sse2-reader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gmap_sse2-reader.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+
+gmap_sse2-reader.obj: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-reader.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-reader.Tpo -c -o gmap_sse2-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-reader.Tpo $(DEPDIR)/gmap_sse2-reader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gmap_sse2-reader.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmap_sse2-oligoindex_hr.Tpo -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-oligoindex_hr.Tpo $(DEPDIR)/gmap_sse2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmap_sse2-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gmap_sse2-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-oligoindex_hr.Tpo -c -o gmap_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-oligoindex_hr.Tpo $(DEPDIR)/gmap_sse2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmap_sse2-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gmap_sse2-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-intron.o -MD -MP -MF $(DEPDIR)/gmap_sse2-intron.Tpo -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-intron.Tpo $(DEPDIR)/gmap_sse2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmap_sse2-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gmap_sse2-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-intron.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-intron.Tpo -c -o gmap_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-intron.Tpo $(DEPDIR)/gmap_sse2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmap_sse2-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gmap_sse2-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-maxent.o -MD -MP -MF $(DEPDIR)/gmap_sse2-maxent.Tpo -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-maxent.Tpo $(DEPDIR)/gmap_sse2-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmap_sse2-maxent.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+
+gmap_sse2-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-maxent.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-maxent.Tpo -c -o gmap_sse2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-maxent.Tpo $(DEPDIR)/gmap_sse2-maxent.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+
+gmap_sse2-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmap_sse2-maxent_hr.Tpo -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-maxent_hr.Tpo $(DEPDIR)/gmap_sse2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap_sse2-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gmap_sse2-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-maxent_hr.Tpo -c -o gmap_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-maxent_hr.Tpo $(DEPDIR)/gmap_sse2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap_sse2-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gmap_sse2-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-pair.o -MD -MP -MF $(DEPDIR)/gmap_sse2-pair.Tpo -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-pair.Tpo $(DEPDIR)/gmap_sse2-pair.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmap_sse2-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-pair.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-pair.Tpo -c -o gmap_sse2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-pair.Tpo $(DEPDIR)/gmap_sse2-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap_sse2-pair.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+
+gmap_sse2-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-pairpool.o -MD -MP -MF $(DEPDIR)/gmap_sse2-pairpool.Tpo -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-pairpool.Tpo $(DEPDIR)/gmap_sse2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap_sse2-pairpool.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmap_sse2-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-pairpool.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-pairpool.Tpo -c -o gmap_sse2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-pairpool.Tpo $(DEPDIR)/gmap_sse2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap_sse2-pairpool.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gmap_sse2-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-cellpool.o -MD -MP -MF $(DEPDIR)/gmap_sse2-cellpool.Tpo -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-cellpool.Tpo $(DEPDIR)/gmap_sse2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap_sse2-cellpool.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gmap_sse2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-cellpool.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-cellpool.Tpo -c -o gmap_sse2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-cellpool.Tpo $(DEPDIR)/gmap_sse2-cellpool.Po
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+
+gmap_sse2-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-stage2.o -MD -MP -MF $(DEPDIR)/gmap_sse2-stage2.Tpo -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-stage2.Tpo $(DEPDIR)/gmap_sse2-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmap_sse2-stage2.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gmap_sse2-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-stage2.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-stage2.Tpo -c -o gmap_sse2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-stage2.Tpo $(DEPDIR)/gmap_sse2-stage2.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gmap_sse2-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-doublelist.o -MD -MP -MF $(DEPDIR)/gmap_sse2-doublelist.Tpo -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-doublelist.Tpo $(DEPDIR)/gmap_sse2-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmap_sse2-doublelist.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
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+gmap_sse2-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-doublelist.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-doublelist.Tpo -c -o gmap_sse2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-doublelist.Tpo $(DEPDIR)/gmap_sse2-doublelist.Po
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+gmap_sse2-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-smooth.o -MD -MP -MF $(DEPDIR)/gmap_sse2-smooth.Tpo -c -o gmap_sse2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
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+gmap_sse2-smooth.obj: smooth.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-smooth.Tpo $(DEPDIR)/gmap_sse2-smooth.Po
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+gmap_sse2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmap_sse2-splicestringpool.Tpo -c -o gmap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmap_sse2-splicestringpool.Tpo -c -o gmap_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-splicestringpool.Tpo $(DEPDIR)/gmap_sse2-splicestringpool.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmap_sse2-splicetrie_build.Tpo -c -o gmap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-splicetrie_build.Tpo $(DEPDIR)/gmap_sse2-splicetrie_build.Po
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+
+gmap_sse2-splicetrie_build.obj: splicetrie_build.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-splicetrie_build.Tpo $(DEPDIR)/gmap_sse2-splicetrie_build.Po
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+
+gmap_sse2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse2_CFLAGS) $(CFLAGS) -MT gmap_sse2-splicetrie.o -MD -MP -MF $(DEPDIR)/gmap_sse2-splicetrie.Tpo -c -o gmap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
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+gmap_sse2-splicetrie.obj: splicetrie.c
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+gmap_sse2-boyer-moore.o: boyer-moore.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-boyer-moore.Tpo $(DEPDIR)/gmap_sse2-boyer-moore.Po
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse2-boyer-moore.Tpo $(DEPDIR)/gmap_sse2-boyer-moore.Po
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+
+gmap_sse2-dynprog.o: dynprog.c
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+gmap_sse2-dynprog.obj: dynprog.c
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+gmap_sse2-dynprog_simd.o: dynprog_simd.c
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+gmap_sse2-dynprog_simd.obj: dynprog_simd.c
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+gmap_sse2-dynprog_single.obj: dynprog_single.c
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+gmap_sse2-dynprog_genome.o: dynprog_genome.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse41_CFLAGS) $(CFLAGS) -MT gmap_sse41-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gmap_sse41-indexdb_hr.Tpo -c -o gmap_sse41-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse41-indexdb_hr.Tpo $(DEPDIR)/gmap_sse41-indexdb_hr.Po
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+
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+
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+
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+
+gmap_sse42-block.o: block.c
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+gmap_sse42-block.obj: block.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-block.Tpo $(DEPDIR)/gmap_sse42-block.Po
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+
+gmap_sse42-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-chrom.o -MD -MP -MF $(DEPDIR)/gmap_sse42-chrom.Tpo -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
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+
+gmap_sse42-chrom.obj: chrom.c
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+gmap_sse42-segmentpos.o: segmentpos.c
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+
+gmap_sse42-segmentpos.obj: segmentpos.c
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+
+gmap_sse42-chrnum.obj: chrnum.c
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+
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+
+gmap_sse42-uinttable.obj: uinttable.c
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+gmap_sse42-gregion.obj: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-gregion.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-gregion.Tpo -c -o gmap_sse42-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
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+gmap_sse42-match.o: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-match.o -MD -MP -MF $(DEPDIR)/gmap_sse42-match.Tpo -c -o gmap_sse42-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
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+
+gmap_sse42-match.obj: match.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-match.Tpo $(DEPDIR)/gmap_sse42-match.Po
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+
+gmap_sse42-matchpool.o: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-matchpool.o -MD -MP -MF $(DEPDIR)/gmap_sse42-matchpool.Tpo -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
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+gmap_sse42-matchpool.obj: matchpool.c
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+gmap_sse42-diagnostic.obj: diagnostic.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-maxent_hr.Tpo -c -o gmap_sse42-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-maxent_hr.Tpo $(DEPDIR)/gmap_sse42-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmap_sse42-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gmap_sse42-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-pair.o -MD -MP -MF $(DEPDIR)/gmap_sse42-pair.Tpo -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-pair.Tpo $(DEPDIR)/gmap_sse42-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap_sse42-pair.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmap_sse42-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-pair.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-pair.Tpo -c -o gmap_sse42-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-pair.Tpo $(DEPDIR)/gmap_sse42-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmap_sse42-pair.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+
+gmap_sse42-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-pairpool.o -MD -MP -MF $(DEPDIR)/gmap_sse42-pairpool.Tpo -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-pairpool.Tpo $(DEPDIR)/gmap_sse42-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap_sse42-pairpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmap_sse42-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-pairpool.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-pairpool.Tpo -c -o gmap_sse42-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-pairpool.Tpo $(DEPDIR)/gmap_sse42-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmap_sse42-pairpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gmap_sse42-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-cellpool.o -MD -MP -MF $(DEPDIR)/gmap_sse42-cellpool.Tpo -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-cellpool.Tpo $(DEPDIR)/gmap_sse42-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap_sse42-cellpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gmap_sse42-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-cellpool.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-cellpool.Tpo -c -o gmap_sse42-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-cellpool.Tpo $(DEPDIR)/gmap_sse42-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmap_sse42-cellpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+
+gmap_sse42-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-stage2.o -MD -MP -MF $(DEPDIR)/gmap_sse42-stage2.Tpo -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-stage2.Tpo $(DEPDIR)/gmap_sse42-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmap_sse42-stage2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gmap_sse42-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-stage2.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-stage2.Tpo -c -o gmap_sse42-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-stage2.Tpo $(DEPDIR)/gmap_sse42-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmap_sse42-stage2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gmap_sse42-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-doublelist.o -MD -MP -MF $(DEPDIR)/gmap_sse42-doublelist.Tpo -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-doublelist.Tpo $(DEPDIR)/gmap_sse42-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmap_sse42-doublelist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmap_sse42-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-doublelist.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-doublelist.Tpo -c -o gmap_sse42-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-doublelist.Tpo $(DEPDIR)/gmap_sse42-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmap_sse42-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmap_sse42-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-smooth.o -MD -MP -MF $(DEPDIR)/gmap_sse42-smooth.Tpo -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-smooth.Tpo $(DEPDIR)/gmap_sse42-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmap_sse42-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmap_sse42-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-smooth.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-smooth.Tpo -c -o gmap_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-smooth.Tpo $(DEPDIR)/gmap_sse42-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmap_sse42-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmap_sse42-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmap_sse42-splicestringpool.Tpo -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-splicestringpool.Tpo $(DEPDIR)/gmap_sse42-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmap_sse42-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmap_sse42-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-splicestringpool.Tpo -c -o gmap_sse42-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-splicestringpool.Tpo $(DEPDIR)/gmap_sse42-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmap_sse42-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmap_sse42-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmap_sse42-splicetrie_build.Tpo -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-splicetrie_build.Tpo $(DEPDIR)/gmap_sse42-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmap_sse42-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmap_sse42-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-splicetrie_build.Tpo -c -o gmap_sse42-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-splicetrie_build.Tpo $(DEPDIR)/gmap_sse42-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmap_sse42-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gmap_sse42-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-splicetrie.o -MD -MP -MF $(DEPDIR)/gmap_sse42-splicetrie.Tpo -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-splicetrie.Tpo $(DEPDIR)/gmap_sse42-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmap_sse42-splicetrie.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmap_sse42-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-splicetrie.Tpo -c -o gmap_sse42-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-splicetrie.Tpo $(DEPDIR)/gmap_sse42-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmap_sse42-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmap_sse42-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmap_sse42-boyer-moore.Tpo -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-boyer-moore.Tpo $(DEPDIR)/gmap_sse42-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmap_sse42-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmap_sse42-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-boyer-moore.Tpo -c -o gmap_sse42-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-boyer-moore.Tpo $(DEPDIR)/gmap_sse42-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmap_sse42-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmap_sse42-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog.o -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog.Tpo -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog.Tpo $(DEPDIR)/gmap_sse42-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmap_sse42-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmap_sse42-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog.Tpo -c -o gmap_sse42-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog.Tpo $(DEPDIR)/gmap_sse42-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmap_sse42-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmap_sse42-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_simd.Tpo -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_simd.Tpo $(DEPDIR)/gmap_sse42-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmap_sse42-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmap_sse42-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_simd.Tpo -c -o gmap_sse42-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_simd.Tpo $(DEPDIR)/gmap_sse42-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmap_sse42-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmap_sse42-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_single.Tpo -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_single.Tpo $(DEPDIR)/gmap_sse42-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmap_sse42-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmap_sse42-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_single.Tpo -c -o gmap_sse42-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_single.Tpo $(DEPDIR)/gmap_sse42-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmap_sse42-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gmap_sse42-dynprog_genome.o: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_genome.Tpo -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_genome.Tpo $(DEPDIR)/gmap_sse42-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmap_sse42-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+
+gmap_sse42-dynprog_genome.obj: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_genome.Tpo -c -o gmap_sse42-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_genome.Tpo $(DEPDIR)/gmap_sse42-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gmap_sse42-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+
+gmap_sse42-dynprog_cdna.o: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_cdna.Tpo -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_cdna.Tpo $(DEPDIR)/gmap_sse42-dynprog_cdna.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gmap_sse42-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+
+gmap_sse42-dynprog_cdna.obj: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_cdna.Tpo -c -o gmap_sse42-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_cdna.Tpo $(DEPDIR)/gmap_sse42-dynprog_cdna.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gmap_sse42-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+
+gmap_sse42-dynprog_end.o: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_end.o -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_end.Tpo -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_end.Tpo $(DEPDIR)/gmap_sse42-dynprog_end.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gmap_sse42-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+
+gmap_sse42-dynprog_end.obj: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-dynprog_end.Tpo -c -o gmap_sse42-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-dynprog_end.Tpo $(DEPDIR)/gmap_sse42-dynprog_end.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gmap_sse42-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+
+gmap_sse42-translation.o: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-translation.o -MD -MP -MF $(DEPDIR)/gmap_sse42-translation.Tpo -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-translation.Tpo $(DEPDIR)/gmap_sse42-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gmap_sse42-translation.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+
+gmap_sse42-translation.obj: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-translation.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-translation.Tpo -c -o gmap_sse42-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-translation.Tpo $(DEPDIR)/gmap_sse42-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gmap_sse42-translation.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+
+gmap_sse42-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-pbinom.o -MD -MP -MF $(DEPDIR)/gmap_sse42-pbinom.Tpo -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-pbinom.Tpo $(DEPDIR)/gmap_sse42-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmap_sse42-pbinom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+
+gmap_sse42-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-pbinom.obj -MD -MP -MF $(DEPDIR)/gmap_sse42-pbinom.Tpo -c -o gmap_sse42-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-pbinom.Tpo $(DEPDIR)/gmap_sse42-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gmap_sse42-pbinom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -c -o gmap_sse42-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+
+gmap_sse42-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_sse42_CFLAGS) $(CFLAGS) -MT gmap_sse42-changepoint.o -MD -MP -MF $(DEPDIR)/gmap_sse42-changepoint.Tpo -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_sse42-changepoint.Tpo $(DEPDIR)/gmap_sse42-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gmap_sse42-changepoint.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-bigendian.Tpo $(DEPDIR)/gmap_ssse3-bigendian.Po
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+gmap_ssse3-bigendian.obj: bigendian.c
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+
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+gmap_ssse3-univinterval.obj: univinterval.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-access.Tpo $(DEPDIR)/gmap_ssse3-access.Po
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+gmap_ssse3-filestring.o: filestring.c
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+gmap_ssse3-filestring.obj: filestring.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-iit-read-univ.Tpo $(DEPDIR)/gmap_ssse3-iit-read-univ.Po
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+
+gmap_ssse3-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_ssse3_CFLAGS) $(CFLAGS) -MT gmap_ssse3-chrom.o -MD -MP -MF $(DEPDIR)/gmap_ssse3-chrom.Tpo -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
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+
+gmap_ssse3-chrom.obj: chrom.c
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+
+gmap_ssse3-segmentpos.o: segmentpos.c
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+
+gmap_ssse3-segmentpos.obj: segmentpos.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-segmentpos.Tpo $(DEPDIR)/gmap_ssse3-segmentpos.Po
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+
+gmap_ssse3-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_ssse3_CFLAGS) $(CFLAGS) -MT gmap_ssse3-chrnum.o -MD -MP -MF $(DEPDIR)/gmap_ssse3-chrnum.Tpo -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-chrnum.Tpo $(DEPDIR)/gmap_ssse3-chrnum.Po
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+
+gmap_ssse3-chrnum.obj: chrnum.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-chrnum.Tpo $(DEPDIR)/gmap_ssse3-chrnum.Po
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+
+gmap_ssse3-uinttable.o: uinttable.c
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+gmap_ssse3-uinttable.obj: uinttable.c
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+
+gmap_ssse3-gregion.obj: gregion.c
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+gmap_ssse3-match.o: match.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-match.Tpo $(DEPDIR)/gmap_ssse3-match.Po
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+
+gmap_ssse3-match.obj: match.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-match.Tpo $(DEPDIR)/gmap_ssse3-match.Po
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+
+gmap_ssse3-matchpool.o: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_ssse3_CFLAGS) $(CFLAGS) -MT gmap_ssse3-matchpool.o -MD -MP -MF $(DEPDIR)/gmap_ssse3-matchpool.Tpo -c -o gmap_ssse3-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmap_ssse3-matchpool.Tpo $(DEPDIR)/gmap_ssse3-matchpool.Po
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+
+gmap_ssse3-matchpool.obj: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_ssse3_CFLAGS) $(CFLAGS) -MT gmap_ssse3-matchpool.obj -MD -MP -MF $(DEPDIR)/gmap_ssse3-matchpool.Tpo -c -o gmap_ssse3-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
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+gmap_ssse3-diagnostic.o: diagnostic.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmap_ssse3_CFLAGS) $(CFLAGS) -MT gmap_ssse3-diagnostic.o -MD -MP -MF $(DEPDIR)/gmap_ssse3-diagnostic.Tpo -c -o gmap_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
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+
+gmap_ssse3-diagnostic.obj: diagnostic.c
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+gmap_ssse3-stage1.o: stage1.c
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+gmap_ssse3-stage1.obj: stage1.c
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+gmap_ssse3-splicetrie.o: splicetrie.c
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+gmap_ssse3-dynprog.obj: dynprog.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-stopwatch.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-stopwatch.Tpo -c -o gmapl_avx2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-stopwatch.Tpo $(DEPDIR)/gmapl_avx2-stopwatch.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+
+gmapl_avx2-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-semaphore.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-semaphore.Tpo -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-semaphore.Tpo $(DEPDIR)/gmapl_avx2-semaphore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+gmapl_avx2-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-semaphore.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-semaphore.Tpo -c -o gmapl_avx2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-semaphore.Tpo $(DEPDIR)/gmapl_avx2-semaphore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
+gmapl_avx2-access.o: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-access.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-access.Tpo -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-access.Tpo $(DEPDIR)/gmapl_avx2-access.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+
+gmapl_avx2-access.obj: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-access.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-access.Tpo -c -o gmapl_avx2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-access.Tpo $(DEPDIR)/gmapl_avx2-access.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+
+gmapl_avx2-filestring.o: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-filestring.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-filestring.Tpo -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-filestring.Tpo $(DEPDIR)/gmapl_avx2-filestring.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+
+gmapl_avx2-filestring.obj: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-filestring.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-filestring.Tpo -c -o gmapl_avx2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-filestring.Tpo $(DEPDIR)/gmapl_avx2-filestring.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+
+gmapl_avx2-iit-read-univ.o: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-iit-read-univ.Tpo -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-iit-read-univ.Tpo $(DEPDIR)/gmapl_avx2-iit-read-univ.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-iit-read-univ.Tpo -c -o gmapl_avx2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-iit-read-univ.Tpo $(DEPDIR)/gmapl_avx2-iit-read-univ.Po
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+
+gmapl_avx2-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-iit-read.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-iit-read.Tpo -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-iit-read.Tpo $(DEPDIR)/gmapl_avx2-iit-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+
+gmapl_avx2-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-iit-read.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-iit-read.Tpo -c -o gmapl_avx2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-iit-read.Tpo $(DEPDIR)/gmapl_avx2-iit-read.Po
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+
+gmapl_avx2-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-md5.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-md5.Tpo -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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+gmapl_avx2-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-md5.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-md5.Tpo -c -o gmapl_avx2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-md5.Tpo $(DEPDIR)/gmapl_avx2-md5.Po
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+gmapl_avx2-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-bzip2.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-bzip2.Tpo -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
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+gmapl_avx2-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-bzip2.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-bzip2.Tpo -c -o gmapl_avx2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-bzip2.Tpo $(DEPDIR)/gmapl_avx2-bzip2.Po
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+gmapl_avx2-sequence.o: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-sequence.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-sequence.Tpo -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-sequence.Tpo $(DEPDIR)/gmapl_avx2-sequence.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
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+gmapl_avx2-sequence.obj: sequence.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-sequence.Tpo $(DEPDIR)/gmapl_avx2-sequence.Po
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+gmapl_avx2-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-reader.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-reader.Tpo -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-uinttable.Tpo $(DEPDIR)/gmapl_avx2-uinttable.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmapl_avx2-uinttable.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
+
+gmapl_avx2-gregion.o: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-gregion.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-gregion.Tpo -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-gregion.Tpo $(DEPDIR)/gmapl_avx2-gregion.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
+
+gmapl_avx2-gregion.obj: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-gregion.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-gregion.Tpo -c -o gmapl_avx2-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-gregion.Tpo $(DEPDIR)/gmapl_avx2-gregion.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
+
+gmapl_avx2-match.o: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-match.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-match.Tpo -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-match.Tpo $(DEPDIR)/gmapl_avx2-match.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
+
+gmapl_avx2-match.obj: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-match.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-match.Tpo -c -o gmapl_avx2-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-match.Tpo $(DEPDIR)/gmapl_avx2-match.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
+
+gmapl_avx2-matchpool.o: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-matchpool.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-matchpool.Tpo -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-matchpool.Tpo $(DEPDIR)/gmapl_avx2-matchpool.Po
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+
+gmapl_avx2-matchpool.obj: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-matchpool.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-matchpool.Tpo -c -o gmapl_avx2-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-matchpool.Tpo $(DEPDIR)/gmapl_avx2-matchpool.Po
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+
+gmapl_avx2-diagnostic.o: diagnostic.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-diagnostic.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-diagnostic.Tpo -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-diagnostic.Tpo $(DEPDIR)/gmapl_avx2-diagnostic.Po
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+
+gmapl_avx2-diagnostic.obj: diagnostic.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-diagnostic.Tpo $(DEPDIR)/gmapl_avx2-diagnostic.Po
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+
+gmapl_avx2-stage1.o: stage1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-stage1.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-stage1.Tpo -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
+
+gmapl_avx2-stage1.obj: stage1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-stage1.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-stage1.Tpo -c -o gmapl_avx2-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-stage1.Tpo $(DEPDIR)/gmapl_avx2-stage1.Po
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+
+gmapl_avx2-diag.o: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-diag.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-diag.Tpo -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-diag.Tpo $(DEPDIR)/gmapl_avx2-diag.Po
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+
+gmapl_avx2-diag.obj: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-diag.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-diag.Tpo -c -o gmapl_avx2-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-diag.Tpo $(DEPDIR)/gmapl_avx2-diag.Po
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+
+gmapl_avx2-diagpool.o: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-diagpool.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-diagpool.Tpo -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-diagpool.Tpo $(DEPDIR)/gmapl_avx2-diagpool.Po
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+
+gmapl_avx2-diagpool.obj: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-diagpool.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-diagpool.Tpo -c -o gmapl_avx2-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-diagpool.Tpo $(DEPDIR)/gmapl_avx2-diagpool.Po
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+
+gmapl_avx2-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-cmet.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-cmet.Tpo -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-cmet.Tpo $(DEPDIR)/gmapl_avx2-cmet.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
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+gmapl_avx2-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-cmet.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-cmet.Tpo -c -o gmapl_avx2-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-cmet.Tpo $(DEPDIR)/gmapl_avx2-cmet.Po
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+gmapl_avx2-atoi.o: atoi.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-atoi.Tpo $(DEPDIR)/gmapl_avx2-atoi.Po
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-atoi.Tpo $(DEPDIR)/gmapl_avx2-atoi.Po
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+
+gmapl_avx2-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-orderstat.Tpo -c -o gmapl_avx2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-oligoindex_hr.Tpo -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-oligoindex_hr.Tpo $(DEPDIR)/gmapl_avx2-oligoindex_hr.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-oligoindex_hr.Tpo -c -o gmapl_avx2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-oligoindex_hr.Tpo $(DEPDIR)/gmapl_avx2-oligoindex_hr.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-intron.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-intron.Tpo -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
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+gmapl_avx2-intron.obj: intron.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-maxent.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-maxent.Tpo -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-maxent.Tpo $(DEPDIR)/gmapl_avx2-maxent.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-maxent_hr.Tpo -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-maxent_hr.Tpo $(DEPDIR)/gmapl_avx2-maxent_hr.Po
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+
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+
+gmapl_avx2-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-pairpool.Tpo -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
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+gmapl_avx2-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-pairpool.Tpo -c -o gmapl_avx2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-pairpool.Tpo $(DEPDIR)/gmapl_avx2-pairpool.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-cellpool.Tpo -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
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+gmapl_avx2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-cellpool.Tpo -c -o gmapl_avx2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-cellpool.Tpo $(DEPDIR)/gmapl_avx2-cellpool.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-stage2.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-stage2.Tpo -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-doublelist.Tpo -c -o gmapl_avx2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-doublelist.Tpo $(DEPDIR)/gmapl_avx2-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_avx2-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmapl_avx2-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-smooth.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-smooth.Tpo -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-smooth.Tpo $(DEPDIR)/gmapl_avx2-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_avx2-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmapl_avx2-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-smooth.Tpo -c -o gmapl_avx2-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-smooth.Tpo $(DEPDIR)/gmapl_avx2-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_avx2-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmapl_avx2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-splicestringpool.Tpo -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-splicestringpool.Tpo $(DEPDIR)/gmapl_avx2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_avx2-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmapl_avx2-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-splicestringpool.Tpo -c -o gmapl_avx2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-splicestringpool.Tpo $(DEPDIR)/gmapl_avx2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_avx2-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmapl_avx2-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-splicetrie_build.Tpo -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-splicetrie_build.Tpo $(DEPDIR)/gmapl_avx2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_avx2-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmapl_avx2-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-splicetrie_build.Tpo -c -o gmapl_avx2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-splicetrie_build.Tpo $(DEPDIR)/gmapl_avx2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_avx2-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gmapl_avx2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-splicetrie.Tpo -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-splicetrie.Tpo $(DEPDIR)/gmapl_avx2-splicetrie.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmapl_avx2-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-splicetrie.Tpo -c -o gmapl_avx2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-splicetrie.Tpo $(DEPDIR)/gmapl_avx2-splicetrie.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmapl_avx2-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-boyer-moore.Tpo -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-boyer-moore.Tpo $(DEPDIR)/gmapl_avx2-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_avx2-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmapl_avx2-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-boyer-moore.Tpo -c -o gmapl_avx2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-boyer-moore.Tpo $(DEPDIR)/gmapl_avx2-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_avx2-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmapl_avx2-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog.Tpo -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog.Tpo $(DEPDIR)/gmapl_avx2-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_avx2-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmapl_avx2-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog.Tpo -c -o gmapl_avx2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog.Tpo $(DEPDIR)/gmapl_avx2-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_avx2-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmapl_avx2-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog_simd.Tpo -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog_simd.Tpo $(DEPDIR)/gmapl_avx2-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_avx2-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmapl_avx2-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog_simd.Tpo -c -o gmapl_avx2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog_simd.Tpo $(DEPDIR)/gmapl_avx2-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_avx2-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmapl_avx2-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog_single.Tpo -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog_single.Tpo $(DEPDIR)/gmapl_avx2-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmapl_avx2-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog_single.Tpo -c -o gmapl_avx2-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog_single.Tpo $(DEPDIR)/gmapl_avx2-dynprog_single.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gmapl_avx2-dynprog_genome.o: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-dynprog_genome.Tpo -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_avx2-dynprog_genome.Tpo $(DEPDIR)/gmapl_avx2-dynprog_genome.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-samheader.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-samheader.Tpo -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
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+gmapl_avx2-samheader.obj: samheader.c
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+gmapl_avx2-outbuffer.obj: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-outbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-outbuffer.Tpo -c -o gmapl_avx2-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-chimera.o -MD -MP -MF $(DEPDIR)/gmapl_avx2-chimera.Tpo -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
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+gmapl_avx2-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_avx2_CFLAGS) $(CFLAGS) -MT gmapl_avx2-chimera.obj -MD -MP -MF $(DEPDIR)/gmapl_avx2-chimera.Tpo -c -o gmapl_avx2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
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+gmapl_avx2-parserange.o: parserange.c
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+gmapl_avx2-getopt.obj: getopt.c
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+gmapl_avx2-getopt1.o: getopt1.c
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+gmapl_avx2-getopt1.obj: getopt1.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-except.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-except.Tpo -c -o gmapl_nosimd-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-except.Tpo $(DEPDIR)/gmapl_nosimd-except.Po
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+
+gmapl_nosimd-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-assert.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-assert.Tpo -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-assert.Tpo $(DEPDIR)/gmapl_nosimd-assert.Po
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+
+gmapl_nosimd-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-assert.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-assert.Tpo -c -o gmapl_nosimd-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-assert.Tpo $(DEPDIR)/gmapl_nosimd-assert.Po
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+
+gmapl_nosimd-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-mem.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-mem.Tpo -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-mem.Tpo $(DEPDIR)/gmapl_nosimd-mem.Po
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+
+gmapl_nosimd-mem.obj: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-mem.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-mem.Tpo -c -o gmapl_nosimd-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-mem.Tpo $(DEPDIR)/gmapl_nosimd-mem.Po
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+
+gmapl_nosimd-intlist.o: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-intlist.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-intlist.Tpo -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-intlist.Tpo $(DEPDIR)/gmapl_nosimd-intlist.Po
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+
+gmapl_nosimd-intlist.obj: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-intlist.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-intlist.Tpo -c -o gmapl_nosimd-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-intlist.Tpo $(DEPDIR)/gmapl_nosimd-intlist.Po
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+
+gmapl_nosimd-list.o: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-list.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-list.Tpo -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-list.Tpo $(DEPDIR)/gmapl_nosimd-list.Po
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+gmapl_nosimd-list.obj: list.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-list.Tpo $(DEPDIR)/gmapl_nosimd-list.Po
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+
+gmapl_nosimd-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-littleendian.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-littleendian.Tpo -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
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+
+gmapl_nosimd-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-littleendian.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-littleendian.Tpo -c -o gmapl_nosimd-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-littleendian.Tpo $(DEPDIR)/gmapl_nosimd-littleendian.Po
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+
+gmapl_nosimd-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-bigendian.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-bigendian.Tpo -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
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+
+gmapl_nosimd-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-bigendian.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-bigendian.Tpo -c -o gmapl_nosimd-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-bigendian.Tpo $(DEPDIR)/gmapl_nosimd-bigendian.Po
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+
+gmapl_nosimd-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-univinterval.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-univinterval.Tpo -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-univinterval.Tpo $(DEPDIR)/gmapl_nosimd-univinterval.Po
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+
+gmapl_nosimd-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-univinterval.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-univinterval.Tpo -c -o gmapl_nosimd-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-univinterval.Tpo $(DEPDIR)/gmapl_nosimd-univinterval.Po
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+
+gmapl_nosimd-interval.o: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-interval.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-interval.Tpo -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-interval.Tpo $(DEPDIR)/gmapl_nosimd-interval.Po
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+
+gmapl_nosimd-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-interval.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-interval.Tpo -c -o gmapl_nosimd-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-interval.Tpo $(DEPDIR)/gmapl_nosimd-interval.Po
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+gmapl_nosimd-uintlist.o: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-uintlist.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-uintlist.Tpo -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-uintlist.Tpo $(DEPDIR)/gmapl_nosimd-uintlist.Po
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+
+gmapl_nosimd-uintlist.obj: uintlist.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-uintlist.Tpo $(DEPDIR)/gmapl_nosimd-uintlist.Po
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+gmapl_nosimd-stopwatch.o: stopwatch.c
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+gmapl_nosimd-stopwatch.obj: stopwatch.c
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+gmapl_nosimd-access.o: access.c
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+gmapl_nosimd-filestring.o: filestring.c
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+gmapl_nosimd-md5.o: md5.c
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+gmapl_nosimd-bzip2.o: bzip2.c
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+gmapl_nosimd-bzip2.obj: bzip2.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-uinttable.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-uinttable.Tpo -c -o gmapl_nosimd-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-uinttable.Tpo $(DEPDIR)/gmapl_nosimd-uinttable.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmapl_nosimd-uinttable.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-uinttable.o `test -f 'uinttable.c' || echo '$(srcdir)/'`uinttable.c
+
+gmapl_nosimd-uinttable.obj: uinttable.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-uinttable.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-uinttable.Tpo -c -o gmapl_nosimd-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-uinttable.Tpo $(DEPDIR)/gmapl_nosimd-uinttable.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uinttable.c' object='gmapl_nosimd-uinttable.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-uinttable.obj `if test -f 'uinttable.c'; then $(CYGPATH_W) 'uinttable.c'; else $(CYGPATH_W) '$(srcdir)/uinttable.c'; fi`
+
+gmapl_nosimd-gregion.o: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-gregion.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-gregion.Tpo -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-gregion.Tpo $(DEPDIR)/gmapl_nosimd-gregion.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmapl_nosimd-gregion.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '$(srcdir)/'`gregion.c
+
+gmapl_nosimd-gregion.obj: gregion.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-gregion.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-gregion.Tpo -c -o gmapl_nosimd-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-gregion.Tpo $(DEPDIR)/gmapl_nosimd-gregion.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gregion.c' object='gmapl_nosimd-gregion.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-gregion.obj `if test -f 'gregion.c'; then $(CYGPATH_W) 'gregion.c'; else $(CYGPATH_W) '$(srcdir)/gregion.c'; fi`
+
+gmapl_nosimd-match.o: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-match.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-match.Tpo -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-match.Tpo $(DEPDIR)/gmapl_nosimd-match.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmapl_nosimd-match.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '$(srcdir)/'`match.c
+
+gmapl_nosimd-match.obj: match.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-match.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-match.Tpo -c -o gmapl_nosimd-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-match.Tpo $(DEPDIR)/gmapl_nosimd-match.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='match.c' object='gmapl_nosimd-match.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-match.obj `if test -f 'match.c'; then $(CYGPATH_W) 'match.c'; else $(CYGPATH_W) '$(srcdir)/match.c'; fi`
+
+gmapl_nosimd-matchpool.o: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-matchpool.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-matchpool.Tpo -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-matchpool.Tpo $(DEPDIR)/gmapl_nosimd-matchpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmapl_nosimd-matchpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '$(srcdir)/'`matchpool.c
+
+gmapl_nosimd-matchpool.obj: matchpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-matchpool.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-matchpool.Tpo -c -o gmapl_nosimd-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-matchpool.Tpo $(DEPDIR)/gmapl_nosimd-matchpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='matchpool.c' object='gmapl_nosimd-matchpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-matchpool.obj `if test -f 'matchpool.c'; then $(CYGPATH_W) 'matchpool.c'; else $(CYGPATH_W) '$(srcdir)/matchpool.c'; fi`
+
+gmapl_nosimd-diagnostic.o: diagnostic.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-diagnostic.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-diagnostic.Tpo -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-diagnostic.Tpo $(DEPDIR)/gmapl_nosimd-diagnostic.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagnostic.c' object='gmapl_nosimd-diagnostic.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '$(srcdir)/'`diagnostic.c
+
+gmapl_nosimd-diagnostic.obj: diagnostic.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-diagnostic.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-diagnostic.Tpo -c -o gmapl_nosimd-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-diagnostic.Tpo $(DEPDIR)/gmapl_nosimd-diagnostic.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-diagnostic.obj `if test -f 'diagnostic.c'; then $(CYGPATH_W) 'diagnostic.c'; else $(CYGPATH_W) '$(srcdir)/diagnostic.c'; fi`
+
+gmapl_nosimd-stage1.o: stage1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-stage1.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-stage1.Tpo -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-stage1.Tpo $(DEPDIR)/gmapl_nosimd-stage1.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1.c' object='gmapl_nosimd-stage1.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '$(srcdir)/'`stage1.c
+
+gmapl_nosimd-stage1.obj: stage1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-stage1.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-stage1.Tpo -c -o gmapl_nosimd-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-stage1.Tpo $(DEPDIR)/gmapl_nosimd-stage1.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-stage1.obj `if test -f 'stage1.c'; then $(CYGPATH_W) 'stage1.c'; else $(CYGPATH_W) '$(srcdir)/stage1.c'; fi`
+
+gmapl_nosimd-diag.o: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-diag.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-diag.Tpo -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-diag.Tpo $(DEPDIR)/gmapl_nosimd-diag.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmapl_nosimd-diag.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+
+gmapl_nosimd-diag.obj: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-diag.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-diag.Tpo -c -o gmapl_nosimd-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-diag.Tpo $(DEPDIR)/gmapl_nosimd-diag.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diag.c' object='gmapl_nosimd-diag.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+
+gmapl_nosimd-diagpool.o: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-diagpool.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-diagpool.Tpo -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-diagpool.Tpo $(DEPDIR)/gmapl_nosimd-diagpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmapl_nosimd-diagpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+
+gmapl_nosimd-diagpool.obj: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-diagpool.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-diagpool.Tpo -c -o gmapl_nosimd-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-diagpool.Tpo $(DEPDIR)/gmapl_nosimd-diagpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gmapl_nosimd-diagpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+
+gmapl_nosimd-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-cmet.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-cmet.Tpo -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-cmet.Tpo $(DEPDIR)/gmapl_nosimd-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmapl_nosimd-cmet.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gmapl_nosimd-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-cmet.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-cmet.Tpo -c -o gmapl_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-cmet.Tpo $(DEPDIR)/gmapl_nosimd-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gmapl_nosimd-cmet.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+
+gmapl_nosimd-atoi.o: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-atoi.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-atoi.Tpo -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-atoi.Tpo $(DEPDIR)/gmapl_nosimd-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmapl_nosimd-atoi.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+
+gmapl_nosimd-atoi.obj: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-atoi.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-atoi.Tpo -c -o gmapl_nosimd-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-atoi.Tpo $(DEPDIR)/gmapl_nosimd-atoi.Po
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-orderstat.Tpo $(DEPDIR)/gmapl_nosimd-orderstat.Po
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+
+gmapl_nosimd-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-orderstat.Tpo -c -o gmapl_nosimd-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-orderstat.Tpo $(DEPDIR)/gmapl_nosimd-orderstat.Po
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+
+gmapl_nosimd-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-oligoindex_hr.Tpo -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-oligoindex_hr.Tpo $(DEPDIR)/gmapl_nosimd-oligoindex_hr.Po
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+
+gmapl_nosimd-oligoindex_hr.obj: oligoindex_hr.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-oligoindex_hr.Tpo $(DEPDIR)/gmapl_nosimd-oligoindex_hr.Po
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+
+gmapl_nosimd-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-intron.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-intron.Tpo -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-intron.Tpo $(DEPDIR)/gmapl_nosimd-intron.Po
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+
+gmapl_nosimd-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-intron.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-intron.Tpo -c -o gmapl_nosimd-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
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+
+gmapl_nosimd-maxent.o: maxent.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-maxent.Tpo $(DEPDIR)/gmapl_nosimd-maxent.Po
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+gmapl_nosimd-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-maxent.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-maxent.Tpo -c -o gmapl_nosimd-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
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+
+gmapl_nosimd-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-maxent_hr.Tpo -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
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+
+gmapl_nosimd-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-maxent_hr.Tpo -c -o gmapl_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-maxent_hr.Tpo $(DEPDIR)/gmapl_nosimd-maxent_hr.Po
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+
+gmapl_nosimd-pair.o: pair.c
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-pair.Tpo $(DEPDIR)/gmapl_nosimd-pair.Po
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+
+gmapl_nosimd-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-pairpool.Tpo -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-pairpool.Tpo $(DEPDIR)/gmapl_nosimd-pairpool.Po
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+
+gmapl_nosimd-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-pairpool.Tpo -c -o gmapl_nosimd-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-pairpool.Tpo $(DEPDIR)/gmapl_nosimd-pairpool.Po
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+
+gmapl_nosimd-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-cellpool.Tpo -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-cellpool.Tpo $(DEPDIR)/gmapl_nosimd-cellpool.Po
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+
+gmapl_nosimd-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-cellpool.Tpo -c -o gmapl_nosimd-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-cellpool.Tpo $(DEPDIR)/gmapl_nosimd-cellpool.Po
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+gmapl_nosimd-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-stage2.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-stage2.Tpo -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-doublelist.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-doublelist.Tpo -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-doublelist.Tpo $(DEPDIR)/gmapl_nosimd-doublelist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmapl_nosimd-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-doublelist.Tpo -c -o gmapl_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-doublelist.Tpo $(DEPDIR)/gmapl_nosimd-doublelist.Po
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+
+gmapl_nosimd-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-smooth.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-smooth.Tpo -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-smooth.Tpo $(DEPDIR)/gmapl_nosimd-smooth.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmapl_nosimd-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-smooth.Tpo -c -o gmapl_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-smooth.Tpo $(DEPDIR)/gmapl_nosimd-smooth.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmapl_nosimd-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-splicestringpool.Tpo -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-splicestringpool.Tpo $(DEPDIR)/gmapl_nosimd-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_nosimd-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmapl_nosimd-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-splicestringpool.Tpo -c -o gmapl_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-splicestringpool.Tpo $(DEPDIR)/gmapl_nosimd-splicestringpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmapl_nosimd-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-splicetrie_build.Tpo -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-splicetrie_build.Tpo $(DEPDIR)/gmapl_nosimd-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_nosimd-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmapl_nosimd-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-splicetrie_build.Tpo -c -o gmapl_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-splicetrie_build.Tpo $(DEPDIR)/gmapl_nosimd-splicetrie_build.Po
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+
+gmapl_nosimd-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-splicetrie.Tpo -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-splicetrie.Tpo $(DEPDIR)/gmapl_nosimd-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmapl_nosimd-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-splicetrie.Tpo -c -o gmapl_nosimd-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-splicetrie.Tpo $(DEPDIR)/gmapl_nosimd-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmapl_nosimd-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-boyer-moore.Tpo -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-boyer-moore.Tpo $(DEPDIR)/gmapl_nosimd-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmapl_nosimd-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-boyer-moore.Tpo -c -o gmapl_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-boyer-moore.Tpo $(DEPDIR)/gmapl_nosimd-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmapl_nosimd-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog.Tpo -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog.Tpo $(DEPDIR)/gmapl_nosimd-dynprog.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmapl_nosimd-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog.Tpo -c -o gmapl_nosimd-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog.Tpo $(DEPDIR)/gmapl_nosimd-dynprog.Po
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+
+gmapl_nosimd-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog_simd.Tpo -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog_simd.Tpo $(DEPDIR)/gmapl_nosimd-dynprog_simd.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
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+gmapl_nosimd-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog_simd.Tpo -c -o gmapl_nosimd-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog_simd.Tpo $(DEPDIR)/gmapl_nosimd-dynprog_simd.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmapl_nosimd-dynprog_single.o: dynprog_single.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
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+gmapl_nosimd-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog_single.Tpo -c -o gmapl_nosimd-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog_single.Tpo $(DEPDIR)/gmapl_nosimd-dynprog_single.Po
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+
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+
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+
+gmapl_nosimd-dynprog_cdna.o: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog_cdna.Tpo -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gmapl_nosimd-dynprog_cdna.Po
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+
+gmapl_nosimd-dynprog_cdna.obj: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog_cdna.Tpo -c -o gmapl_nosimd-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gmapl_nosimd-dynprog_cdna.Po
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+
+gmapl_nosimd-dynprog_end.o: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-dynprog_end.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-dynprog_end.Tpo -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
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+
+gmapl_nosimd-translation.o: translation.c
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+
+gmapl_nosimd-pbinom.o: pbinom.c
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+
+gmapl_nosimd-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-pbinom.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-pbinom.Tpo -c -o gmapl_nosimd-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
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+gmapl_nosimd-stage3.o: stage3.c
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+gmapl_nosimd-request.obj: request.c
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+gmapl_nosimd-result.o: result.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-output.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-output.Tpo -c -o gmapl_nosimd-output.obj `if test -f 'output.c'; then $(CYGPATH_W) 'output.c'; else $(CYGPATH_W) '$(srcdir)/output.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-output.Tpo $(DEPDIR)/gmapl_nosimd-output.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-output.obj `if test -f 'output.c'; then $(CYGPATH_W) 'output.c'; else $(CYGPATH_W) '$(srcdir)/output.c'; fi`
+
+gmapl_nosimd-inbuffer.o: inbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-inbuffer.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-inbuffer.Tpo -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-inbuffer.Tpo $(DEPDIR)/gmapl_nosimd-inbuffer.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
+
+gmapl_nosimd-inbuffer.obj: inbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-inbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-inbuffer.Tpo -c -o gmapl_nosimd-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-inbuffer.Tpo $(DEPDIR)/gmapl_nosimd-inbuffer.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-inbuffer.obj `if test -f 'inbuffer.c'; then $(CYGPATH_W) 'inbuffer.c'; else $(CYGPATH_W) '$(srcdir)/inbuffer.c'; fi`
+
+gmapl_nosimd-samheader.o: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-samheader.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-samheader.Tpo -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-samheader.Tpo $(DEPDIR)/gmapl_nosimd-samheader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gmapl_nosimd-samheader.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+
+gmapl_nosimd-samheader.obj: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-samheader.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-samheader.Tpo -c -o gmapl_nosimd-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-samheader.Tpo $(DEPDIR)/gmapl_nosimd-samheader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gmapl_nosimd-samheader.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
+
+gmapl_nosimd-outbuffer.o: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-outbuffer.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-outbuffer.Tpo -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-outbuffer.Tpo $(DEPDIR)/gmapl_nosimd-outbuffer.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
+
+gmapl_nosimd-outbuffer.obj: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-outbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-outbuffer.Tpo -c -o gmapl_nosimd-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-outbuffer.Tpo $(DEPDIR)/gmapl_nosimd-outbuffer.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='outbuffer.c' object='gmapl_nosimd-outbuffer.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
+
+gmapl_nosimd-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-chimera.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-chimera.Tpo -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-chimera.Tpo $(DEPDIR)/gmapl_nosimd-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gmapl_nosimd-chimera.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gmapl_nosimd-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-chimera.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-chimera.Tpo -c -o gmapl_nosimd-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-chimera.Tpo $(DEPDIR)/gmapl_nosimd-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gmapl_nosimd-chimera.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gmapl_nosimd-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-datadir.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-datadir.Tpo -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-datadir.Tpo $(DEPDIR)/gmapl_nosimd-datadir.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+
+gmapl_nosimd-datadir.obj: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-datadir.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-datadir.Tpo -c -o gmapl_nosimd-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-datadir.Tpo $(DEPDIR)/gmapl_nosimd-datadir.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='datadir.c' object='gmapl_nosimd-datadir.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+
+gmapl_nosimd-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-parserange.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-parserange.Tpo -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-parserange.Tpo $(DEPDIR)/gmapl_nosimd-parserange.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+gmapl_nosimd-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-parserange.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-parserange.Tpo -c -o gmapl_nosimd-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-parserange.Tpo $(DEPDIR)/gmapl_nosimd-parserange.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
+gmapl_nosimd-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-getopt.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-getopt.Tpo -c -o gmapl_nosimd-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-getopt.Tpo $(DEPDIR)/gmapl_nosimd-getopt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='getopt.c' object='gmapl_nosimd-getopt.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+
+gmapl_nosimd-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-getopt.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-getopt.Tpo -c -o gmapl_nosimd-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-getopt.Tpo $(DEPDIR)/gmapl_nosimd-getopt.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+
+gmapl_nosimd-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-getopt1.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-getopt1.Tpo -c -o gmapl_nosimd-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-getopt1.Tpo $(DEPDIR)/gmapl_nosimd-getopt1.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+
+gmapl_nosimd-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-getopt1.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-getopt1.Tpo -c -o gmapl_nosimd-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-getopt1.Tpo $(DEPDIR)/gmapl_nosimd-getopt1.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+
+gmapl_nosimd-gmap.o: gmap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-gmap.o -MD -MP -MF $(DEPDIR)/gmapl_nosimd-gmap.Tpo -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-gmap.Tpo $(DEPDIR)/gmapl_nosimd-gmap.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
+
+gmapl_nosimd-gmap.obj: gmap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -MT gmapl_nosimd-gmap.obj -MD -MP -MF $(DEPDIR)/gmapl_nosimd-gmap.Tpo -c -o gmapl_nosimd-gmap.obj `if test -f 'gmap.c'; then $(CYGPATH_W) 'gmap.c'; else $(CYGPATH_W) '$(srcdir)/gmap.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_nosimd-gmap.Tpo $(DEPDIR)/gmapl_nosimd-gmap.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gmap.c' object='gmapl_nosimd-gmap.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_nosimd_CFLAGS) $(CFLAGS) -c -o gmapl_nosimd-gmap.obj `if test -f 'gmap.c'; then $(CYGPATH_W) 'gmap.c'; else $(CYGPATH_W) '$(srcdir)/gmap.c'; fi`
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-atoi.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-atoi.Tpo -c -o gmapl_sse2-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-atoi.Tpo $(DEPDIR)/gmapl_sse2-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmapl_sse2-atoi.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+
+gmapl_sse2-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-orderstat.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-orderstat.Tpo -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-orderstat.Tpo $(DEPDIR)/gmapl_sse2-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmapl_sse2-orderstat.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+
+gmapl_sse2-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-orderstat.Tpo -c -o gmapl_sse2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-orderstat.Tpo $(DEPDIR)/gmapl_sse2-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmapl_sse2-orderstat.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+
+gmapl_sse2-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-oligoindex_hr.Tpo -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-oligoindex_hr.Tpo $(DEPDIR)/gmapl_sse2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl_sse2-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gmapl_sse2-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-oligoindex_hr.Tpo -c -o gmapl_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-oligoindex_hr.Tpo $(DEPDIR)/gmapl_sse2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl_sse2-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gmapl_sse2-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-intron.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-intron.Tpo -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-intron.Tpo $(DEPDIR)/gmapl_sse2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmapl_sse2-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gmapl_sse2-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-intron.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-intron.Tpo -c -o gmapl_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-intron.Tpo $(DEPDIR)/gmapl_sse2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmapl_sse2-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gmapl_sse2-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-maxent.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-maxent.Tpo -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-maxent.Tpo $(DEPDIR)/gmapl_sse2-maxent.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+
+gmapl_sse2-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-maxent.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-maxent.Tpo -c -o gmapl_sse2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-maxent.Tpo $(DEPDIR)/gmapl_sse2-maxent.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+
+gmapl_sse2-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-maxent_hr.Tpo -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-maxent_hr.Tpo $(DEPDIR)/gmapl_sse2-maxent_hr.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gmapl_sse2-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-maxent_hr.Tpo -c -o gmapl_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-maxent_hr.Tpo $(DEPDIR)/gmapl_sse2-maxent_hr.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gmapl_sse2-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-pair.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-pair.Tpo -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-pair.Tpo $(DEPDIR)/gmapl_sse2-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmapl_sse2-pair.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmapl_sse2-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-pair.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-pair.Tpo -c -o gmapl_sse2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-pair.Tpo $(DEPDIR)/gmapl_sse2-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmapl_sse2-pair.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+
+gmapl_sse2-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-pairpool.Tpo -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-pairpool.Tpo $(DEPDIR)/gmapl_sse2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl_sse2-pairpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmapl_sse2-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-pairpool.Tpo -c -o gmapl_sse2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-pairpool.Tpo $(DEPDIR)/gmapl_sse2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl_sse2-pairpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gmapl_sse2-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-cellpool.Tpo -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-cellpool.Tpo $(DEPDIR)/gmapl_sse2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmapl_sse2-cellpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gmapl_sse2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-cellpool.Tpo -c -o gmapl_sse2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-cellpool.Tpo $(DEPDIR)/gmapl_sse2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmapl_sse2-cellpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+gmapl_sse2-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-stage2.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-stage2.Tpo -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-stage2.Tpo $(DEPDIR)/gmapl_sse2-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmapl_sse2-stage2.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gmapl_sse2-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-stage2.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-stage2.Tpo -c -o gmapl_sse2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-stage2.Tpo $(DEPDIR)/gmapl_sse2-stage2.Po
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+
+gmapl_sse2-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-doublelist.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-doublelist.Tpo -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-doublelist.Tpo $(DEPDIR)/gmapl_sse2-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_sse2-doublelist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmapl_sse2-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-doublelist.Tpo -c -o gmapl_sse2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-doublelist.Tpo $(DEPDIR)/gmapl_sse2-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_sse2-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmapl_sse2-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-smooth.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-smooth.Tpo -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-smooth.Tpo $(DEPDIR)/gmapl_sse2-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_sse2-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmapl_sse2-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-smooth.Tpo -c -o gmapl_sse2-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-smooth.Tpo $(DEPDIR)/gmapl_sse2-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_sse2-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmapl_sse2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-splicestringpool.Tpo -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-splicestringpool.Tpo $(DEPDIR)/gmapl_sse2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_sse2-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmapl_sse2-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-splicestringpool.Tpo -c -o gmapl_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-splicestringpool.Tpo $(DEPDIR)/gmapl_sse2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_sse2-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmapl_sse2-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-splicetrie_build.Tpo -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-splicetrie_build.Tpo $(DEPDIR)/gmapl_sse2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_sse2-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmapl_sse2-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-splicetrie_build.Tpo -c -o gmapl_sse2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-splicetrie_build.Tpo $(DEPDIR)/gmapl_sse2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_sse2-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gmapl_sse2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-splicetrie.Tpo -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-splicetrie.Tpo $(DEPDIR)/gmapl_sse2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmapl_sse2-splicetrie.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmapl_sse2-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-splicetrie.Tpo -c -o gmapl_sse2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-splicetrie.Tpo $(DEPDIR)/gmapl_sse2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmapl_sse2-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmapl_sse2-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-boyer-moore.Tpo -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-boyer-moore.Tpo $(DEPDIR)/gmapl_sse2-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_sse2-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmapl_sse2-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-boyer-moore.Tpo -c -o gmapl_sse2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-boyer-moore.Tpo $(DEPDIR)/gmapl_sse2-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_sse2-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmapl_sse2-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-dynprog.Tpo -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-dynprog.Tpo $(DEPDIR)/gmapl_sse2-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_sse2-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmapl_sse2-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-dynprog.Tpo -c -o gmapl_sse2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-dynprog.Tpo $(DEPDIR)/gmapl_sse2-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_sse2-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmapl_sse2-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-dynprog_simd.Tpo -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-dynprog_simd.Tpo $(DEPDIR)/gmapl_sse2-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_sse2-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmapl_sse2-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-dynprog_simd.Tpo -c -o gmapl_sse2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-dynprog_simd.Tpo $(DEPDIR)/gmapl_sse2-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_sse2-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmapl_sse2-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-dynprog_single.Tpo -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-dynprog_single.Tpo $(DEPDIR)/gmapl_sse2-dynprog_single.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmapl_sse2-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-dynprog_single.Tpo -c -o gmapl_sse2-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-dynprog_single.Tpo $(DEPDIR)/gmapl_sse2-dynprog_single.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -c -o gmapl_sse2-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-output.Tpo $(DEPDIR)/gmapl_sse2-output.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-inbuffer.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-inbuffer.Tpo -c -o gmapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
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+
+gmapl_sse2-samheader.o: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-samheader.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-samheader.Tpo -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-samheader.Tpo $(DEPDIR)/gmapl_sse2-samheader.Po
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+
+gmapl_sse2-samheader.obj: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-samheader.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-samheader.Tpo -c -o gmapl_sse2-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-samheader.Tpo $(DEPDIR)/gmapl_sse2-samheader.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-outbuffer.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-outbuffer.Tpo -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-outbuffer.Tpo $(DEPDIR)/gmapl_sse2-outbuffer.Po
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+
+gmapl_sse2-outbuffer.obj: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-outbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-outbuffer.Tpo -c -o gmapl_sse2-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-outbuffer.Tpo $(DEPDIR)/gmapl_sse2-outbuffer.Po
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+
+gmapl_sse2-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-chimera.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-chimera.Tpo -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-chimera.Tpo $(DEPDIR)/gmapl_sse2-chimera.Po
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+
+gmapl_sse2-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-chimera.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-chimera.Tpo -c -o gmapl_sse2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
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+
+gmapl_sse2-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-datadir.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-datadir.Tpo -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-datadir.Tpo $(DEPDIR)/gmapl_sse2-datadir.Po
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+
+gmapl_sse2-datadir.obj: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-datadir.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-datadir.Tpo -c -o gmapl_sse2-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
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+
+gmapl_sse2-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-parserange.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-parserange.Tpo -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
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+gmapl_sse2-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-parserange.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-parserange.Tpo -c -o gmapl_sse2-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
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+
+gmapl_sse2-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-getopt.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-getopt.Tpo -c -o gmapl_sse2-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-getopt.Tpo $(DEPDIR)/gmapl_sse2-getopt.Po
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+
+gmapl_sse2-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-getopt.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-getopt.Tpo -c -o gmapl_sse2-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-getopt.Tpo $(DEPDIR)/gmapl_sse2-getopt.Po
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+
+gmapl_sse2-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-getopt1.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-getopt1.Tpo -c -o gmapl_sse2-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
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+gmapl_sse2-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-getopt1.obj -MD -MP -MF $(DEPDIR)/gmapl_sse2-getopt1.Tpo -c -o gmapl_sse2-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-getopt1.Tpo $(DEPDIR)/gmapl_sse2-getopt1.Po
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+gmapl_sse2-gmap.o: gmap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse2_CFLAGS) $(CFLAGS) -MT gmapl_sse2-gmap.o -MD -MP -MF $(DEPDIR)/gmapl_sse2-gmap.Tpo -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-gmap.Tpo $(DEPDIR)/gmapl_sse2-gmap.Po
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse2-gmap.Tpo $(DEPDIR)/gmapl_sse2-gmap.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-atoi.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-atoi.Tpo -c -o gmapl_sse41-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-atoi.Tpo $(DEPDIR)/gmapl_sse41-atoi.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+gmapl_sse41-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-orderstat.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-orderstat.Tpo -c -o gmapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-orderstat.Tpo $(DEPDIR)/gmapl_sse41-orderstat.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+
+gmapl_sse41-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-orderstat.Tpo -c -o gmapl_sse41-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-orderstat.Tpo $(DEPDIR)/gmapl_sse41-orderstat.Po
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+
+gmapl_sse41-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-oligoindex_hr.Tpo -c -o gmapl_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-oligoindex_hr.Tpo $(DEPDIR)/gmapl_sse41-oligoindex_hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gmapl_sse41-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-oligoindex_hr.Tpo -c -o gmapl_sse41-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-oligoindex_hr.Tpo $(DEPDIR)/gmapl_sse41-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl_sse41-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gmapl_sse41-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-intron.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-intron.Tpo -c -o gmapl_sse41-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-intron.Tpo $(DEPDIR)/gmapl_sse41-intron.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gmapl_sse41-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-intron.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-intron.Tpo -c -o gmapl_sse41-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-intron.Tpo $(DEPDIR)/gmapl_sse41-intron.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-maxent.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-maxent.Tpo -c -o gmapl_sse41-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-maxent.Tpo $(DEPDIR)/gmapl_sse41-maxent.Po
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+
+gmapl_sse41-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-maxent.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-maxent.Tpo -c -o gmapl_sse41-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-maxent.Tpo $(DEPDIR)/gmapl_sse41-maxent.Po
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+
+gmapl_sse41-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-maxent_hr.Tpo -c -o gmapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-maxent_hr.Tpo $(DEPDIR)/gmapl_sse41-maxent_hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gmapl_sse41-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-maxent_hr.Tpo -c -o gmapl_sse41-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-maxent_hr.Tpo $(DEPDIR)/gmapl_sse41-maxent_hr.Po
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+
+gmapl_sse41-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-pair.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-pair.Tpo -c -o gmapl_sse41-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-pair.Tpo $(DEPDIR)/gmapl_sse41-pair.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmapl_sse41-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-pair.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-pair.Tpo -c -o gmapl_sse41-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-pair.Tpo $(DEPDIR)/gmapl_sse41-pair.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+
+gmapl_sse41-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-pairpool.Tpo -c -o gmapl_sse41-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-pairpool.Tpo $(DEPDIR)/gmapl_sse41-pairpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmapl_sse41-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-pairpool.Tpo -c -o gmapl_sse41-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-pairpool.Tpo $(DEPDIR)/gmapl_sse41-pairpool.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gmapl_sse41-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-cellpool.Tpo -c -o gmapl_sse41-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-cellpool.Tpo $(DEPDIR)/gmapl_sse41-cellpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gmapl_sse41-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-cellpool.Tpo -c -o gmapl_sse41-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-cellpool.Tpo $(DEPDIR)/gmapl_sse41-cellpool.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-stage2.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-stage2.Tpo -c -o gmapl_sse41-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
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+gmapl_sse41-stage2.obj: stage2.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-stage2.Tpo $(DEPDIR)/gmapl_sse41-stage2.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-doublelist.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-doublelist.Tpo -c -o gmapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-doublelist.Tpo $(DEPDIR)/gmapl_sse41-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_sse41-doublelist.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmapl_sse41-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-doublelist.Tpo -c -o gmapl_sse41-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-doublelist.Tpo $(DEPDIR)/gmapl_sse41-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_sse41-doublelist.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmapl_sse41-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-smooth.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-smooth.Tpo -c -o gmapl_sse41-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-smooth.Tpo $(DEPDIR)/gmapl_sse41-smooth.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmapl_sse41-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-smooth.Tpo -c -o gmapl_sse41-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-smooth.Tpo $(DEPDIR)/gmapl_sse41-smooth.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmapl_sse41-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-splicestringpool.Tpo -c -o gmapl_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-splicestringpool.Tpo $(DEPDIR)/gmapl_sse41-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_sse41-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmapl_sse41-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-splicestringpool.Tpo -c -o gmapl_sse41-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-splicestringpool.Tpo $(DEPDIR)/gmapl_sse41-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_sse41-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmapl_sse41-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-splicetrie_build.Tpo -c -o gmapl_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-splicetrie_build.Tpo $(DEPDIR)/gmapl_sse41-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_sse41-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmapl_sse41-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-splicetrie_build.Tpo -c -o gmapl_sse41-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-splicetrie_build.Tpo $(DEPDIR)/gmapl_sse41-splicetrie_build.Po
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+
+gmapl_sse41-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-splicetrie.Tpo -c -o gmapl_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-splicetrie.Tpo $(DEPDIR)/gmapl_sse41-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmapl_sse41-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-splicetrie.Tpo -c -o gmapl_sse41-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-splicetrie.Tpo $(DEPDIR)/gmapl_sse41-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmapl_sse41-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-boyer-moore.Tpo -c -o gmapl_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-boyer-moore.Tpo $(DEPDIR)/gmapl_sse41-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_sse41-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-boyer-moore.Tpo -c -o gmapl_sse41-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-boyer-moore.Tpo $(DEPDIR)/gmapl_sse41-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmapl_sse41-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-dynprog.Tpo -c -o gmapl_sse41-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-dynprog.Tpo $(DEPDIR)/gmapl_sse41-dynprog.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmapl_sse41-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-dynprog.Tpo -c -o gmapl_sse41-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-dynprog.Tpo $(DEPDIR)/gmapl_sse41-dynprog.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmapl_sse41-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl_sse41-dynprog_simd.Tpo -c -o gmapl_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-dynprog_simd.Tpo $(DEPDIR)/gmapl_sse41-dynprog_simd.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmapl_sse41-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-dynprog_simd.Tpo -c -o gmapl_sse41-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-dynprog_simd.Tpo $(DEPDIR)/gmapl_sse41-dynprog_simd.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmapl_sse41-dynprog_single.o: dynprog_single.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-dynprog_single.Tpo $(DEPDIR)/gmapl_sse41-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmapl_sse41-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -MT gmapl_sse41-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl_sse41-dynprog_single.Tpo -c -o gmapl_sse41-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse41-dynprog_single.Tpo $(DEPDIR)/gmapl_sse41-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse41_CFLAGS) $(CFLAGS) -c -o gmapl_sse41-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
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+gmapl_sse42-univinterval.obj: univinterval.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-genome-write.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-genome-write.Tpo -c -o gmapl_sse42-genome-write.obj `if test -f 'genome-write.c'; then $(CYGPATH_W) 'genome-write.c'; else $(CYGPATH_W) '$(srcdir)/genome-write.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-genome-write.Tpo $(DEPDIR)/gmapl_sse42-genome-write.Po
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+
+gmapl_sse42-bitpack64-read.o: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-bitpack64-read.Tpo -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-bitpack64-read.Tpo $(DEPDIR)/gmapl_sse42-bitpack64-read.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-bitpack64-read.Tpo -c -o gmapl_sse42-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-bitpack64-read.Tpo $(DEPDIR)/gmapl_sse42-bitpack64-read.Po
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+
+gmapl_sse42-bitpack64-readtwo.o: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-bitpack64-readtwo.Tpo -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-bitpack64-readtwo.Tpo $(DEPDIR)/gmapl_sse42-bitpack64-readtwo.Po
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+
+gmapl_sse42-bitpack64-readtwo.obj: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-bitpack64-readtwo.Tpo -c -o gmapl_sse42-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-bitpack64-readtwo.Tpo $(DEPDIR)/gmapl_sse42-bitpack64-readtwo.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-indexdb.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-indexdb.Tpo -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
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+
+gmapl_sse42-indexdb.obj: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-indexdb.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-indexdb.Tpo -c -o gmapl_sse42-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-indexdb.Tpo $(DEPDIR)/gmapl_sse42-indexdb.Po
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+gmapl_sse42-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-indexdb_hr.Tpo -c -o gmapl_sse42-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
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+
+gmapl_sse42-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-indexdb_hr.Tpo -c -o gmapl_sse42-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
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+
+gmapl_sse42-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-oligo.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-oligo.Tpo -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-oligo.Tpo $(DEPDIR)/gmapl_sse42-oligo.Po
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+
+gmapl_sse42-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-oligo.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-oligo.Tpo -c -o gmapl_sse42-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-chrom.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-chrom.Tpo -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
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+
+gmapl_sse42-chrom.obj: chrom.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-atoi.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-atoi.Tpo -c -o gmapl_sse42-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-atoi.Tpo $(DEPDIR)/gmapl_sse42-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gmapl_sse42-atoi.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+
+gmapl_sse42-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-orderstat.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-orderstat.Tpo -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-orderstat.Tpo $(DEPDIR)/gmapl_sse42-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmapl_sse42-orderstat.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+
+gmapl_sse42-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-orderstat.Tpo -c -o gmapl_sse42-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-orderstat.Tpo $(DEPDIR)/gmapl_sse42-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gmapl_sse42-orderstat.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+
+gmapl_sse42-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-oligoindex_hr.Tpo -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-oligoindex_hr.Tpo $(DEPDIR)/gmapl_sse42-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl_sse42-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gmapl_sse42-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-oligoindex_hr.Tpo -c -o gmapl_sse42-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-oligoindex_hr.Tpo $(DEPDIR)/gmapl_sse42-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gmapl_sse42-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gmapl_sse42-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-intron.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-intron.Tpo -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-intron.Tpo $(DEPDIR)/gmapl_sse42-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmapl_sse42-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gmapl_sse42-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-intron.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-intron.Tpo -c -o gmapl_sse42-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-intron.Tpo $(DEPDIR)/gmapl_sse42-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gmapl_sse42-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gmapl_sse42-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-maxent.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-maxent.Tpo -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-maxent.Tpo $(DEPDIR)/gmapl_sse42-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmapl_sse42-maxent.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+
+gmapl_sse42-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-maxent.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-maxent.Tpo -c -o gmapl_sse42-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-maxent.Tpo $(DEPDIR)/gmapl_sse42-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gmapl_sse42-maxent.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+
+gmapl_sse42-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-maxent_hr.Tpo -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-maxent_hr.Tpo $(DEPDIR)/gmapl_sse42-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmapl_sse42-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gmapl_sse42-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-maxent_hr.Tpo -c -o gmapl_sse42-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-maxent_hr.Tpo $(DEPDIR)/gmapl_sse42-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gmapl_sse42-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gmapl_sse42-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-pair.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-pair.Tpo -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-pair.Tpo $(DEPDIR)/gmapl_sse42-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmapl_sse42-pair.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmapl_sse42-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-pair.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-pair.Tpo -c -o gmapl_sse42-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-pair.Tpo $(DEPDIR)/gmapl_sse42-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gmapl_sse42-pair.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+
+gmapl_sse42-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-pairpool.Tpo -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-pairpool.Tpo $(DEPDIR)/gmapl_sse42-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl_sse42-pairpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmapl_sse42-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-pairpool.Tpo -c -o gmapl_sse42-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-pairpool.Tpo $(DEPDIR)/gmapl_sse42-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl_sse42-pairpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gmapl_sse42-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-cellpool.Tpo -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-cellpool.Tpo $(DEPDIR)/gmapl_sse42-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmapl_sse42-cellpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gmapl_sse42-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-cellpool.Tpo -c -o gmapl_sse42-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-cellpool.Tpo $(DEPDIR)/gmapl_sse42-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gmapl_sse42-cellpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+
+gmapl_sse42-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-stage2.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-stage2.Tpo -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-stage2.Tpo $(DEPDIR)/gmapl_sse42-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmapl_sse42-stage2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gmapl_sse42-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-stage2.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-stage2.Tpo -c -o gmapl_sse42-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-stage2.Tpo $(DEPDIR)/gmapl_sse42-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gmapl_sse42-stage2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gmapl_sse42-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-doublelist.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-doublelist.Tpo -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-doublelist.Tpo $(DEPDIR)/gmapl_sse42-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_sse42-doublelist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmapl_sse42-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-doublelist.Tpo -c -o gmapl_sse42-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-doublelist.Tpo $(DEPDIR)/gmapl_sse42-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_sse42-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmapl_sse42-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-smooth.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-smooth.Tpo -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-smooth.Tpo $(DEPDIR)/gmapl_sse42-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_sse42-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmapl_sse42-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-smooth.Tpo -c -o gmapl_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-smooth.Tpo $(DEPDIR)/gmapl_sse42-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_sse42-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmapl_sse42-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-splicestringpool.Tpo -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-splicestringpool.Tpo $(DEPDIR)/gmapl_sse42-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_sse42-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmapl_sse42-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-splicestringpool.Tpo -c -o gmapl_sse42-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-splicestringpool.Tpo $(DEPDIR)/gmapl_sse42-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_sse42-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmapl_sse42-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-splicetrie_build.Tpo -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-splicetrie_build.Tpo $(DEPDIR)/gmapl_sse42-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_sse42-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmapl_sse42-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-splicetrie_build.Tpo -c -o gmapl_sse42-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-splicetrie_build.Tpo $(DEPDIR)/gmapl_sse42-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_sse42-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gmapl_sse42-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-splicetrie.Tpo -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-splicetrie.Tpo $(DEPDIR)/gmapl_sse42-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmapl_sse42-splicetrie.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmapl_sse42-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-splicetrie.Tpo -c -o gmapl_sse42-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-splicetrie.Tpo $(DEPDIR)/gmapl_sse42-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gmapl_sse42-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmapl_sse42-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-boyer-moore.Tpo -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-boyer-moore.Tpo $(DEPDIR)/gmapl_sse42-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_sse42-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmapl_sse42-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-boyer-moore.Tpo -c -o gmapl_sse42-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-boyer-moore.Tpo $(DEPDIR)/gmapl_sse42-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_sse42-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmapl_sse42-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog.Tpo -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog.Tpo $(DEPDIR)/gmapl_sse42-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_sse42-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmapl_sse42-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog.Tpo -c -o gmapl_sse42-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog.Tpo $(DEPDIR)/gmapl_sse42-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_sse42-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmapl_sse42-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog_simd.Tpo -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_simd.Tpo $(DEPDIR)/gmapl_sse42-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_sse42-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmapl_sse42-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog_simd.Tpo -c -o gmapl_sse42-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_simd.Tpo $(DEPDIR)/gmapl_sse42-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_sse42-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmapl_sse42-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog_single.Tpo -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_single.Tpo $(DEPDIR)/gmapl_sse42-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmapl_sse42-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmapl_sse42-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog_single.Tpo -c -o gmapl_sse42-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_single.Tpo $(DEPDIR)/gmapl_sse42-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gmapl_sse42-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gmapl_sse42-dynprog_genome.o: dynprog_genome.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_genome.Tpo $(DEPDIR)/gmapl_sse42-dynprog_genome.Po
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_genome.Tpo $(DEPDIR)/gmapl_sse42-dynprog_genome.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-dynprog_cdna.Tpo -c -o gmapl_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_cdna.Tpo $(DEPDIR)/gmapl_sse42-dynprog_cdna.Po
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-dynprog_cdna.Tpo $(DEPDIR)/gmapl_sse42-dynprog_cdna.Po
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+
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+gmapl_sse42-pbinom.obj: pbinom.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-output.Tpo $(DEPDIR)/gmapl_sse42-output.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-inbuffer.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-inbuffer.Tpo -c -o gmapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
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+
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+
+gmapl_sse42-samheader.o: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-samheader.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-samheader.Tpo -c -o gmapl_sse42-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-samheader.Tpo $(DEPDIR)/gmapl_sse42-samheader.Po
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+
+gmapl_sse42-samheader.obj: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-samheader.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-samheader.Tpo -c -o gmapl_sse42-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-samheader.Tpo $(DEPDIR)/gmapl_sse42-samheader.Po
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+
+gmapl_sse42-outbuffer.o: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-outbuffer.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-outbuffer.Tpo -c -o gmapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-outbuffer.Tpo $(DEPDIR)/gmapl_sse42-outbuffer.Po
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+
+gmapl_sse42-outbuffer.obj: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-outbuffer.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-outbuffer.Tpo -c -o gmapl_sse42-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-outbuffer.Tpo $(DEPDIR)/gmapl_sse42-outbuffer.Po
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+
+gmapl_sse42-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-chimera.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-chimera.Tpo -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-chimera.Tpo $(DEPDIR)/gmapl_sse42-chimera.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gmapl_sse42-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-chimera.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-chimera.Tpo -c -o gmapl_sse42-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-chimera.Tpo $(DEPDIR)/gmapl_sse42-chimera.Po
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+
+gmapl_sse42-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-datadir.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-datadir.Tpo -c -o gmapl_sse42-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-datadir.Tpo $(DEPDIR)/gmapl_sse42-datadir.Po
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+
+gmapl_sse42-datadir.obj: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-datadir.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-datadir.Tpo -c -o gmapl_sse42-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-datadir.Tpo $(DEPDIR)/gmapl_sse42-datadir.Po
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+
+gmapl_sse42-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-parserange.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-parserange.Tpo -c -o gmapl_sse42-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
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+
+gmapl_sse42-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-parserange.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-parserange.Tpo -c -o gmapl_sse42-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-parserange.Tpo $(DEPDIR)/gmapl_sse42-parserange.Po
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+
+gmapl_sse42-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-getopt.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-getopt.Tpo -c -o gmapl_sse42-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-getopt.Tpo $(DEPDIR)/gmapl_sse42-getopt.Po
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+
+gmapl_sse42-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-getopt.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-getopt.Tpo -c -o gmapl_sse42-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-getopt.Tpo $(DEPDIR)/gmapl_sse42-getopt.Po
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+
+gmapl_sse42-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-getopt1.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-getopt1.Tpo -c -o gmapl_sse42-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
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+gmapl_sse42-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-getopt1.obj -MD -MP -MF $(DEPDIR)/gmapl_sse42-getopt1.Tpo -c -o gmapl_sse42-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-getopt1.Tpo $(DEPDIR)/gmapl_sse42-getopt1.Po
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+gmapl_sse42-gmap.o: gmap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_sse42_CFLAGS) $(CFLAGS) -MT gmapl_sse42-gmap.o -MD -MP -MF $(DEPDIR)/gmapl_sse42-gmap.Tpo -c -o gmapl_sse42-gmap.o `test -f 'gmap.c' || echo '$(srcdir)/'`gmap.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-gmap.Tpo $(DEPDIR)/gmapl_sse42-gmap.Po
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_sse42-gmap.Tpo $(DEPDIR)/gmapl_sse42-gmap.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-atoi.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-atoi.Tpo -c -o gmapl_ssse3-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-atoi.Tpo $(DEPDIR)/gmapl_ssse3-atoi.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-orderstat.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-orderstat.Tpo -c -o gmapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-orderstat.Tpo $(DEPDIR)/gmapl_ssse3-orderstat.Po
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+
+gmapl_ssse3-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-orderstat.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-orderstat.Tpo -c -o gmapl_ssse3-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-orderstat.Tpo $(DEPDIR)/gmapl_ssse3-orderstat.Po
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+
+gmapl_ssse3-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-oligoindex_hr.Tpo -c -o gmapl_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-oligoindex_hr.Tpo $(DEPDIR)/gmapl_ssse3-oligoindex_hr.Po
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+
+gmapl_ssse3-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-oligoindex_hr.Tpo -c -o gmapl_ssse3-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-oligoindex_hr.Tpo $(DEPDIR)/gmapl_ssse3-oligoindex_hr.Po
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+
+gmapl_ssse3-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-intron.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-intron.Tpo -c -o gmapl_ssse3-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-intron.Tpo $(DEPDIR)/gmapl_ssse3-intron.Po
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+
+gmapl_ssse3-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-intron.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-intron.Tpo -c -o gmapl_ssse3-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-intron.Tpo $(DEPDIR)/gmapl_ssse3-intron.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-maxent.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-maxent.Tpo -c -o gmapl_ssse3-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-maxent.Tpo $(DEPDIR)/gmapl_ssse3-maxent.Po
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+
+gmapl_ssse3-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-maxent.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-maxent.Tpo -c -o gmapl_ssse3-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-maxent.Tpo $(DEPDIR)/gmapl_ssse3-maxent.Po
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+
+gmapl_ssse3-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-maxent_hr.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-maxent_hr.Tpo -c -o gmapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-maxent_hr.Tpo $(DEPDIR)/gmapl_ssse3-maxent_hr.Po
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+
+gmapl_ssse3-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-maxent_hr.Tpo -c -o gmapl_ssse3-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-maxent_hr.Tpo $(DEPDIR)/gmapl_ssse3-maxent_hr.Po
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+
+gmapl_ssse3-pair.o: pair.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-pair.Tpo $(DEPDIR)/gmapl_ssse3-pair.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gmapl_ssse3-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-pair.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-pair.Tpo -c -o gmapl_ssse3-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-pair.Tpo $(DEPDIR)/gmapl_ssse3-pair.Po
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+
+gmapl_ssse3-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-pairpool.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-pairpool.Tpo -c -o gmapl_ssse3-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-pairpool.Tpo $(DEPDIR)/gmapl_ssse3-pairpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gmapl_ssse3-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-pairpool.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-pairpool.Tpo -c -o gmapl_ssse3-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-pairpool.Tpo $(DEPDIR)/gmapl_ssse3-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gmapl_ssse3-pairpool.obj' libtool=no @AMDEPBACKSLASH@
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+
+gmapl_ssse3-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-cellpool.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-cellpool.Tpo -c -o gmapl_ssse3-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-cellpool.Tpo $(DEPDIR)/gmapl_ssse3-cellpool.Po
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+
+gmapl_ssse3-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-cellpool.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-cellpool.Tpo -c -o gmapl_ssse3-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-cellpool.Tpo $(DEPDIR)/gmapl_ssse3-cellpool.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-stage2.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-stage2.Tpo -c -o gmapl_ssse3-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-doublelist.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-doublelist.Tpo -c -o gmapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-doublelist.Tpo $(DEPDIR)/gmapl_ssse3-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_ssse3-doublelist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gmapl_ssse3-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-doublelist.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-doublelist.Tpo -c -o gmapl_ssse3-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-doublelist.Tpo $(DEPDIR)/gmapl_ssse3-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gmapl_ssse3-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gmapl_ssse3-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-smooth.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-smooth.Tpo -c -o gmapl_ssse3-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-smooth.Tpo $(DEPDIR)/gmapl_ssse3-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_ssse3-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gmapl_ssse3-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-smooth.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-smooth.Tpo -c -o gmapl_ssse3-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-smooth.Tpo $(DEPDIR)/gmapl_ssse3-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gmapl_ssse3-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gmapl_ssse3-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-splicestringpool.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-splicestringpool.Tpo -c -o gmapl_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-splicestringpool.Tpo $(DEPDIR)/gmapl_ssse3-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_ssse3-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gmapl_ssse3-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-splicestringpool.Tpo -c -o gmapl_ssse3-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-splicestringpool.Tpo $(DEPDIR)/gmapl_ssse3-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gmapl_ssse3-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gmapl_ssse3-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-splicetrie_build.Tpo -c -o gmapl_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-splicetrie_build.Tpo $(DEPDIR)/gmapl_ssse3-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_ssse3-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gmapl_ssse3-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-splicetrie_build.Tpo -c -o gmapl_ssse3-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-splicetrie_build.Tpo $(DEPDIR)/gmapl_ssse3-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gmapl_ssse3-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gmapl_ssse3-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-splicetrie.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-splicetrie.Tpo -c -o gmapl_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-splicetrie.Tpo $(DEPDIR)/gmapl_ssse3-splicetrie.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gmapl_ssse3-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-splicetrie.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-splicetrie.Tpo -c -o gmapl_ssse3-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-splicetrie.Tpo $(DEPDIR)/gmapl_ssse3-splicetrie.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gmapl_ssse3-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-boyer-moore.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-boyer-moore.Tpo -c -o gmapl_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-boyer-moore.Tpo $(DEPDIR)/gmapl_ssse3-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_ssse3-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gmapl_ssse3-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-boyer-moore.Tpo -c -o gmapl_ssse3-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-boyer-moore.Tpo $(DEPDIR)/gmapl_ssse3-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gmapl_ssse3-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gmapl_ssse3-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-dynprog.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-dynprog.Tpo -c -o gmapl_ssse3-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-dynprog.Tpo $(DEPDIR)/gmapl_ssse3-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_ssse3-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gmapl_ssse3-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-dynprog.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-dynprog.Tpo -c -o gmapl_ssse3-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-dynprog.Tpo $(DEPDIR)/gmapl_ssse3-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gmapl_ssse3-dynprog.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gmapl_ssse3-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-dynprog_simd.Tpo -c -o gmapl_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-dynprog_simd.Tpo $(DEPDIR)/gmapl_ssse3-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gmapl_ssse3-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gmapl_ssse3-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-dynprog_simd.Tpo -c -o gmapl_ssse3-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-dynprog_simd.Tpo $(DEPDIR)/gmapl_ssse3-dynprog_simd.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gmapl_ssse3-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-dynprog_single.o -MD -MP -MF $(DEPDIR)/gmapl_ssse3-dynprog_single.Tpo -c -o gmapl_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-dynprog_single.Tpo $(DEPDIR)/gmapl_ssse3-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gmapl_ssse3-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -MT gmapl_ssse3-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gmapl_ssse3-dynprog_single.Tpo -c -o gmapl_ssse3-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gmapl_ssse3-dynprog_single.Tpo $(DEPDIR)/gmapl_ssse3-dynprog_single.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapl_ssse3_CFLAGS) $(CFLAGS) -c -o gmapl_ssse3-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
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+gmapl_ssse3-getopt1.o: getopt1.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-cpuid.o -MD -MP -MF $(DEPDIR)/gsnap-cpuid.Tpo -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '$(srcdir)/'`cpuid.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-cpuid.Tpo $(DEPDIR)/gsnap-cpuid.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '$(srcdir)/'`cpuid.c
+
+gsnap-cpuid.obj: cpuid.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-cpuid.obj -MD -MP -MF $(DEPDIR)/gsnap-cpuid.Tpo -c -o gsnap-cpuid.obj `if test -f 'cpuid.c'; then $(CYGPATH_W) 'cpuid.c'; else $(CYGPATH_W) '$(srcdir)/cpuid.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-cpuid.Tpo $(DEPDIR)/gsnap-cpuid.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-cpuid.obj `if test -f 'cpuid.c'; then $(CYGPATH_W) 'cpuid.c'; else $(CYGPATH_W) '$(srcdir)/cpuid.c'; fi`
+
+gsnap-gsnap_select.o: gsnap_select.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-gsnap_select.o -MD -MP -MF $(DEPDIR)/gsnap-gsnap_select.Tpo -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '$(srcdir)/'`gsnap_select.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-gsnap_select.Tpo $(DEPDIR)/gsnap-gsnap_select.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '$(srcdir)/'`gsnap_select.c
+
+gsnap-gsnap_select.obj: gsnap_select.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-gsnap_select.obj -MD -MP -MF $(DEPDIR)/gsnap-gsnap_select.Tpo -c -o gsnap-gsnap_select.obj `if test -f 'gsnap_select.c'; then $(CYGPATH_W) 'gsnap_select.c'; else $(CYGPATH_W) '$(srcdir)/gsnap_select.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap-gsnap_select.Tpo $(DEPDIR)/gsnap-gsnap_select.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -c -o gsnap-gsnap_select.obj `if test -f 'gsnap_select.c'; then $(CYGPATH_W) 'gsnap_select.c'; else $(CYGPATH_W) '$(srcdir)/gsnap_select.c'; fi`
+
+gsnap_avx2-except.o: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-except.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-except.Tpo -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-except.Tpo $(DEPDIR)/gsnap_avx2-except.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+
+gsnap_avx2-except.obj: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-except.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-except.Tpo -c -o gsnap_avx2-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-except.Tpo $(DEPDIR)/gsnap_avx2-except.Po
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+
+gsnap_avx2-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-assert.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-assert.Tpo -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-assert.Tpo $(DEPDIR)/gsnap_avx2-assert.Po
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+
+gsnap_avx2-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-assert.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-assert.Tpo -c -o gsnap_avx2-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-assert.Tpo $(DEPDIR)/gsnap_avx2-assert.Po
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+gsnap_avx2-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-mem.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-mem.Tpo -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-mem.Tpo $(DEPDIR)/gsnap_avx2-mem.Po
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+
+gsnap_avx2-mem.obj: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-mem.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-mem.Tpo -c -o gsnap_avx2-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-mem.Tpo $(DEPDIR)/gsnap_avx2-mem.Po
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+
+gsnap_avx2-intlist.o: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-intlist.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-intlist.Tpo -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-intlist.Tpo $(DEPDIR)/gsnap_avx2-intlist.Po
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+
+gsnap_avx2-intlist.obj: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-intlist.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-intlist.Tpo -c -o gsnap_avx2-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-intlist.Tpo $(DEPDIR)/gsnap_avx2-intlist.Po
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+
+gsnap_avx2-list.o: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-list.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-list.Tpo -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-list.Tpo $(DEPDIR)/gsnap_avx2-list.Po
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+
+gsnap_avx2-list.obj: list.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-list.Tpo $(DEPDIR)/gsnap_avx2-list.Po
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+gsnap_avx2-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-littleendian.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-littleendian.Tpo -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-littleendian.Tpo $(DEPDIR)/gsnap_avx2-littleendian.Po
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+gsnap_avx2-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-littleendian.Tpo -c -o gsnap_avx2-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-littleendian.Tpo $(DEPDIR)/gsnap_avx2-littleendian.Po
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+
+gsnap_avx2-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bigendian.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-bigendian.Tpo -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
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+gsnap_avx2-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-bigendian.Tpo -c -o gsnap_avx2-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bigendian.Tpo $(DEPDIR)/gsnap_avx2-bigendian.Po
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+gsnap_avx2-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-univinterval.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-univinterval.Tpo -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-univinterval.Tpo $(DEPDIR)/gsnap_avx2-univinterval.Po
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+gsnap_avx2-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-univinterval.Tpo -c -o gsnap_avx2-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-univinterval.Tpo $(DEPDIR)/gsnap_avx2-univinterval.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-interval.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-interval.Tpo -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-interval.Tpo $(DEPDIR)/gsnap_avx2-interval.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+
+gsnap_avx2-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-interval.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-interval.Tpo -c -o gsnap_avx2-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-interval.Tpo $(DEPDIR)/gsnap_avx2-interval.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+
+gsnap_avx2-uintlist.o: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-uintlist.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-uintlist.Tpo -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-uintlist.Tpo $(DEPDIR)/gsnap_avx2-uintlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnap_avx2-uintlist.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+
+gsnap_avx2-uintlist.obj: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-uintlist.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-uintlist.Tpo -c -o gsnap_avx2-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-uintlist.Tpo $(DEPDIR)/gsnap_avx2-uintlist.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
+
+gsnap_avx2-stopwatch.o: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-stopwatch.Tpo -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stopwatch.Tpo $(DEPDIR)/gsnap_avx2-stopwatch.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
+
+gsnap_avx2-stopwatch.obj: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stopwatch.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-stopwatch.Tpo -c -o gsnap_avx2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stopwatch.Tpo $(DEPDIR)/gsnap_avx2-stopwatch.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+
+gsnap_avx2-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-semaphore.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-semaphore.Tpo -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-semaphore.Tpo $(DEPDIR)/gsnap_avx2-semaphore.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+gsnap_avx2-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-semaphore.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-semaphore.Tpo -c -o gsnap_avx2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-semaphore.Tpo $(DEPDIR)/gsnap_avx2-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='gsnap_avx2-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
+gsnap_avx2-access.o: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-access.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-access.Tpo -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-access.Tpo $(DEPDIR)/gsnap_avx2-access.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+
+gsnap_avx2-access.obj: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-access.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-access.Tpo -c -o gsnap_avx2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-access.Tpo $(DEPDIR)/gsnap_avx2-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap_avx2-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+
+gsnap_avx2-filestring.o: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-filestring.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-filestring.Tpo -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-filestring.Tpo $(DEPDIR)/gsnap_avx2-filestring.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+
+gsnap_avx2-filestring.obj: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-filestring.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-filestring.Tpo -c -o gsnap_avx2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-filestring.Tpo $(DEPDIR)/gsnap_avx2-filestring.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+
+gsnap_avx2-iit-read-univ.o: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-iit-read-univ.Tpo -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-iit-read-univ.Tpo $(DEPDIR)/gsnap_avx2-iit-read-univ.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+
+gsnap_avx2-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-iit-read-univ.Tpo -c -o gsnap_avx2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-iit-read-univ.Tpo $(DEPDIR)/gsnap_avx2-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap_avx2-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+
+gsnap_avx2-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-iit-read.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-iit-read.Tpo -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-iit-read.Tpo $(DEPDIR)/gsnap_avx2-iit-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+
+gsnap_avx2-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-iit-read.Tpo -c -o gsnap_avx2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-iit-read.Tpo $(DEPDIR)/gsnap_avx2-iit-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+
+gsnap_avx2-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-md5.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-md5.Tpo -c -o gsnap_avx2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-md5.Tpo $(DEPDIR)/gsnap_avx2-md5.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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+gsnap_avx2-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-md5.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-md5.Tpo -c -o gsnap_avx2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-md5.Tpo $(DEPDIR)/gsnap_avx2-md5.Po
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+gsnap_avx2-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bzip2.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-bzip2.Tpo -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bzip2.Tpo $(DEPDIR)/gsnap_avx2-bzip2.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+
+gsnap_avx2-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-bzip2.Tpo -c -o gsnap_avx2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bzip2.Tpo $(DEPDIR)/gsnap_avx2-bzip2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnap_avx2-bzip2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+
+gsnap_avx2-sequence.o: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-sequence.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-sequence.Tpo -c -o gsnap_avx2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-sequence.Tpo $(DEPDIR)/gsnap_avx2-sequence.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnap_avx2-sequence.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+
+gsnap_avx2-sequence.obj: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-sequence.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-sequence.Tpo -c -o gsnap_avx2-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-sequence.Tpo $(DEPDIR)/gsnap_avx2-sequence.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnap_avx2-sequence.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+
+gsnap_avx2-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-reader.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-reader.Tpo -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-reader.Tpo $(DEPDIR)/gsnap_avx2-reader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnap_avx2-reader.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+
+gsnap_avx2-reader.obj: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-reader.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-reader.Tpo -c -o gsnap_avx2-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-reader.Tpo $(DEPDIR)/gsnap_avx2-reader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnap_avx2-reader.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+
+gsnap_avx2-genomicpos.o: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-genomicpos.Tpo -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genomicpos.Tpo $(DEPDIR)/gsnap_avx2-genomicpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnap_avx2-genomicpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
+
+gsnap_avx2-genomicpos.obj: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genomicpos.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-genomicpos.Tpo -c -o gsnap_avx2-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genomicpos.Tpo $(DEPDIR)/gsnap_avx2-genomicpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnap_avx2-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
+
+gsnap_avx2-compress.o: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-compress.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-compress.Tpo -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-compress.Tpo $(DEPDIR)/gsnap_avx2-compress.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnap_avx2-compress.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
+
+gsnap_avx2-compress.obj: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-compress.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-compress.Tpo -c -o gsnap_avx2-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-compress.Tpo $(DEPDIR)/gsnap_avx2-compress.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnap_avx2-compress.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
+
+gsnap_avx2-genome.o: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genome.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-genome.Tpo -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genome.Tpo $(DEPDIR)/gsnap_avx2-genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnap_avx2-genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+
+gsnap_avx2-genome.obj: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genome.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-genome.Tpo -c -o gsnap_avx2-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genome.Tpo $(DEPDIR)/gsnap_avx2-genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnap_avx2-genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
+
+gsnap_avx2-popcount.o: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-popcount.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-popcount.Tpo -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-popcount.Tpo $(DEPDIR)/gsnap_avx2-popcount.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnap_avx2-popcount.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+
+gsnap_avx2-popcount.obj: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-popcount.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-popcount.Tpo -c -o gsnap_avx2-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-popcount.Tpo $(DEPDIR)/gsnap_avx2-popcount.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnap_avx2-popcount.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+
+gsnap_avx2-genome128_hr.o: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genome128_hr.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-genome128_hr.Tpo -c -o gsnap_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genome128_hr.Tpo $(DEPDIR)/gsnap_avx2-genome128_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnap_avx2-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
+
+gsnap_avx2-genome128_hr.obj: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-genome128_hr.Tpo -c -o gsnap_avx2-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genome128_hr.Tpo $(DEPDIR)/gsnap_avx2-genome128_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnap_avx2-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
+
+gsnap_avx2-genome_sites.o: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genome_sites.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-genome_sites.Tpo -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genome_sites.Tpo $(DEPDIR)/gsnap_avx2-genome_sites.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnap_avx2-genome_sites.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
+
+gsnap_avx2-genome_sites.obj: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-genome_sites.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-genome_sites.Tpo -c -o gsnap_avx2-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-genome_sites.Tpo $(DEPDIR)/gsnap_avx2-genome_sites.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnap_avx2-genome_sites.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
+
+gsnap_avx2-bitpack64-read.o: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-bitpack64-read.Tpo -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bitpack64-read.Tpo $(DEPDIR)/gsnap_avx2-bitpack64-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gsnap_avx2-bitpack64-read.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+
+gsnap_avx2-bitpack64-read.obj: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-bitpack64-read.Tpo -c -o gsnap_avx2-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bitpack64-read.Tpo $(DEPDIR)/gsnap_avx2-bitpack64-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-read.c' object='gsnap_avx2-bitpack64-read.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+
+gsnap_avx2-bitpack64-readtwo.o: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-bitpack64-readtwo.Tpo -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap_avx2-bitpack64-readtwo.Po
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+
+gsnap_avx2-bitpack64-readtwo.obj: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-bitpack64-readtwo.Tpo -c -o gsnap_avx2-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap_avx2-bitpack64-readtwo.Po
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+
+gsnap_avx2-indexdb.o: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-indexdb.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-indexdb.Tpo -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-indexdb.Tpo $(DEPDIR)/gsnap_avx2-indexdb.Po
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+
+gsnap_avx2-indexdb.obj: indexdb.c
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+
+gsnap_avx2-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-indexdb_hr.Tpo -c -o gsnap_avx2-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-indexdb_hr.Tpo $(DEPDIR)/gsnap_avx2-indexdb_hr.Po
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+
+gsnap_avx2-indexdb_hr.obj: indexdb_hr.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-indexdb_hr.Tpo $(DEPDIR)/gsnap_avx2-indexdb_hr.Po
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+
+gsnap_avx2-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-oligo.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-oligo.Tpo -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-oligo.Tpo $(DEPDIR)/gsnap_avx2-oligo.Po
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+gsnap_avx2-oligo.obj: oligo.c
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+gsnap_avx2-chrom.o: chrom.c
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+gsnap_avx2-chrom.obj: chrom.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-chrom.Tpo $(DEPDIR)/gsnap_avx2-chrom.Po
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+gsnap_avx2-segmentpos.o: segmentpos.c
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+gsnap_avx2-segmentpos.obj: segmentpos.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-chrnum.Tpo $(DEPDIR)/gsnap_avx2-chrnum.Po
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+gsnap_avx2-chrnum.obj: chrnum.c
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+gsnap_avx2-maxent_hr.o: maxent_hr.c
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+gsnap_avx2-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-maxent_hr.Tpo -c -o gsnap_avx2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
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+gsnap_avx2-samprint.o: samprint.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-samprint.Tpo $(DEPDIR)/gsnap_avx2-samprint.Po
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+gsnap_avx2-samprint.obj: samprint.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-samprint.Tpo $(DEPDIR)/gsnap_avx2-samprint.Po
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+gsnap_avx2-mapq.o: mapq.c
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+gsnap_avx2-mapq.obj: mapq.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-mapq.Tpo $(DEPDIR)/gsnap_avx2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_avx2-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnap_avx2-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-shortread.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-shortread.Tpo -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-shortread.Tpo $(DEPDIR)/gsnap_avx2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_avx2-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnap_avx2-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-shortread.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-shortread.Tpo -c -o gsnap_avx2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-shortread.Tpo $(DEPDIR)/gsnap_avx2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_avx2-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnap_avx2-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-substring.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-substring.Tpo -c -o gsnap_avx2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-substring.Tpo $(DEPDIR)/gsnap_avx2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_avx2-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnap_avx2-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-substring.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-substring.Tpo -c -o gsnap_avx2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-substring.Tpo $(DEPDIR)/gsnap_avx2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_avx2-substring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnap_avx2-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-junction.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-junction.Tpo -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-junction.Tpo $(DEPDIR)/gsnap_avx2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_avx2-junction.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+
+gsnap_avx2-junction.obj: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-junction.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-junction.Tpo -c -o gsnap_avx2-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-junction.Tpo $(DEPDIR)/gsnap_avx2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_avx2-junction.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+
+gsnap_avx2-stage3hr.o: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-stage3hr.Tpo -c -o gsnap_avx2-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage3hr.Tpo $(DEPDIR)/gsnap_avx2-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap_avx2-stage3hr.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+
+gsnap_avx2-stage3hr.obj: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-stage3hr.Tpo -c -o gsnap_avx2-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage3hr.Tpo $(DEPDIR)/gsnap_avx2-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap_avx2-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+
+gsnap_avx2-spanningelt.o: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-spanningelt.Tpo -c -o gsnap_avx2-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-spanningelt.Tpo $(DEPDIR)/gsnap_avx2-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap_avx2-spanningelt.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+
+gsnap_avx2-spanningelt.obj: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-spanningelt.Tpo -c -o gsnap_avx2-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-spanningelt.Tpo $(DEPDIR)/gsnap_avx2-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap_avx2-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+
+gsnap_avx2-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-cmet.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-cmet.Tpo -c -o gsnap_avx2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-cmet.Tpo $(DEPDIR)/gsnap_avx2-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnap_avx2-cmet.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gsnap_avx2-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-cmet.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-cmet.Tpo -c -o gsnap_avx2-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-cmet.Tpo $(DEPDIR)/gsnap_avx2-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnap_avx2-cmet.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+
+gsnap_avx2-atoi.o: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-atoi.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-atoi.Tpo -c -o gsnap_avx2-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-atoi.Tpo $(DEPDIR)/gsnap_avx2-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnap_avx2-atoi.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+
+gsnap_avx2-atoi.obj: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-atoi.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-atoi.Tpo -c -o gsnap_avx2-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-atoi.Tpo $(DEPDIR)/gsnap_avx2-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnap_avx2-atoi.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+
+gsnap_avx2-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-maxent.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-maxent.Tpo -c -o gsnap_avx2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-maxent.Tpo $(DEPDIR)/gsnap_avx2-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnap_avx2-maxent.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+
+gsnap_avx2-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-maxent.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-maxent.Tpo -c -o gsnap_avx2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-maxent.Tpo $(DEPDIR)/gsnap_avx2-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnap_avx2-maxent.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
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+gsnap_avx2-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-pair.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-pair.Tpo -c -o gsnap_avx2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-pair.Tpo $(DEPDIR)/gsnap_avx2-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnap_avx2-pair.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gsnap_avx2-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-pair.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-pair.Tpo -c -o gsnap_avx2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-pair.Tpo $(DEPDIR)/gsnap_avx2-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnap_avx2-pair.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
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+gsnap_avx2-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-pairpool.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-pairpool.Tpo -c -o gsnap_avx2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-pairpool.Tpo $(DEPDIR)/gsnap_avx2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnap_avx2-pairpool.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
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+gsnap_avx2-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-pairpool.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-pairpool.Tpo -c -o gsnap_avx2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-pairpool.Tpo $(DEPDIR)/gsnap_avx2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnap_avx2-pairpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+
+gsnap_avx2-diag.o: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-diag.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-diag.Tpo -c -o gsnap_avx2-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-diag.Tpo $(DEPDIR)/gsnap_avx2-diag.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+
+gsnap_avx2-diag.obj: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-diag.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-diag.Tpo -c -o gsnap_avx2-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-diag.Tpo $(DEPDIR)/gsnap_avx2-diag.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-diag.obj `if test -f 'diag.c'; then $(CYGPATH_W) 'diag.c'; else $(CYGPATH_W) '$(srcdir)/diag.c'; fi`
+
+gsnap_avx2-diagpool.o: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-diagpool.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-diagpool.Tpo -c -o gsnap_avx2-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-diagpool.Tpo $(DEPDIR)/gsnap_avx2-diagpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+
+gsnap_avx2-diagpool.obj: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-diagpool.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-diagpool.Tpo -c -o gsnap_avx2-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-diagpool.Tpo $(DEPDIR)/gsnap_avx2-diagpool.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+
+gsnap_avx2-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-orderstat.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-orderstat.Tpo -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-orderstat.Tpo $(DEPDIR)/gsnap_avx2-orderstat.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+
+gsnap_avx2-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-orderstat.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-orderstat.Tpo -c -o gsnap_avx2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-orderstat.Tpo $(DEPDIR)/gsnap_avx2-orderstat.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+
+gsnap_avx2-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-oligoindex_hr.Tpo -c -o gsnap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-oligoindex_hr.Tpo $(DEPDIR)/gsnap_avx2-oligoindex_hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gsnap_avx2-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-oligoindex_hr.Tpo -c -o gsnap_avx2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-oligoindex_hr.Tpo $(DEPDIR)/gsnap_avx2-oligoindex_hr.Po
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+
+gsnap_avx2-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-cellpool.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-cellpool.Tpo -c -o gsnap_avx2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-cellpool.Tpo $(DEPDIR)/gsnap_avx2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnap_avx2-cellpool.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gsnap_avx2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-cellpool.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-cellpool.Tpo -c -o gsnap_avx2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-cellpool.Tpo $(DEPDIR)/gsnap_avx2-cellpool.Po
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+gsnap_avx2-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stage2.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-stage2.Tpo -c -o gsnap_avx2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage2.Tpo $(DEPDIR)/gsnap_avx2-stage2.Po
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+gsnap_avx2-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stage2.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-stage2.Tpo -c -o gsnap_avx2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage2.Tpo $(DEPDIR)/gsnap_avx2-stage2.Po
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+gsnap_avx2-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-intron.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-intron.Tpo -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-intron.Tpo $(DEPDIR)/gsnap_avx2-intron.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gsnap_avx2-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-intron.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-intron.Tpo -c -o gsnap_avx2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-intron.Tpo $(DEPDIR)/gsnap_avx2-intron.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
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+gsnap_avx2-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-boyer-moore.Tpo -c -o gsnap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-boyer-moore.Tpo $(DEPDIR)/gsnap_avx2-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
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+gsnap_avx2-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-boyer-moore.Tpo -c -o gsnap_avx2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-boyer-moore.Tpo $(DEPDIR)/gsnap_avx2-boyer-moore.Po
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+gsnap_avx2-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-changepoint.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-changepoint.Tpo -c -o gsnap_avx2-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-changepoint.Tpo $(DEPDIR)/gsnap_avx2-changepoint.Po
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+gsnap_avx2-changepoint.obj: changepoint.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-changepoint.Tpo $(DEPDIR)/gsnap_avx2-changepoint.Po
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+gsnap_avx2-pbinom.o: pbinom.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-pbinom.Tpo $(DEPDIR)/gsnap_avx2-pbinom.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-doublelist.Tpo -c -o gsnap_avx2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-doublelist.Tpo $(DEPDIR)/gsnap_avx2-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnap_avx2-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gsnap_avx2-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-smooth.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-smooth.Tpo -c -o gsnap_avx2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-smooth.Tpo $(DEPDIR)/gsnap_avx2-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnap_avx2-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gsnap_avx2-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-smooth.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-smooth.Tpo -c -o gsnap_avx2-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-smooth.Tpo $(DEPDIR)/gsnap_avx2-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnap_avx2-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gsnap_avx2-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-chimera.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-chimera.Tpo -c -o gsnap_avx2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-chimera.Tpo $(DEPDIR)/gsnap_avx2-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap_avx2-chimera.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gsnap_avx2-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-chimera.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-chimera.Tpo -c -o gsnap_avx2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-chimera.Tpo $(DEPDIR)/gsnap_avx2-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap_avx2-chimera.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnap_avx2-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stage3.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-stage3.Tpo -c -o gsnap_avx2-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage3.Tpo $(DEPDIR)/gsnap_avx2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap_avx2-stage3.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnap_avx2-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-stage3.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-stage3.Tpo -c -o gsnap_avx2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage3.Tpo $(DEPDIR)/gsnap_avx2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap_avx2-stage3.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnap_avx2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-splicestringpool.Tpo -c -o gsnap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splicestringpool.Tpo $(DEPDIR)/gsnap_avx2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap_avx2-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnap_avx2-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-splicestringpool.Tpo -c -o gsnap_avx2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splicestringpool.Tpo $(DEPDIR)/gsnap_avx2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap_avx2-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnap_avx2-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-splicetrie_build.Tpo -c -o gsnap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splicetrie_build.Tpo $(DEPDIR)/gsnap_avx2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap_avx2-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnap_avx2-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-splicetrie_build.Tpo -c -o gsnap_avx2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splicetrie_build.Tpo $(DEPDIR)/gsnap_avx2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap_avx2-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnap_avx2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-splicetrie.Tpo -c -o gsnap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splicetrie.Tpo $(DEPDIR)/gsnap_avx2-splicetrie.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gsnap_avx2-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-splicetrie.Tpo -c -o gsnap_avx2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splicetrie.Tpo $(DEPDIR)/gsnap_avx2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnap_avx2-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gsnap_avx2-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splice.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-splice.Tpo -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splice.Tpo $(DEPDIR)/gsnap_avx2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap_avx2-splice.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnap_avx2-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-splice.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-splice.Tpo -c -o gsnap_avx2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-splice.Tpo $(DEPDIR)/gsnap_avx2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap_avx2-splice.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+
+gsnap_avx2-indel.o: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-indel.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-indel.Tpo -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-indel.Tpo $(DEPDIR)/gsnap_avx2-indel.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnap_avx2-indel.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+
+gsnap_avx2-indel.obj: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-indel.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-indel.Tpo -c -o gsnap_avx2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-indel.Tpo $(DEPDIR)/gsnap_avx2-indel.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnap_avx2-indel.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+
+gsnap_avx2-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-bitpack64-access.Tpo -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bitpack64-access.Tpo $(DEPDIR)/gsnap_avx2-bitpack64-access.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+gsnap_avx2-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-bitpack64-access.Tpo -c -o gsnap_avx2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bitpack64-access.Tpo $(DEPDIR)/gsnap_avx2-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnap_avx2-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bytecoding.Tpo $(DEPDIR)/gsnap_avx2-bytecoding.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
+
+gsnap_avx2-bytecoding.obj: bytecoding.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-bytecoding.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-bytecoding.Tpo -c -o gsnap_avx2-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-bytecoding.Tpo $(DEPDIR)/gsnap_avx2-bytecoding.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -c -o gsnap_avx2-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
+
+gsnap_avx2-univdiag.o: univdiag.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-univdiag.Tpo $(DEPDIR)/gsnap_avx2-univdiag.Po
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+
+gsnap_avx2-univdiag.obj: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-univdiag.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-univdiag.Tpo -c -o gsnap_avx2-univdiag.obj `if test -f 'univdiag.c'; then $(CYGPATH_W) 'univdiag.c'; else $(CYGPATH_W) '$(srcdir)/univdiag.c'; fi`
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+
+gsnap_avx2-sarray-read.o: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-sarray-read.o -MD -MP -MF $(DEPDIR)/gsnap_avx2-sarray-read.Tpo -c -o gsnap_avx2-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
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+gsnap_avx2-sarray-read.obj: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_avx2_CFLAGS) $(CFLAGS) -MT gsnap_avx2-sarray-read.obj -MD -MP -MF $(DEPDIR)/gsnap_avx2-sarray-read.Tpo -c -o gsnap_avx2-sarray-read.obj `if test -f 'sarray-read.c'; then $(CYGPATH_W) 'sarray-read.c'; else $(CYGPATH_W) '$(srcdir)/sarray-read.c'; fi`
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+
+gsnap_avx2-stage1hr.o: stage1hr.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_avx2-stage1hr.Tpo $(DEPDIR)/gsnap_avx2-stage1hr.Po
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+gsnap_avx2-stage1hr.obj: stage1hr.c
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+gsnap_avx2-request.obj: request.c
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+gsnap_avx2-resulthr.obj: resulthr.c
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+gsnap_avx2-output.obj: output.c
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+gsnap_avx2-inbuffer.obj: inbuffer.c
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+gsnap_avx2-samheader.o: samheader.c
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+gsnap_avx2-outbuffer.obj: outbuffer.c
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+gsnap_nosimd-intlist.obj: intlist.c
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+gsnap_nosimd-list.obj: list.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-list.Tpo $(DEPDIR)/gsnap_nosimd-list.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='list.c' object='gsnap_nosimd-list.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
+
+gsnap_nosimd-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-littleendian.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-littleendian.Tpo -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-littleendian.Tpo $(DEPDIR)/gsnap_nosimd-littleendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gsnap_nosimd-littleendian.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+
+gsnap_nosimd-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-littleendian.Tpo -c -o gsnap_nosimd-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-littleendian.Tpo $(DEPDIR)/gsnap_nosimd-littleendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='littleendian.c' object='gsnap_nosimd-littleendian.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+
+gsnap_nosimd-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-bigendian.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-bigendian.Tpo -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-bigendian.Tpo $(DEPDIR)/gsnap_nosimd-bigendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gsnap_nosimd-bigendian.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+
+gsnap_nosimd-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-bigendian.Tpo -c -o gsnap_nosimd-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-bigendian.Tpo $(DEPDIR)/gsnap_nosimd-bigendian.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bigendian.c' object='gsnap_nosimd-bigendian.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+
+gsnap_nosimd-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-univinterval.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-univinterval.Tpo -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-univinterval.Tpo $(DEPDIR)/gsnap_nosimd-univinterval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gsnap_nosimd-univinterval.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+
+gsnap_nosimd-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-univinterval.Tpo -c -o gsnap_nosimd-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-univinterval.Tpo $(DEPDIR)/gsnap_nosimd-univinterval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univinterval.c' object='gsnap_nosimd-univinterval.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+
+gsnap_nosimd-interval.o: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-interval.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-interval.Tpo -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-interval.Tpo $(DEPDIR)/gsnap_nosimd-interval.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='interval.c' object='gsnap_nosimd-interval.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+
+gsnap_nosimd-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-interval.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-interval.Tpo -c -o gsnap_nosimd-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-interval.Tpo $(DEPDIR)/gsnap_nosimd-interval.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+
+gsnap_nosimd-uintlist.o: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-uintlist.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-uintlist.Tpo -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-uintlist.Tpo $(DEPDIR)/gsnap_nosimd-uintlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnap_nosimd-uintlist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+
+gsnap_nosimd-uintlist.obj: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-uintlist.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-uintlist.Tpo -c -o gsnap_nosimd-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-uintlist.Tpo $(DEPDIR)/gsnap_nosimd-uintlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnap_nosimd-uintlist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
+
+gsnap_nosimd-stopwatch.o: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stopwatch.Tpo -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stopwatch.Tpo $(DEPDIR)/gsnap_nosimd-stopwatch.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gsnap_nosimd-stopwatch.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
+
+gsnap_nosimd-stopwatch.obj: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stopwatch.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stopwatch.Tpo -c -o gsnap_nosimd-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stopwatch.Tpo $(DEPDIR)/gsnap_nosimd-stopwatch.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+
+gsnap_nosimd-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-semaphore.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-semaphore.Tpo -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-semaphore.Tpo $(DEPDIR)/gsnap_nosimd-semaphore.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+gsnap_nosimd-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-semaphore.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-semaphore.Tpo -c -o gsnap_nosimd-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-semaphore.Tpo $(DEPDIR)/gsnap_nosimd-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='gsnap_nosimd-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
+gsnap_nosimd-access.o: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-access.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-access.Tpo -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-access.Tpo $(DEPDIR)/gsnap_nosimd-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap_nosimd-access.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+
+gsnap_nosimd-access.obj: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-access.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-access.Tpo -c -o gsnap_nosimd-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-access.Tpo $(DEPDIR)/gsnap_nosimd-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap_nosimd-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+
+gsnap_nosimd-filestring.o: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-filestring.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-filestring.Tpo -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-filestring.Tpo $(DEPDIR)/gsnap_nosimd-filestring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='filestring.c' object='gsnap_nosimd-filestring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+
+gsnap_nosimd-filestring.obj: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-filestring.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-filestring.Tpo -c -o gsnap_nosimd-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-filestring.Tpo $(DEPDIR)/gsnap_nosimd-filestring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='filestring.c' object='gsnap_nosimd-filestring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+
+gsnap_nosimd-iit-read-univ.o: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-iit-read-univ.Tpo -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-iit-read-univ.Tpo $(DEPDIR)/gsnap_nosimd-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap_nosimd-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+
+gsnap_nosimd-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-iit-read-univ.Tpo -c -o gsnap_nosimd-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-iit-read-univ.Tpo $(DEPDIR)/gsnap_nosimd-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap_nosimd-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+
+gsnap_nosimd-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-iit-read.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-iit-read.Tpo -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-iit-read.Tpo $(DEPDIR)/gsnap_nosimd-iit-read.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+
+gsnap_nosimd-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-iit-read.Tpo -c -o gsnap_nosimd-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-iit-read.Tpo $(DEPDIR)/gsnap_nosimd-iit-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnap_nosimd-iit-read.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+
+gsnap_nosimd-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-md5.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-md5.Tpo -c -o gsnap_nosimd-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-md5.Tpo $(DEPDIR)/gsnap_nosimd-md5.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+
+gsnap_nosimd-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-md5.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-md5.Tpo -c -o gsnap_nosimd-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-md5.Tpo $(DEPDIR)/gsnap_nosimd-md5.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+
+gsnap_nosimd-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-bzip2.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-bzip2.Tpo -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-bzip2.Tpo $(DEPDIR)/gsnap_nosimd-bzip2.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+
+gsnap_nosimd-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-bzip2.Tpo -c -o gsnap_nosimd-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-bzip2.Tpo $(DEPDIR)/gsnap_nosimd-bzip2.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+
+gsnap_nosimd-sequence.o: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-sequence.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-sequence.Tpo -c -o gsnap_nosimd-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-sequence.Tpo $(DEPDIR)/gsnap_nosimd-sequence.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+
+gsnap_nosimd-sequence.obj: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-sequence.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-sequence.Tpo -c -o gsnap_nosimd-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-sequence.Tpo $(DEPDIR)/gsnap_nosimd-sequence.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+
+gsnap_nosimd-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-reader.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-reader.Tpo -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-reader.Tpo $(DEPDIR)/gsnap_nosimd-reader.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+
+gsnap_nosimd-reader.obj: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-reader.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-reader.Tpo -c -o gsnap_nosimd-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-reader.Tpo $(DEPDIR)/gsnap_nosimd-reader.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+
+gsnap_nosimd-genomicpos.o: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-genomicpos.Tpo -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-genomicpos.Tpo $(DEPDIR)/gsnap_nosimd-genomicpos.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
+
+gsnap_nosimd-genomicpos.obj: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-genomicpos.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-genomicpos.Tpo -c -o gsnap_nosimd-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-genomicpos.Tpo $(DEPDIR)/gsnap_nosimd-genomicpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genomicpos.c' object='gsnap_nosimd-genomicpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
+
+gsnap_nosimd-compress.o: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-compress.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-compress.Tpo -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-compress.Tpo $(DEPDIR)/gsnap_nosimd-compress.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
+
+gsnap_nosimd-compress.obj: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-compress.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-compress.Tpo -c -o gsnap_nosimd-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-compress.Tpo $(DEPDIR)/gsnap_nosimd-compress.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='compress.c' object='gsnap_nosimd-compress.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
+
+gsnap_nosimd-genome.o: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-genome.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-genome.Tpo -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-genome.Tpo $(DEPDIR)/gsnap_nosimd-genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnap_nosimd-genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+
+gsnap_nosimd-genome.obj: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-genome.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-genome.Tpo -c -o gsnap_nosimd-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-genome.Tpo $(DEPDIR)/gsnap_nosimd-genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnap_nosimd-genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
+
+gsnap_nosimd-popcount.o: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-popcount.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-popcount.Tpo -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-popcount.Tpo $(DEPDIR)/gsnap_nosimd-popcount.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnap_nosimd-popcount.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+
+gsnap_nosimd-popcount.obj: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-popcount.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-popcount.Tpo -c -o gsnap_nosimd-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
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+
+gsnap_nosimd-genome_sites.o: genome_sites.c
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+gsnap_nosimd-genome_sites.obj: genome_sites.c
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+
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+gsnap_nosimd-indexdb.obj: indexdb.c
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+gsnap_nosimd-indexdb_hr.obj: indexdb_hr.c
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+gsnap_nosimd-oligo.o: oligo.c
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+gsnap_nosimd-oligo.obj: oligo.c
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+gsnap_nosimd-chrom.o: chrom.c
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+gsnap_nosimd-chrom.obj: chrom.c
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+gsnap_nosimd-segmentpos.o: segmentpos.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-chrnum.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-chrnum.Tpo -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-chrnum.Tpo $(DEPDIR)/gsnap_nosimd-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_nosimd-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnap_nosimd-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-chrnum.Tpo -c -o gsnap_nosimd-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-chrnum.Tpo $(DEPDIR)/gsnap_nosimd-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_nosimd-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnap_nosimd-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-maxent_hr.Tpo -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-maxent_hr.Tpo $(DEPDIR)/gsnap_nosimd-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_nosimd-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnap_nosimd-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-maxent_hr.Tpo -c -o gsnap_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-maxent_hr.Tpo $(DEPDIR)/gsnap_nosimd-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_nosimd-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnap_nosimd-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-samprint.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-samprint.Tpo -c -o gsnap_nosimd-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-samprint.Tpo $(DEPDIR)/gsnap_nosimd-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_nosimd-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnap_nosimd-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-samprint.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-samprint.Tpo -c -o gsnap_nosimd-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-samprint.Tpo $(DEPDIR)/gsnap_nosimd-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_nosimd-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnap_nosimd-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-mapq.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-mapq.Tpo -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-mapq.Tpo $(DEPDIR)/gsnap_nosimd-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_nosimd-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnap_nosimd-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-mapq.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-mapq.Tpo -c -o gsnap_nosimd-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-mapq.Tpo $(DEPDIR)/gsnap_nosimd-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_nosimd-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnap_nosimd-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-shortread.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-shortread.Tpo -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-shortread.Tpo $(DEPDIR)/gsnap_nosimd-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_nosimd-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnap_nosimd-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-shortread.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-shortread.Tpo -c -o gsnap_nosimd-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-shortread.Tpo $(DEPDIR)/gsnap_nosimd-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_nosimd-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnap_nosimd-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-substring.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-substring.Tpo -c -o gsnap_nosimd-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-substring.Tpo $(DEPDIR)/gsnap_nosimd-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_nosimd-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnap_nosimd-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-substring.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-substring.Tpo -c -o gsnap_nosimd-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-substring.Tpo $(DEPDIR)/gsnap_nosimd-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_nosimd-substring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnap_nosimd-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-junction.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-junction.Tpo -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-junction.Tpo $(DEPDIR)/gsnap_nosimd-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_nosimd-junction.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+
+gsnap_nosimd-junction.obj: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-junction.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-junction.Tpo -c -o gsnap_nosimd-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-junction.Tpo $(DEPDIR)/gsnap_nosimd-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_nosimd-junction.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+
+gsnap_nosimd-stage3hr.o: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage3hr.Tpo -c -o gsnap_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stage3hr.Tpo $(DEPDIR)/gsnap_nosimd-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap_nosimd-stage3hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+
+gsnap_nosimd-stage3hr.obj: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage3hr.Tpo -c -o gsnap_nosimd-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stage3hr.Tpo $(DEPDIR)/gsnap_nosimd-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap_nosimd-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+
+gsnap_nosimd-spanningelt.o: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-spanningelt.Tpo -c -o gsnap_nosimd-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-spanningelt.Tpo $(DEPDIR)/gsnap_nosimd-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap_nosimd-spanningelt.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+
+gsnap_nosimd-spanningelt.obj: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-spanningelt.Tpo -c -o gsnap_nosimd-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-spanningelt.Tpo $(DEPDIR)/gsnap_nosimd-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap_nosimd-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+
+gsnap_nosimd-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-cmet.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-cmet.Tpo -c -o gsnap_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-cmet.Tpo $(DEPDIR)/gsnap_nosimd-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnap_nosimd-cmet.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gsnap_nosimd-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-cmet.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-cmet.Tpo -c -o gsnap_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-cmet.Tpo $(DEPDIR)/gsnap_nosimd-cmet.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cmet.c' object='gsnap_nosimd-cmet.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+gsnap_nosimd-pair.obj: pair.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-pair.Tpo $(DEPDIR)/gsnap_nosimd-pair.Po
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+gsnap_nosimd-diag.obj: diag.c
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+gsnap_nosimd-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage2.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage2.Tpo -c -o gsnap_nosimd-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stage2.Tpo $(DEPDIR)/gsnap_nosimd-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnap_nosimd-stage2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gsnap_nosimd-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-intron.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-intron.Tpo -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-intron.Tpo $(DEPDIR)/gsnap_nosimd-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnap_nosimd-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gsnap_nosimd-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-intron.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-intron.Tpo -c -o gsnap_nosimd-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-intron.Tpo $(DEPDIR)/gsnap_nosimd-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnap_nosimd-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gsnap_nosimd-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-boyer-moore.Tpo -c -o gsnap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-boyer-moore.Tpo $(DEPDIR)/gsnap_nosimd-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnap_nosimd-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gsnap_nosimd-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-boyer-moore.Tpo -c -o gsnap_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-boyer-moore.Tpo $(DEPDIR)/gsnap_nosimd-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnap_nosimd-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gsnap_nosimd-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-changepoint.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-changepoint.Tpo -c -o gsnap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-changepoint.Tpo $(DEPDIR)/gsnap_nosimd-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnap_nosimd-changepoint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+
+gsnap_nosimd-changepoint.obj: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-changepoint.Tpo -c -o gsnap_nosimd-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-changepoint.Tpo $(DEPDIR)/gsnap_nosimd-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnap_nosimd-changepoint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+
+gsnap_nosimd-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-pbinom.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-pbinom.Tpo -c -o gsnap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-pbinom.Tpo $(DEPDIR)/gsnap_nosimd-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnap_nosimd-pbinom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+
+gsnap_nosimd-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-pbinom.Tpo -c -o gsnap_nosimd-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-pbinom.Tpo $(DEPDIR)/gsnap_nosimd-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnap_nosimd-pbinom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+
+gsnap_nosimd-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog.Tpo -c -o gsnap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog.Tpo $(DEPDIR)/gsnap_nosimd-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnap_nosimd-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gsnap_nosimd-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog.Tpo -c -o gsnap_nosimd-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog.Tpo $(DEPDIR)/gsnap_nosimd-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnap_nosimd-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gsnap_nosimd-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_simd.Tpo -c -o gsnap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_simd.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap_nosimd-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gsnap_nosimd-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_simd.Tpo -c -o gsnap_nosimd-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_simd.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap_nosimd-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gsnap_nosimd-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_single.Tpo -c -o gsnap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_single.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap_nosimd-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gsnap_nosimd-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_single.Tpo -c -o gsnap_nosimd-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_single.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap_nosimd-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gsnap_nosimd-dynprog_genome.o: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_genome.Tpo -c -o gsnap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_genome.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap_nosimd-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+
+gsnap_nosimd-dynprog_genome.obj: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_genome.Tpo -c -o gsnap_nosimd-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_genome.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap_nosimd-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+
+gsnap_nosimd-dynprog_cdna.o: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_cdna.Tpo -c -o gsnap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_cdna.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnap_nosimd-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+
+gsnap_nosimd-dynprog_cdna.obj: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_cdna.Tpo -c -o gsnap_nosimd-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_cdna.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnap_nosimd-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+
+gsnap_nosimd-dynprog_end.o: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_end.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_end.Tpo -c -o gsnap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_end.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_end.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+
+gsnap_nosimd-dynprog_end.obj: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-dynprog_end.Tpo -c -o gsnap_nosimd-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-dynprog_end.Tpo $(DEPDIR)/gsnap_nosimd-dynprog_end.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+
+gsnap_nosimd-gbuffer.o: gbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-gbuffer.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-gbuffer.Tpo -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-gbuffer.Tpo $(DEPDIR)/gsnap_nosimd-gbuffer.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnap_nosimd-gbuffer.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
+
+gsnap_nosimd-gbuffer.obj: gbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-gbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-gbuffer.Tpo -c -o gsnap_nosimd-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-gbuffer.Tpo $(DEPDIR)/gsnap_nosimd-gbuffer.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnap_nosimd-gbuffer.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
+
+gsnap_nosimd-translation.o: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-translation.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-translation.Tpo -c -o gsnap_nosimd-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-translation.Tpo $(DEPDIR)/gsnap_nosimd-translation.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+
+gsnap_nosimd-translation.obj: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-translation.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-translation.Tpo -c -o gsnap_nosimd-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-translation.Tpo $(DEPDIR)/gsnap_nosimd-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnap_nosimd-translation.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+
+gsnap_nosimd-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-doublelist.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-doublelist.Tpo -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-doublelist.Tpo $(DEPDIR)/gsnap_nosimd-doublelist.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gsnap_nosimd-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-doublelist.Tpo -c -o gsnap_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-doublelist.Tpo $(DEPDIR)/gsnap_nosimd-doublelist.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gsnap_nosimd-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-smooth.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-smooth.Tpo -c -o gsnap_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-smooth.Tpo $(DEPDIR)/gsnap_nosimd-smooth.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gsnap_nosimd-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-smooth.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-smooth.Tpo -c -o gsnap_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-smooth.Tpo $(DEPDIR)/gsnap_nosimd-smooth.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gsnap_nosimd-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-chimera.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-chimera.Tpo -c -o gsnap_nosimd-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-chimera.Tpo $(DEPDIR)/gsnap_nosimd-chimera.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gsnap_nosimd-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-chimera.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-chimera.Tpo -c -o gsnap_nosimd-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-chimera.Tpo $(DEPDIR)/gsnap_nosimd-chimera.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnap_nosimd-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage3.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage3.Tpo -c -o gsnap_nosimd-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stage3.Tpo $(DEPDIR)/gsnap_nosimd-stage3.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnap_nosimd-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage3.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage3.Tpo -c -o gsnap_nosimd-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stage3.Tpo $(DEPDIR)/gsnap_nosimd-stage3.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnap_nosimd-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-splicestringpool.Tpo -c -o gsnap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-splicestringpool.Tpo $(DEPDIR)/gsnap_nosimd-splicestringpool.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnap_nosimd-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-splicestringpool.Tpo -c -o gsnap_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-splicestringpool.Tpo $(DEPDIR)/gsnap_nosimd-splicestringpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnap_nosimd-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-splicetrie_build.Tpo -c -o gsnap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-splicetrie_build.Tpo $(DEPDIR)/gsnap_nosimd-splicetrie_build.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnap_nosimd-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-splicetrie_build.Tpo -c -o gsnap_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-splicetrie_build.Tpo $(DEPDIR)/gsnap_nosimd-splicetrie_build.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -c -o gsnap_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
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+gsnap_nosimd-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-splicetrie.Tpo -c -o gsnap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-splicetrie.Tpo $(DEPDIR)/gsnap_nosimd-splicetrie.Po
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+gsnap_nosimd-splicetrie.obj: splicetrie.c
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+gsnap_nosimd-splice.obj: splice.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-splice.Tpo $(DEPDIR)/gsnap_nosimd-splice.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-indel.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-indel.Tpo -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
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+gsnap_nosimd-indel.obj: indel.c
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+
+gsnap_nosimd-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-bitpack64-access.Tpo -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-bitpack64-access.Tpo $(DEPDIR)/gsnap_nosimd-bitpack64-access.Po
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+gsnap_nosimd-bitpack64-access.obj: bitpack64-access.c
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+gsnap_nosimd-bytecoding.o: bytecoding.c
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+
+gsnap_nosimd-bytecoding.obj: bytecoding.c
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+gsnap_nosimd-univdiag.o: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-univdiag.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-univdiag.Tpo -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '$(srcdir)/'`univdiag.c
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+gsnap_nosimd-univdiag.obj: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-univdiag.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-univdiag.Tpo -c -o gsnap_nosimd-univdiag.obj `if test -f 'univdiag.c'; then $(CYGPATH_W) 'univdiag.c'; else $(CYGPATH_W) '$(srcdir)/univdiag.c'; fi`
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+gsnap_nosimd-sarray-read.o: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-sarray-read.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-sarray-read.Tpo -c -o gsnap_nosimd-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
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+gsnap_nosimd-sarray-read.obj: sarray-read.c
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+gsnap_nosimd-stage1hr.o: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage1hr.o -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage1hr.Tpo -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
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+gsnap_nosimd-stage1hr.obj: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_nosimd_CFLAGS) $(CFLAGS) -MT gsnap_nosimd-stage1hr.obj -MD -MP -MF $(DEPDIR)/gsnap_nosimd-stage1hr.Tpo -c -o gsnap_nosimd-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-stage1hr.Tpo $(DEPDIR)/gsnap_nosimd-stage1hr.Po
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+gsnap_nosimd-request.o: request.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_nosimd-request.Tpo $(DEPDIR)/gsnap_nosimd-request.Po
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+gsnap_nosimd-request.obj: request.c
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+gsnap_nosimd-resulthr.obj: resulthr.c
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+gsnap_nosimd-getopt1.obj: getopt1.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-except.Tpo $(DEPDIR)/gsnap_sse2-except.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+
+gsnap_sse2-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-assert.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-assert.Tpo -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-assert.Tpo $(DEPDIR)/gsnap_sse2-assert.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+
+gsnap_sse2-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-assert.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-assert.Tpo -c -o gsnap_sse2-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-assert.Tpo $(DEPDIR)/gsnap_sse2-assert.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+
+gsnap_sse2-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-mem.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-mem.Tpo -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-mem.Tpo $(DEPDIR)/gsnap_sse2-mem.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+
+gsnap_sse2-mem.obj: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-mem.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-mem.Tpo -c -o gsnap_sse2-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-mem.Tpo $(DEPDIR)/gsnap_sse2-mem.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
+
+gsnap_sse2-intlist.o: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-intlist.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-intlist.Tpo -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-intlist.Tpo $(DEPDIR)/gsnap_sse2-intlist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+
+gsnap_sse2-intlist.obj: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-intlist.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-intlist.Tpo -c -o gsnap_sse2-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-intlist.Tpo $(DEPDIR)/gsnap_sse2-intlist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+
+gsnap_sse2-list.o: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-list.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-list.Tpo -c -o gsnap_sse2-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-list.Tpo $(DEPDIR)/gsnap_sse2-list.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+gsnap_sse2-list.obj: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-list.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-list.Tpo -c -o gsnap_sse2-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-list.Tpo $(DEPDIR)/gsnap_sse2-list.Po
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+
+gsnap_sse2-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-littleendian.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-littleendian.Tpo -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
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+gsnap_sse2-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-littleendian.Tpo -c -o gsnap_sse2-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-littleendian.Tpo $(DEPDIR)/gsnap_sse2-littleendian.Po
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+
+gsnap_sse2-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bigendian.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-bigendian.Tpo -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bigendian.Tpo $(DEPDIR)/gsnap_sse2-bigendian.Po
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+
+gsnap_sse2-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-bigendian.Tpo -c -o gsnap_sse2-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bigendian.Tpo $(DEPDIR)/gsnap_sse2-bigendian.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+
+gsnap_sse2-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-univinterval.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-univinterval.Tpo -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-univinterval.Tpo $(DEPDIR)/gsnap_sse2-univinterval.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+
+gsnap_sse2-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-univinterval.Tpo -c -o gsnap_sse2-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-univinterval.Tpo $(DEPDIR)/gsnap_sse2-univinterval.Po
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+
+gsnap_sse2-interval.o: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-interval.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-interval.Tpo -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-interval.Tpo $(DEPDIR)/gsnap_sse2-interval.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+
+gsnap_sse2-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-interval.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-interval.Tpo -c -o gsnap_sse2-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-interval.Tpo $(DEPDIR)/gsnap_sse2-interval.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
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+gsnap_sse2-uintlist.o: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-uintlist.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-uintlist.Tpo -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-uintlist.Tpo $(DEPDIR)/gsnap_sse2-uintlist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+
+gsnap_sse2-uintlist.obj: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-uintlist.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-uintlist.Tpo -c -o gsnap_sse2-uintlist.obj `if test -f 'uintlist.c'; then $(CYGPATH_W) 'uintlist.c'; else $(CYGPATH_W) '$(srcdir)/uintlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-uintlist.Tpo $(DEPDIR)/gsnap_sse2-uintlist.Po
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+gsnap_sse2-stopwatch.o: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-stopwatch.Tpo -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
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+
+gsnap_sse2-stopwatch.obj: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stopwatch.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-stopwatch.Tpo -c -o gsnap_sse2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-stopwatch.Tpo $(DEPDIR)/gsnap_sse2-stopwatch.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stopwatch.c' object='gsnap_sse2-stopwatch.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+
+gsnap_sse2-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-semaphore.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-semaphore.Tpo -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-semaphore.Tpo $(DEPDIR)/gsnap_sse2-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='gsnap_sse2-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+gsnap_sse2-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-semaphore.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-semaphore.Tpo -c -o gsnap_sse2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-semaphore.Tpo $(DEPDIR)/gsnap_sse2-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='gsnap_sse2-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
+gsnap_sse2-access.o: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-access.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-access.Tpo -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-access.Tpo $(DEPDIR)/gsnap_sse2-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap_sse2-access.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
+
+gsnap_sse2-access.obj: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-access.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-access.Tpo -c -o gsnap_sse2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-access.Tpo $(DEPDIR)/gsnap_sse2-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='access.c' object='gsnap_sse2-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-access.obj `if test -f 'access.c'; then $(CYGPATH_W) 'access.c'; else $(CYGPATH_W) '$(srcdir)/access.c'; fi`
+
+gsnap_sse2-filestring.o: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-filestring.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-filestring.Tpo -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-filestring.Tpo $(DEPDIR)/gsnap_sse2-filestring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='filestring.c' object='gsnap_sse2-filestring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
+
+gsnap_sse2-filestring.obj: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-filestring.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-filestring.Tpo -c -o gsnap_sse2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-filestring.Tpo $(DEPDIR)/gsnap_sse2-filestring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='filestring.c' object='gsnap_sse2-filestring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+
+gsnap_sse2-iit-read-univ.o: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-iit-read-univ.Tpo -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-iit-read-univ.Tpo $(DEPDIR)/gsnap_sse2-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap_sse2-iit-read-univ.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+
+gsnap_sse2-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-iit-read-univ.Tpo -c -o gsnap_sse2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-iit-read-univ.Tpo $(DEPDIR)/gsnap_sse2-iit-read-univ.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read-univ.c' object='gsnap_sse2-iit-read-univ.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+
+gsnap_sse2-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-iit-read.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-iit-read.Tpo -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-iit-read.Tpo $(DEPDIR)/gsnap_sse2-iit-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnap_sse2-iit-read.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+
+gsnap_sse2-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-iit-read.Tpo -c -o gsnap_sse2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-iit-read.Tpo $(DEPDIR)/gsnap_sse2-iit-read.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='iit-read.c' object='gsnap_sse2-iit-read.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+
+gsnap_sse2-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-md5.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-md5.Tpo -c -o gsnap_sse2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-md5.Tpo $(DEPDIR)/gsnap_sse2-md5.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gsnap_sse2-md5.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
+
+gsnap_sse2-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-md5.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-md5.Tpo -c -o gsnap_sse2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-md5.Tpo $(DEPDIR)/gsnap_sse2-md5.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='md5.c' object='gsnap_sse2-md5.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+
+gsnap_sse2-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bzip2.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-bzip2.Tpo -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bzip2.Tpo $(DEPDIR)/gsnap_sse2-bzip2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnap_sse2-bzip2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+
+gsnap_sse2-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-bzip2.Tpo -c -o gsnap_sse2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bzip2.Tpo $(DEPDIR)/gsnap_sse2-bzip2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bzip2.c' object='gsnap_sse2-bzip2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+
+gsnap_sse2-sequence.o: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-sequence.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-sequence.Tpo -c -o gsnap_sse2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-sequence.Tpo $(DEPDIR)/gsnap_sse2-sequence.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnap_sse2-sequence.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+
+gsnap_sse2-sequence.obj: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-sequence.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-sequence.Tpo -c -o gsnap_sse2-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-sequence.Tpo $(DEPDIR)/gsnap_sse2-sequence.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='sequence.c' object='gsnap_sse2-sequence.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+
+gsnap_sse2-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-reader.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-reader.Tpo -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-reader.Tpo $(DEPDIR)/gsnap_sse2-reader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnap_sse2-reader.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+
+gsnap_sse2-reader.obj: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-reader.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-reader.Tpo -c -o gsnap_sse2-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-reader.Tpo $(DEPDIR)/gsnap_sse2-reader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='reader.c' object='gsnap_sse2-reader.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+
+gsnap_sse2-genomicpos.o: genomicpos.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-genomicpos.Tpo $(DEPDIR)/gsnap_sse2-genomicpos.Po
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+
+gsnap_sse2-genomicpos.obj: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-genomicpos.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-genomicpos.Tpo -c -o gsnap_sse2-genomicpos.obj `if test -f 'genomicpos.c'; then $(CYGPATH_W) 'genomicpos.c'; else $(CYGPATH_W) '$(srcdir)/genomicpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-genomicpos.Tpo $(DEPDIR)/gsnap_sse2-genomicpos.Po
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+
+gsnap_sse2-compress.o: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-compress.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-compress.Tpo -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-compress.Tpo $(DEPDIR)/gsnap_sse2-compress.Po
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+
+gsnap_sse2-compress.obj: compress.c
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+
+gsnap_sse2-genome.o: genome.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-genome.Tpo $(DEPDIR)/gsnap_sse2-genome.Po
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+
+gsnap_sse2-genome.obj: genome.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-genome.Tpo $(DEPDIR)/gsnap_sse2-genome.Po
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+
+gsnap_sse2-popcount.o: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-popcount.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-popcount.Tpo -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
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+
+gsnap_sse2-popcount.obj: popcount.c
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+gsnap_sse2-genome128_hr.o: genome128_hr.c
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+gsnap_sse2-genome_sites.o: genome_sites.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-genome_sites.Tpo $(DEPDIR)/gsnap_sse2-genome_sites.Po
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+gsnap_sse2-genome_sites.obj: genome_sites.c
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+
+gsnap_sse2-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-indexdb_hr.Tpo -c -o gsnap_sse2-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-indexdb_hr.Tpo $(DEPDIR)/gsnap_sse2-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnap_sse2-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+
+gsnap_sse2-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-oligo.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-oligo.Tpo -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-oligo.Tpo $(DEPDIR)/gsnap_sse2-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnap_sse2-oligo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gsnap_sse2-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-oligo.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-oligo.Tpo -c -o gsnap_sse2-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-oligo.Tpo $(DEPDIR)/gsnap_sse2-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnap_sse2-oligo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+
+gsnap_sse2-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-chrom.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-chrom.Tpo -c -o gsnap_sse2-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-chrom.Tpo $(DEPDIR)/gsnap_sse2-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnap_sse2-chrom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+
+gsnap_sse2-chrom.obj: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-chrom.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-chrom.Tpo -c -o gsnap_sse2-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-chrom.Tpo $(DEPDIR)/gsnap_sse2-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnap_sse2-chrom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+
+gsnap_sse2-segmentpos.o: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-segmentpos.Tpo -c -o gsnap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-segmentpos.Tpo $(DEPDIR)/gsnap_sse2-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap_sse2-segmentpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+
+gsnap_sse2-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-segmentpos.Tpo -c -o gsnap_sse2-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-segmentpos.Tpo $(DEPDIR)/gsnap_sse2-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap_sse2-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gsnap_sse2-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-chrnum.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-chrnum.Tpo -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-chrnum.Tpo $(DEPDIR)/gsnap_sse2-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_sse2-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnap_sse2-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-chrnum.Tpo -c -o gsnap_sse2-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-chrnum.Tpo $(DEPDIR)/gsnap_sse2-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_sse2-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnap_sse2-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-maxent_hr.Tpo -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-maxent_hr.Tpo $(DEPDIR)/gsnap_sse2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_sse2-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnap_sse2-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-maxent_hr.Tpo -c -o gsnap_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-maxent_hr.Tpo $(DEPDIR)/gsnap_sse2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_sse2-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnap_sse2-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-samprint.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-samprint.Tpo -c -o gsnap_sse2-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-samprint.Tpo $(DEPDIR)/gsnap_sse2-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_sse2-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnap_sse2-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-samprint.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-samprint.Tpo -c -o gsnap_sse2-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-samprint.Tpo $(DEPDIR)/gsnap_sse2-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_sse2-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnap_sse2-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-mapq.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-mapq.Tpo -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-mapq.Tpo $(DEPDIR)/gsnap_sse2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_sse2-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnap_sse2-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-mapq.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-mapq.Tpo -c -o gsnap_sse2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-mapq.Tpo $(DEPDIR)/gsnap_sse2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_sse2-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnap_sse2-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-shortread.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-shortread.Tpo -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-shortread.Tpo $(DEPDIR)/gsnap_sse2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_sse2-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnap_sse2-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-shortread.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-shortread.Tpo -c -o gsnap_sse2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-shortread.Tpo $(DEPDIR)/gsnap_sse2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_sse2-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnap_sse2-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-substring.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-substring.Tpo -c -o gsnap_sse2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-substring.Tpo $(DEPDIR)/gsnap_sse2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_sse2-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnap_sse2-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-substring.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-substring.Tpo -c -o gsnap_sse2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-substring.Tpo $(DEPDIR)/gsnap_sse2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_sse2-substring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnap_sse2-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-junction.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-junction.Tpo -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-junction.Tpo $(DEPDIR)/gsnap_sse2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_sse2-junction.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+gsnap_sse2-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-orderstat.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-orderstat.Tpo -c -o gsnap_sse2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-orderstat.Tpo $(DEPDIR)/gsnap_sse2-orderstat.Po
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+
+gsnap_sse2-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-oligoindex_hr.Tpo -c -o gsnap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-oligoindex_hr.Tpo $(DEPDIR)/gsnap_sse2-oligoindex_hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gsnap_sse2-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-oligoindex_hr.Tpo -c -o gsnap_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-oligoindex_hr.Tpo $(DEPDIR)/gsnap_sse2-oligoindex_hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gsnap_sse2-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-cellpool.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-cellpool.Tpo -c -o gsnap_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-cellpool.Tpo $(DEPDIR)/gsnap_sse2-cellpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gsnap_sse2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-cellpool.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-cellpool.Tpo -c -o gsnap_sse2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-cellpool.Tpo $(DEPDIR)/gsnap_sse2-cellpool.Po
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+
+gsnap_sse2-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stage2.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-stage2.Tpo -c -o gsnap_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
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+gsnap_sse2-stage2.obj: stage2.c
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+gsnap_sse2-intron.o: intron.c
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+gsnap_sse2-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-intron.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-intron.Tpo -c -o gsnap_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
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+gsnap_sse2-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-boyer-moore.Tpo -c -o gsnap_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-boyer-moore.Tpo $(DEPDIR)/gsnap_sse2-boyer-moore.Po
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+gsnap_sse2-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-boyer-moore.Tpo -c -o gsnap_sse2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-boyer-moore.Tpo $(DEPDIR)/gsnap_sse2-boyer-moore.Po
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+gsnap_sse2-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-changepoint.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-changepoint.Tpo -c -o gsnap_sse2-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-changepoint.Tpo $(DEPDIR)/gsnap_sse2-changepoint.Po
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+gsnap_sse2-changepoint.obj: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-changepoint.Tpo -c -o gsnap_sse2-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
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+gsnap_sse2-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-pbinom.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-pbinom.Tpo -c -o gsnap_sse2-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-pbinom.Tpo $(DEPDIR)/gsnap_sse2-pbinom.Po
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+gsnap_sse2-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-pbinom.Tpo -c -o gsnap_sse2-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-pbinom.Tpo $(DEPDIR)/gsnap_sse2-pbinom.Po
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+gsnap_sse2-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog.Tpo -c -o gsnap_sse2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
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+gsnap_sse2-dynprog.obj: dynprog.c
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+gsnap_sse2-dynprog_simd.o: dynprog_simd.c
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+gsnap_sse2-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_simd.Tpo -c -o gsnap_sse2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_simd.Tpo $(DEPDIR)/gsnap_sse2-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap_sse2-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gsnap_sse2-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_single.Tpo -c -o gsnap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_single.Tpo $(DEPDIR)/gsnap_sse2-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap_sse2-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gsnap_sse2-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_single.Tpo -c -o gsnap_sse2-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_single.Tpo $(DEPDIR)/gsnap_sse2-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap_sse2-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gsnap_sse2-dynprog_genome.o: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_genome.Tpo -c -o gsnap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_genome.Tpo $(DEPDIR)/gsnap_sse2-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap_sse2-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+
+gsnap_sse2-dynprog_genome.obj: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_genome.Tpo -c -o gsnap_sse2-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_genome.Tpo $(DEPDIR)/gsnap_sse2-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap_sse2-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+
+gsnap_sse2-dynprog_cdna.o: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_cdna.Tpo -c -o gsnap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_cdna.Tpo $(DEPDIR)/gsnap_sse2-dynprog_cdna.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+
+gsnap_sse2-dynprog_cdna.obj: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_cdna.Tpo -c -o gsnap_sse2-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_cdna.Tpo $(DEPDIR)/gsnap_sse2-dynprog_cdna.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+
+gsnap_sse2-dynprog_end.o: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_end.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_end.Tpo -c -o gsnap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_end.Tpo $(DEPDIR)/gsnap_sse2-dynprog_end.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+
+gsnap_sse2-dynprog_end.obj: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-dynprog_end.Tpo -c -o gsnap_sse2-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-dynprog_end.Tpo $(DEPDIR)/gsnap_sse2-dynprog_end.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+
+gsnap_sse2-gbuffer.o: gbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-gbuffer.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-gbuffer.Tpo -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-gbuffer.Tpo $(DEPDIR)/gsnap_sse2-gbuffer.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
+
+gsnap_sse2-gbuffer.obj: gbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-gbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-gbuffer.Tpo -c -o gsnap_sse2-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-gbuffer.Tpo $(DEPDIR)/gsnap_sse2-gbuffer.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
+
+gsnap_sse2-translation.o: translation.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-translation.Tpo $(DEPDIR)/gsnap_sse2-translation.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+
+gsnap_sse2-translation.obj: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-translation.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-translation.Tpo -c -o gsnap_sse2-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-translation.Tpo $(DEPDIR)/gsnap_sse2-translation.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+
+gsnap_sse2-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-doublelist.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-doublelist.Tpo -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-doublelist.Tpo $(DEPDIR)/gsnap_sse2-doublelist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gsnap_sse2-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-doublelist.Tpo -c -o gsnap_sse2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-doublelist.Tpo $(DEPDIR)/gsnap_sse2-doublelist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
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+gsnap_sse2-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-smooth.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-smooth.Tpo -c -o gsnap_sse2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-smooth.Tpo $(DEPDIR)/gsnap_sse2-smooth.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gsnap_sse2-smooth.obj: smooth.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-smooth.Tpo $(DEPDIR)/gsnap_sse2-smooth.Po
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+gsnap_sse2-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-chimera.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-chimera.Tpo -c -o gsnap_sse2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-chimera.Tpo $(DEPDIR)/gsnap_sse2-chimera.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
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+gsnap_sse2-chimera.obj: chimera.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-chimera.Tpo $(DEPDIR)/gsnap_sse2-chimera.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnap_sse2-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stage3.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-stage3.Tpo -c -o gsnap_sse2-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-stage3.Tpo $(DEPDIR)/gsnap_sse2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap_sse2-stage3.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnap_sse2-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stage3.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-stage3.Tpo -c -o gsnap_sse2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-stage3.Tpo $(DEPDIR)/gsnap_sse2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap_sse2-stage3.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnap_sse2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-splicestringpool.Tpo -c -o gsnap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splicestringpool.Tpo $(DEPDIR)/gsnap_sse2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap_sse2-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnap_sse2-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-splicestringpool.Tpo -c -o gsnap_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splicestringpool.Tpo $(DEPDIR)/gsnap_sse2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap_sse2-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnap_sse2-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-splicetrie_build.Tpo -c -o gsnap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splicetrie_build.Tpo $(DEPDIR)/gsnap_sse2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap_sse2-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnap_sse2-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-splicetrie_build.Tpo -c -o gsnap_sse2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splicetrie_build.Tpo $(DEPDIR)/gsnap_sse2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap_sse2-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnap_sse2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-splicetrie.Tpo -c -o gsnap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splicetrie.Tpo $(DEPDIR)/gsnap_sse2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnap_sse2-splicetrie.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gsnap_sse2-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-splicetrie.Tpo -c -o gsnap_sse2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splicetrie.Tpo $(DEPDIR)/gsnap_sse2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnap_sse2-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gsnap_sse2-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splice.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-splice.Tpo -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splice.Tpo $(DEPDIR)/gsnap_sse2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap_sse2-splice.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnap_sse2-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-splice.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-splice.Tpo -c -o gsnap_sse2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-splice.Tpo $(DEPDIR)/gsnap_sse2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap_sse2-splice.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+
+gsnap_sse2-indel.o: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-indel.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-indel.Tpo -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-indel.Tpo $(DEPDIR)/gsnap_sse2-indel.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnap_sse2-indel.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+
+gsnap_sse2-indel.obj: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-indel.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-indel.Tpo -c -o gsnap_sse2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-indel.Tpo $(DEPDIR)/gsnap_sse2-indel.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+
+gsnap_sse2-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-bitpack64-access.Tpo -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bitpack64-access.Tpo $(DEPDIR)/gsnap_sse2-bitpack64-access.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+gsnap_sse2-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-bitpack64-access.Tpo -c -o gsnap_sse2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bitpack64-access.Tpo $(DEPDIR)/gsnap_sse2-bitpack64-access.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+
+gsnap_sse2-bytecoding.o: bytecoding.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bytecoding.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-bytecoding.Tpo -c -o gsnap_sse2-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bytecoding.Tpo $(DEPDIR)/gsnap_sse2-bytecoding.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bytecoding.c' object='gsnap_sse2-bytecoding.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
+
+gsnap_sse2-bytecoding.obj: bytecoding.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-bytecoding.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-bytecoding.Tpo -c -o gsnap_sse2-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-bytecoding.Tpo $(DEPDIR)/gsnap_sse2-bytecoding.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
+
+gsnap_sse2-univdiag.o: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-univdiag.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-univdiag.Tpo -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo '$(srcdir)/'`univdiag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-univdiag.Tpo $(DEPDIR)/gsnap_sse2-univdiag.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='univdiag.c' object='gsnap_sse2-univdiag.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo '$(srcdir)/'`univdiag.c
+
+gsnap_sse2-univdiag.obj: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-univdiag.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-univdiag.Tpo -c -o gsnap_sse2-univdiag.obj `if test -f 'univdiag.c'; then $(CYGPATH_W) 'univdiag.c'; else $(CYGPATH_W) '$(srcdir)/univdiag.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-univdiag.Tpo $(DEPDIR)/gsnap_sse2-univdiag.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-univdiag.obj `if test -f 'univdiag.c'; then $(CYGPATH_W) 'univdiag.c'; else $(CYGPATH_W) '$(srcdir)/univdiag.c'; fi`
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+gsnap_sse2-sarray-read.o: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-sarray-read.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-sarray-read.Tpo -c -o gsnap_sse2-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-sarray-read.Tpo $(DEPDIR)/gsnap_sse2-sarray-read.Po
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+
+gsnap_sse2-sarray-read.obj: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-sarray-read.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-sarray-read.Tpo -c -o gsnap_sse2-sarray-read.obj `if test -f 'sarray-read.c'; then $(CYGPATH_W) 'sarray-read.c'; else $(CYGPATH_W) '$(srcdir)/sarray-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-sarray-read.Tpo $(DEPDIR)/gsnap_sse2-sarray-read.Po
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+
+gsnap_sse2-stage1hr.o: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stage1hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-stage1hr.Tpo -c -o gsnap_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-stage1hr.Tpo $(DEPDIR)/gsnap_sse2-stage1hr.Po
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+gsnap_sse2-stage1hr.obj: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-stage1hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-stage1hr.Tpo -c -o gsnap_sse2-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-stage1hr.Tpo $(DEPDIR)/gsnap_sse2-stage1hr.Po
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+
+gsnap_sse2-request.o: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-request.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-request.Tpo -c -o gsnap_sse2-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-request.Tpo $(DEPDIR)/gsnap_sse2-request.Po
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+
+gsnap_sse2-request.obj: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-request.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-request.Tpo -c -o gsnap_sse2-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-request.Tpo $(DEPDIR)/gsnap_sse2-request.Po
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+gsnap_sse2-resulthr.o: resulthr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-resulthr.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-resulthr.Tpo -c -o gsnap_sse2-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
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+gsnap_sse2-resulthr.obj: resulthr.c
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+gsnap_sse2-output.o: output.c
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+gsnap_sse2-output.obj: output.c
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+gsnap_sse2-outbuffer.obj: outbuffer.c
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+gsnap_sse2-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-datadir.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-datadir.Tpo -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-getopt.Tpo $(DEPDIR)/gsnap_sse2-getopt.Po
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+
+gsnap_sse2-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-getopt.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-getopt.Tpo -c -o gsnap_sse2-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-getopt.Tpo $(DEPDIR)/gsnap_sse2-getopt.Po
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+
+gsnap_sse2-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-getopt1.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-getopt1.Tpo -c -o gsnap_sse2-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-getopt1.Tpo $(DEPDIR)/gsnap_sse2-getopt1.Po
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+
+gsnap_sse2-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-getopt1.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-getopt1.Tpo -c -o gsnap_sse2-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-getopt1.Tpo $(DEPDIR)/gsnap_sse2-getopt1.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-gsnap.o -MD -MP -MF $(DEPDIR)/gsnap_sse2-gsnap.Tpo -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-gsnap.Tpo $(DEPDIR)/gsnap_sse2-gsnap.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
+
+gsnap_sse2-gsnap.obj: gsnap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse2_CFLAGS) $(CFLAGS) -MT gsnap_sse2-gsnap.obj -MD -MP -MF $(DEPDIR)/gsnap_sse2-gsnap.Tpo -c -o gsnap_sse2-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse2-gsnap.Tpo $(DEPDIR)/gsnap_sse2-gsnap.Po
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+
+gsnap_sse41-except.o: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-except.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-except.Tpo -c -o gsnap_sse41-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-except.Tpo $(DEPDIR)/gsnap_sse41-except.Po
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+
+gsnap_sse41-except.obj: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-except.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-except.Tpo -c -o gsnap_sse41-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-except.Tpo $(DEPDIR)/gsnap_sse41-except.Po
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+
+gsnap_sse41-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-assert.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-assert.Tpo -c -o gsnap_sse41-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-assert.Tpo $(DEPDIR)/gsnap_sse41-assert.Po
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+
+gsnap_sse41-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-assert.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-assert.Tpo -c -o gsnap_sse41-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-assert.Tpo $(DEPDIR)/gsnap_sse41-assert.Po
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+gsnap_sse41-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-mem.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-mem.Tpo -c -o gsnap_sse41-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-mem.Tpo $(DEPDIR)/gsnap_sse41-mem.Po
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+
+gsnap_sse41-mem.obj: mem.c
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+
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+gsnap_sse41-intlist.obj: intlist.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-list.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-list.Tpo -c -o gsnap_sse41-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-list.Tpo $(DEPDIR)/gsnap_sse41-list.Po
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+
+gsnap_sse41-list.obj: list.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-list.Tpo $(DEPDIR)/gsnap_sse41-list.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-littleendian.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-littleendian.Tpo -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
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+gsnap_sse41-littleendian.obj: littleendian.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-littleendian.Tpo $(DEPDIR)/gsnap_sse41-littleendian.Po
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+gsnap_sse41-bigendian.o: bigendian.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-md5.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-md5.Tpo -c -o gsnap_sse41-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-md5.Tpo $(DEPDIR)/gsnap_sse41-md5.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+
+gsnap_sse41-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-bzip2.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-bzip2.Tpo -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-bzip2.Tpo $(DEPDIR)/gsnap_sse41-bzip2.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
+
+gsnap_sse41-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-bzip2.Tpo -c -o gsnap_sse41-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-bzip2.Tpo $(DEPDIR)/gsnap_sse41-bzip2.Po
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+
+gsnap_sse41-sequence.o: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-sequence.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-sequence.Tpo -c -o gsnap_sse41-sequence.o `test -f 'sequence.c' || echo '$(srcdir)/'`sequence.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-sequence.Tpo $(DEPDIR)/gsnap_sse41-sequence.Po
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+
+gsnap_sse41-sequence.obj: sequence.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-sequence.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-sequence.Tpo -c -o gsnap_sse41-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-sequence.Tpo $(DEPDIR)/gsnap_sse41-sequence.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-sequence.obj `if test -f 'sequence.c'; then $(CYGPATH_W) 'sequence.c'; else $(CYGPATH_W) '$(srcdir)/sequence.c'; fi`
+
+gsnap_sse41-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-reader.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-reader.Tpo -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-reader.Tpo $(DEPDIR)/gsnap_sse41-reader.Po
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+
+gsnap_sse41-reader.obj: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-reader.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-reader.Tpo -c -o gsnap_sse41-reader.obj `if test -f 'reader.c'; then $(CYGPATH_W) 'reader.c'; else $(CYGPATH_W) '$(srcdir)/reader.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-reader.Tpo $(DEPDIR)/gsnap_sse41-reader.Po
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+
+gsnap_sse41-genomicpos.o: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-genomicpos.Tpo -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genomicpos.Tpo $(DEPDIR)/gsnap_sse41-genomicpos.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
+
+gsnap_sse41-genomicpos.obj: genomicpos.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genomicpos.Tpo $(DEPDIR)/gsnap_sse41-genomicpos.Po
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+
+gsnap_sse41-compress.o: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-compress.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-compress.Tpo -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-compress.Tpo $(DEPDIR)/gsnap_sse41-compress.Po
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+
+gsnap_sse41-compress.obj: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-compress.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-compress.Tpo -c -o gsnap_sse41-compress.obj `if test -f 'compress.c'; then $(CYGPATH_W) 'compress.c'; else $(CYGPATH_W) '$(srcdir)/compress.c'; fi`
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+
+gsnap_sse41-genome.o: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-genome.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-genome.Tpo -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genome.Tpo $(DEPDIR)/gsnap_sse41-genome.Po
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+
+gsnap_sse41-genome.obj: genome.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genome.Tpo $(DEPDIR)/gsnap_sse41-genome.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-popcount.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-popcount.Tpo -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-popcount.Tpo $(DEPDIR)/gsnap_sse41-popcount.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+
+gsnap_sse41-popcount.obj: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-popcount.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-popcount.Tpo -c -o gsnap_sse41-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-popcount.Tpo $(DEPDIR)/gsnap_sse41-popcount.Po
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+gsnap_sse41-genome128_hr.o: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-genome128_hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-genome128_hr.Tpo -c -o gsnap_sse41-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genome128_hr.Tpo $(DEPDIR)/gsnap_sse41-genome128_hr.Po
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+gsnap_sse41-genome128_hr.obj: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-genome128_hr.Tpo -c -o gsnap_sse41-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genome128_hr.Tpo $(DEPDIR)/gsnap_sse41-genome128_hr.Po
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+gsnap_sse41-genome_sites.o: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-genome_sites.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-genome_sites.Tpo -c -o gsnap_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-genome_sites.Tpo $(DEPDIR)/gsnap_sse41-genome_sites.Po
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+gsnap_sse41-genome_sites.obj: genome_sites.c
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+gsnap_sse41-doublelist.obj: doublelist.c
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+gsnap_sse41-smooth.obj: smooth.c
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+gsnap_sse41-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-chimera.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-chimera.Tpo -c -o gsnap_sse41-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
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+gsnap_sse41-chimera.obj: chimera.c
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+gsnap_sse41-splicetrie.o: splicetrie.c
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+gsnap_sse41-splicetrie.obj: splicetrie.c
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+gsnap_sse41-splice.obj: splice.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-samheader.Tpo $(DEPDIR)/gsnap_sse41-samheader.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samheader.c' object='gsnap_sse41-samheader.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-samheader.obj `if test -f 'samheader.c'; then $(CYGPATH_W) 'samheader.c'; else $(CYGPATH_W) '$(srcdir)/samheader.c'; fi`
+
+gsnap_sse41-outbuffer.o: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-outbuffer.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-outbuffer.Tpo -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-outbuffer.Tpo $(DEPDIR)/gsnap_sse41-outbuffer.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '$(srcdir)/'`outbuffer.c
+
+gsnap_sse41-outbuffer.obj: outbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-outbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-outbuffer.Tpo -c -o gsnap_sse41-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-outbuffer.Tpo $(DEPDIR)/gsnap_sse41-outbuffer.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-outbuffer.obj `if test -f 'outbuffer.c'; then $(CYGPATH_W) 'outbuffer.c'; else $(CYGPATH_W) '$(srcdir)/outbuffer.c'; fi`
+
+gsnap_sse41-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-datadir.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-datadir.Tpo -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-datadir.Tpo $(DEPDIR)/gsnap_sse41-datadir.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
+
+gsnap_sse41-datadir.obj: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-datadir.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-datadir.Tpo -c -o gsnap_sse41-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-datadir.Tpo $(DEPDIR)/gsnap_sse41-datadir.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+
+gsnap_sse41-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-parserange.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-parserange.Tpo -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-parserange.Tpo $(DEPDIR)/gsnap_sse41-parserange.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+gsnap_sse41-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-parserange.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-parserange.Tpo -c -o gsnap_sse41-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-parserange.Tpo $(DEPDIR)/gsnap_sse41-parserange.Po
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+
+gsnap_sse41-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-getopt.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-getopt.Tpo -c -o gsnap_sse41-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-getopt.Tpo $(DEPDIR)/gsnap_sse41-getopt.Po
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+
+gsnap_sse41-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-getopt.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-getopt.Tpo -c -o gsnap_sse41-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-getopt.Tpo $(DEPDIR)/gsnap_sse41-getopt.Po
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+
+gsnap_sse41-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-getopt1.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-getopt1.Tpo -c -o gsnap_sse41-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-getopt1.Tpo $(DEPDIR)/gsnap_sse41-getopt1.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+
+gsnap_sse41-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-getopt1.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-getopt1.Tpo -c -o gsnap_sse41-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-getopt1.Tpo $(DEPDIR)/gsnap_sse41-getopt1.Po
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+
+gsnap_sse41-gsnap.o: gsnap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-gsnap.o -MD -MP -MF $(DEPDIR)/gsnap_sse41-gsnap.Tpo -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-gsnap.Tpo $(DEPDIR)/gsnap_sse41-gsnap.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
+
+gsnap_sse41-gsnap.obj: gsnap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -MT gsnap_sse41-gsnap.obj -MD -MP -MF $(DEPDIR)/gsnap_sse41-gsnap.Tpo -c -o gsnap_sse41-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse41-gsnap.Tpo $(DEPDIR)/gsnap_sse41-gsnap.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse41_CFLAGS) $(CFLAGS) -c -o gsnap_sse41-gsnap.obj `if test -f 'gsnap.c'; then $(CYGPATH_W) 'gsnap.c'; else $(CYGPATH_W) '$(srcdir)/gsnap.c'; fi`
+
+gsnap_sse42-except.o: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-except.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-except.Tpo -c -o gsnap_sse42-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-except.Tpo $(DEPDIR)/gsnap_sse42-except.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+
+gsnap_sse42-except.obj: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-except.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-except.Tpo -c -o gsnap_sse42-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-except.Tpo $(DEPDIR)/gsnap_sse42-except.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+
+gsnap_sse42-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-assert.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-assert.Tpo -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-assert.Tpo $(DEPDIR)/gsnap_sse42-assert.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+
+gsnap_sse42-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-assert.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-assert.Tpo -c -o gsnap_sse42-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-assert.Tpo $(DEPDIR)/gsnap_sse42-assert.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
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+gsnap_sse42-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-mem.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-mem.Tpo -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-mem.Tpo $(DEPDIR)/gsnap_sse42-mem.Po
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+gsnap_sse42-mem.obj: mem.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-intlist.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-intlist.Tpo -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-intlist.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-intlist.Tpo -c -o gsnap_sse42-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-intlist.Tpo $(DEPDIR)/gsnap_sse42-intlist.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+
+gsnap_sse42-list.o: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-list.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-list.Tpo -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-list.Tpo $(DEPDIR)/gsnap_sse42-list.Po
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+
+gsnap_sse42-list.obj: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-list.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-list.Tpo -c -o gsnap_sse42-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-list.Tpo $(DEPDIR)/gsnap_sse42-list.Po
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+
+gsnap_sse42-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-littleendian.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-littleendian.Tpo -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-littleendian.Tpo $(DEPDIR)/gsnap_sse42-littleendian.Po
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+gsnap_sse42-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-littleendian.Tpo -c -o gsnap_sse42-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-littleendian.Tpo $(DEPDIR)/gsnap_sse42-littleendian.Po
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+
+gsnap_sse42-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bigendian.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-bigendian.Tpo -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bigendian.Tpo $(DEPDIR)/gsnap_sse42-bigendian.Po
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+
+gsnap_sse42-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-bigendian.Tpo -c -o gsnap_sse42-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bigendian.Tpo $(DEPDIR)/gsnap_sse42-bigendian.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-univinterval.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-univinterval.Tpo -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-univinterval.Tpo $(DEPDIR)/gsnap_sse42-univinterval.Po
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+
+gsnap_sse42-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-univinterval.Tpo -c -o gsnap_sse42-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-univinterval.Tpo $(DEPDIR)/gsnap_sse42-univinterval.Po
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+
+gsnap_sse42-interval.o: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-interval.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-interval.Tpo -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-interval.Tpo $(DEPDIR)/gsnap_sse42-interval.Po
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+
+gsnap_sse42-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-interval.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-interval.Tpo -c -o gsnap_sse42-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-interval.Tpo $(DEPDIR)/gsnap_sse42-interval.Po
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+gsnap_sse42-uintlist.o: uintlist.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-uintlist.Tpo $(DEPDIR)/gsnap_sse42-uintlist.Po
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+
+gsnap_sse42-uintlist.obj: uintlist.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-uintlist.Tpo $(DEPDIR)/gsnap_sse42-uintlist.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-stopwatch.Tpo -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
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+gsnap_sse42-stopwatch.obj: stopwatch.c
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+gsnap_sse42-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-semaphore.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-semaphore.Tpo -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-semaphore.Tpo $(DEPDIR)/gsnap_sse42-semaphore.Po
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+gsnap_sse42-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-semaphore.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-semaphore.Tpo -c -o gsnap_sse42-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-semaphore.Tpo $(DEPDIR)/gsnap_sse42-semaphore.Po
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+gsnap_sse42-filestring.obj: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-filestring.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-filestring.Tpo -c -o gsnap_sse42-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-iit-read-univ.Tpo $(DEPDIR)/gsnap_sse42-iit-read-univ.Po
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+gsnap_sse42-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-iit-read-univ.Tpo -c -o gsnap_sse42-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-iit-read-univ.Tpo $(DEPDIR)/gsnap_sse42-iit-read-univ.Po
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+gsnap_sse42-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-iit-read.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-iit-read.Tpo -c -o gsnap_sse42-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
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+
+gsnap_sse42-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-iit-read.Tpo -c -o gsnap_sse42-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
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+
+gsnap_sse42-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-md5.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-md5.Tpo -c -o gsnap_sse42-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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+gsnap_sse42-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-md5.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-md5.Tpo -c -o gsnap_sse42-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
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+gsnap_sse42-bzip2.o: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bzip2.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-bzip2.Tpo -c -o gsnap_sse42-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
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+gsnap_sse42-bzip2.obj: bzip2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bzip2.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-bzip2.Tpo -c -o gsnap_sse42-bzip2.obj `if test -f 'bzip2.c'; then $(CYGPATH_W) 'bzip2.c'; else $(CYGPATH_W) '$(srcdir)/bzip2.c'; fi`
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+gsnap_sse42-sequence.o: sequence.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-sequence.Tpo $(DEPDIR)/gsnap_sse42-sequence.Po
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+gsnap_sse42-sequence.obj: sequence.c
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+gsnap_sse42-reader.o: reader.c
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+gsnap_sse42-reader.obj: reader.c
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+gsnap_sse42-genomicpos.o: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-genomicpos.Tpo -c -o gsnap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
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+gsnap_sse42-genomicpos.obj: genomicpos.c
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+gsnap_sse42-compress.o: compress.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-compress.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-compress.Tpo -c -o gsnap_sse42-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
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+gsnap_sse42-compress.obj: compress.c
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+gsnap_sse42-genome.o: genome.c
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+gsnap_sse42-genome.obj: genome.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-genome.Tpo $(DEPDIR)/gsnap_sse42-genome.Po
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-popcount.Tpo $(DEPDIR)/gsnap_sse42-popcount.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+
+gsnap_sse42-popcount.obj: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-popcount.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-popcount.Tpo -c -o gsnap_sse42-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-popcount.Tpo $(DEPDIR)/gsnap_sse42-popcount.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+
+gsnap_sse42-genome128_hr.o: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-genome128_hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-genome128_hr.Tpo -c -o gsnap_sse42-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-genome128_hr.Tpo $(DEPDIR)/gsnap_sse42-genome128_hr.Po
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+
+gsnap_sse42-genome128_hr.obj: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-genome128_hr.Tpo -c -o gsnap_sse42-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-genome128_hr.Tpo $(DEPDIR)/gsnap_sse42-genome128_hr.Po
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+
+gsnap_sse42-genome_sites.o: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-genome_sites.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-genome_sites.Tpo -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-genome_sites.Tpo $(DEPDIR)/gsnap_sse42-genome_sites.Po
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+
+gsnap_sse42-genome_sites.obj: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-genome_sites.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-genome_sites.Tpo -c -o gsnap_sse42-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-genome_sites.Tpo $(DEPDIR)/gsnap_sse42-genome_sites.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-bitpack64-read.Tpo -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bitpack64-read.Tpo $(DEPDIR)/gsnap_sse42-bitpack64-read.Po
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap_sse42-bitpack64-readtwo.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-bitpack64-readtwo.Tpo -c -o gsnap_sse42-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bitpack64-readtwo.Tpo $(DEPDIR)/gsnap_sse42-bitpack64-readtwo.Po
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+
+gsnap_sse42-indexdb.o: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-indexdb.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-indexdb.Tpo -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-indexdb.Tpo $(DEPDIR)/gsnap_sse42-indexdb.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+
+gsnap_sse42-indexdb.obj: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-indexdb.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-indexdb.Tpo -c -o gsnap_sse42-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
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+
+gsnap_sse42-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-indexdb_hr.Tpo -c -o gsnap_sse42-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-indexdb_hr.Tpo $(DEPDIR)/gsnap_sse42-indexdb_hr.Po
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+
+gsnap_sse42-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-indexdb_hr.Tpo -c -o gsnap_sse42-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-indexdb_hr.Tpo $(DEPDIR)/gsnap_sse42-indexdb_hr.Po
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+
+gsnap_sse42-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-oligo.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-oligo.Tpo -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gsnap_sse42-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-oligo.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-oligo.Tpo -c -o gsnap_sse42-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
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+gsnap_sse42-chrom.o: chrom.c
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+gsnap_sse42-chrom.obj: chrom.c
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+
+gsnap_sse42-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-segmentpos.Tpo -c -o gsnap_sse42-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-segmentpos.Tpo $(DEPDIR)/gsnap_sse42-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap_sse42-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gsnap_sse42-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-chrnum.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-chrnum.Tpo -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-chrnum.Tpo $(DEPDIR)/gsnap_sse42-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_sse42-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnap_sse42-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-chrnum.Tpo -c -o gsnap_sse42-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-chrnum.Tpo $(DEPDIR)/gsnap_sse42-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_sse42-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnap_sse42-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-maxent_hr.Tpo -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-maxent_hr.Tpo $(DEPDIR)/gsnap_sse42-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_sse42-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnap_sse42-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-maxent_hr.Tpo -c -o gsnap_sse42-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-maxent_hr.Tpo $(DEPDIR)/gsnap_sse42-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_sse42-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnap_sse42-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-samprint.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-samprint.Tpo -c -o gsnap_sse42-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-samprint.Tpo $(DEPDIR)/gsnap_sse42-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_sse42-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnap_sse42-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-samprint.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-samprint.Tpo -c -o gsnap_sse42-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-samprint.Tpo $(DEPDIR)/gsnap_sse42-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_sse42-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnap_sse42-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-mapq.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-mapq.Tpo -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-mapq.Tpo $(DEPDIR)/gsnap_sse42-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_sse42-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnap_sse42-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-mapq.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-mapq.Tpo -c -o gsnap_sse42-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-mapq.Tpo $(DEPDIR)/gsnap_sse42-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_sse42-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnap_sse42-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-shortread.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-shortread.Tpo -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-shortread.Tpo $(DEPDIR)/gsnap_sse42-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_sse42-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnap_sse42-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-shortread.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-shortread.Tpo -c -o gsnap_sse42-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-shortread.Tpo $(DEPDIR)/gsnap_sse42-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_sse42-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnap_sse42-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-substring.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-substring.Tpo -c -o gsnap_sse42-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-substring.Tpo $(DEPDIR)/gsnap_sse42-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_sse42-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnap_sse42-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-substring.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-substring.Tpo -c -o gsnap_sse42-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-substring.Tpo $(DEPDIR)/gsnap_sse42-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_sse42-substring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnap_sse42-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-junction.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-junction.Tpo -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-junction.Tpo $(DEPDIR)/gsnap_sse42-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_sse42-junction.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+
+gsnap_sse42-junction.obj: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-junction.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-junction.Tpo -c -o gsnap_sse42-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-junction.Tpo $(DEPDIR)/gsnap_sse42-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnap_sse42-junction.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+
+gsnap_sse42-stage3hr.o: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage3hr.Tpo -c -o gsnap_sse42-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage3hr.Tpo $(DEPDIR)/gsnap_sse42-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap_sse42-stage3hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+
+gsnap_sse42-stage3hr.obj: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage3hr.Tpo -c -o gsnap_sse42-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage3hr.Tpo $(DEPDIR)/gsnap_sse42-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnap_sse42-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+
+gsnap_sse42-spanningelt.o: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-spanningelt.Tpo -c -o gsnap_sse42-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-spanningelt.Tpo $(DEPDIR)/gsnap_sse42-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap_sse42-spanningelt.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+
+gsnap_sse42-spanningelt.obj: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-spanningelt.Tpo -c -o gsnap_sse42-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-spanningelt.Tpo $(DEPDIR)/gsnap_sse42-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnap_sse42-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+
+gsnap_sse42-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-cmet.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-cmet.Tpo -c -o gsnap_sse42-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-cmet.Tpo $(DEPDIR)/gsnap_sse42-cmet.Po
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+gsnap_sse42-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage2.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage2.Tpo -c -o gsnap_sse42-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage2.Tpo $(DEPDIR)/gsnap_sse42-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnap_sse42-stage2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gsnap_sse42-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage2.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage2.Tpo -c -o gsnap_sse42-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage2.Tpo $(DEPDIR)/gsnap_sse42-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnap_sse42-stage2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gsnap_sse42-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-intron.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-intron.Tpo -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-intron.Tpo $(DEPDIR)/gsnap_sse42-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnap_sse42-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gsnap_sse42-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-intron.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-intron.Tpo -c -o gsnap_sse42-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-intron.Tpo $(DEPDIR)/gsnap_sse42-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnap_sse42-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gsnap_sse42-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-boyer-moore.Tpo -c -o gsnap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-boyer-moore.Tpo $(DEPDIR)/gsnap_sse42-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnap_sse42-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gsnap_sse42-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-boyer-moore.Tpo -c -o gsnap_sse42-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-boyer-moore.Tpo $(DEPDIR)/gsnap_sse42-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnap_sse42-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gsnap_sse42-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-changepoint.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-changepoint.Tpo -c -o gsnap_sse42-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-changepoint.Tpo $(DEPDIR)/gsnap_sse42-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnap_sse42-changepoint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+
+gsnap_sse42-changepoint.obj: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-changepoint.Tpo -c -o gsnap_sse42-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-changepoint.Tpo $(DEPDIR)/gsnap_sse42-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnap_sse42-changepoint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+
+gsnap_sse42-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-pbinom.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-pbinom.Tpo -c -o gsnap_sse42-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-pbinom.Tpo $(DEPDIR)/gsnap_sse42-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnap_sse42-pbinom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+
+gsnap_sse42-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-pbinom.Tpo -c -o gsnap_sse42-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-pbinom.Tpo $(DEPDIR)/gsnap_sse42-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnap_sse42-pbinom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+
+gsnap_sse42-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog.Tpo -c -o gsnap_sse42-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog.Tpo $(DEPDIR)/gsnap_sse42-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnap_sse42-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gsnap_sse42-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog.Tpo -c -o gsnap_sse42-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog.Tpo $(DEPDIR)/gsnap_sse42-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnap_sse42-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gsnap_sse42-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_simd.Tpo -c -o gsnap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_simd.Tpo $(DEPDIR)/gsnap_sse42-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap_sse42-dynprog_simd.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gsnap_sse42-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_simd.Tpo -c -o gsnap_sse42-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_simd.Tpo $(DEPDIR)/gsnap_sse42-dynprog_simd.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_simd.c' object='gsnap_sse42-dynprog_simd.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gsnap_sse42-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_single.Tpo -c -o gsnap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_single.Tpo $(DEPDIR)/gsnap_sse42-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap_sse42-dynprog_single.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
+
+gsnap_sse42-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_single.Tpo -c -o gsnap_sse42-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_single.Tpo $(DEPDIR)/gsnap_sse42-dynprog_single.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_single.c' object='gsnap_sse42-dynprog_single.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
+
+gsnap_sse42-dynprog_genome.o: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_genome.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_genome.Tpo -c -o gsnap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_genome.Tpo $(DEPDIR)/gsnap_sse42-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap_sse42-dynprog_genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '$(srcdir)/'`dynprog_genome.c
+
+gsnap_sse42-dynprog_genome.obj: dynprog_genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_genome.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_genome.Tpo -c -o gsnap_sse42-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_genome.Tpo $(DEPDIR)/gsnap_sse42-dynprog_genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_genome.c' object='gsnap_sse42-dynprog_genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_genome.obj `if test -f 'dynprog_genome.c'; then $(CYGPATH_W) 'dynprog_genome.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_genome.c'; fi`
+
+gsnap_sse42-dynprog_cdna.o: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_cdna.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_cdna.Tpo -c -o gsnap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_cdna.Tpo $(DEPDIR)/gsnap_sse42-dynprog_cdna.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnap_sse42-dynprog_cdna.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '$(srcdir)/'`dynprog_cdna.c
+
+gsnap_sse42-dynprog_cdna.obj: dynprog_cdna.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_cdna.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_cdna.Tpo -c -o gsnap_sse42-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_cdna.Tpo $(DEPDIR)/gsnap_sse42-dynprog_cdna.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_cdna.c' object='gsnap_sse42-dynprog_cdna.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_cdna.obj `if test -f 'dynprog_cdna.c'; then $(CYGPATH_W) 'dynprog_cdna.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_cdna.c'; fi`
+
+gsnap_sse42-dynprog_end.o: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_end.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_end.Tpo -c -o gsnap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_end.Tpo $(DEPDIR)/gsnap_sse42-dynprog_end.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gsnap_sse42-dynprog_end.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '$(srcdir)/'`dynprog_end.c
+
+gsnap_sse42-dynprog_end.obj: dynprog_end.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-dynprog_end.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-dynprog_end.Tpo -c -o gsnap_sse42-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-dynprog_end.Tpo $(DEPDIR)/gsnap_sse42-dynprog_end.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog_end.c' object='gsnap_sse42-dynprog_end.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-dynprog_end.obj `if test -f 'dynprog_end.c'; then $(CYGPATH_W) 'dynprog_end.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_end.c'; fi`
+
+gsnap_sse42-gbuffer.o: gbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-gbuffer.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-gbuffer.Tpo -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-gbuffer.Tpo $(DEPDIR)/gsnap_sse42-gbuffer.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnap_sse42-gbuffer.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '$(srcdir)/'`gbuffer.c
+
+gsnap_sse42-gbuffer.obj: gbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-gbuffer.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-gbuffer.Tpo -c -o gsnap_sse42-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-gbuffer.Tpo $(DEPDIR)/gsnap_sse42-gbuffer.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='gbuffer.c' object='gsnap_sse42-gbuffer.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-gbuffer.obj `if test -f 'gbuffer.c'; then $(CYGPATH_W) 'gbuffer.c'; else $(CYGPATH_W) '$(srcdir)/gbuffer.c'; fi`
+
+gsnap_sse42-translation.o: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-translation.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-translation.Tpo -c -o gsnap_sse42-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-translation.Tpo $(DEPDIR)/gsnap_sse42-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnap_sse42-translation.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+
+gsnap_sse42-translation.obj: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-translation.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-translation.Tpo -c -o gsnap_sse42-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-translation.Tpo $(DEPDIR)/gsnap_sse42-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnap_sse42-translation.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+
+gsnap_sse42-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-doublelist.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-doublelist.Tpo -c -o gsnap_sse42-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-doublelist.Tpo $(DEPDIR)/gsnap_sse42-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnap_sse42-doublelist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gsnap_sse42-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-doublelist.Tpo -c -o gsnap_sse42-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-doublelist.Tpo $(DEPDIR)/gsnap_sse42-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnap_sse42-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gsnap_sse42-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-smooth.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-smooth.Tpo -c -o gsnap_sse42-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-smooth.Tpo $(DEPDIR)/gsnap_sse42-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnap_sse42-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gsnap_sse42-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-smooth.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-smooth.Tpo -c -o gsnap_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-smooth.Tpo $(DEPDIR)/gsnap_sse42-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnap_sse42-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gsnap_sse42-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-chimera.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-chimera.Tpo -c -o gsnap_sse42-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-chimera.Tpo $(DEPDIR)/gsnap_sse42-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap_sse42-chimera.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gsnap_sse42-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-chimera.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-chimera.Tpo -c -o gsnap_sse42-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-chimera.Tpo $(DEPDIR)/gsnap_sse42-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap_sse42-chimera.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnap_sse42-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage3.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage3.Tpo -c -o gsnap_sse42-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage3.Tpo $(DEPDIR)/gsnap_sse42-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnap_sse42-stage3.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnap_sse42-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage3.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage3.Tpo -c -o gsnap_sse42-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage3.Tpo $(DEPDIR)/gsnap_sse42-stage3.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnap_sse42-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-splicestringpool.Tpo -c -o gsnap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splicestringpool.Tpo $(DEPDIR)/gsnap_sse42-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap_sse42-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnap_sse42-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-splicestringpool.Tpo -c -o gsnap_sse42-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splicestringpool.Tpo $(DEPDIR)/gsnap_sse42-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnap_sse42-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnap_sse42-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-splicetrie_build.Tpo -c -o gsnap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splicetrie_build.Tpo $(DEPDIR)/gsnap_sse42-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnap_sse42-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnap_sse42-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-splicetrie_build.Tpo -c -o gsnap_sse42-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splicetrie_build.Tpo $(DEPDIR)/gsnap_sse42-splicetrie_build.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnap_sse42-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-splicetrie.Tpo -c -o gsnap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splicetrie.Tpo $(DEPDIR)/gsnap_sse42-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gsnap_sse42-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-splicetrie.Tpo -c -o gsnap_sse42-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splicetrie.Tpo $(DEPDIR)/gsnap_sse42-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnap_sse42-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gsnap_sse42-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splice.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-splice.Tpo -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splice.Tpo $(DEPDIR)/gsnap_sse42-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnap_sse42-splice.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnap_sse42-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-splice.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-splice.Tpo -c -o gsnap_sse42-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-splice.Tpo $(DEPDIR)/gsnap_sse42-splice.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+
+gsnap_sse42-indel.o: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-indel.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-indel.Tpo -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-indel.Tpo $(DEPDIR)/gsnap_sse42-indel.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+
+gsnap_sse42-indel.obj: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-indel.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-indel.Tpo -c -o gsnap_sse42-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-indel.Tpo $(DEPDIR)/gsnap_sse42-indel.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+
+gsnap_sse42-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-bitpack64-access.Tpo -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bitpack64-access.Tpo $(DEPDIR)/gsnap_sse42-bitpack64-access.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+gsnap_sse42-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-bitpack64-access.Tpo -c -o gsnap_sse42-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bitpack64-access.Tpo $(DEPDIR)/gsnap_sse42-bitpack64-access.Po
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+
+gsnap_sse42-bytecoding.o: bytecoding.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bytecoding.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-bytecoding.Tpo -c -o gsnap_sse42-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bytecoding.Tpo $(DEPDIR)/gsnap_sse42-bytecoding.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
+
+gsnap_sse42-bytecoding.obj: bytecoding.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-bytecoding.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-bytecoding.Tpo -c -o gsnap_sse42-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-bytecoding.Tpo $(DEPDIR)/gsnap_sse42-bytecoding.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-bytecoding.obj `if test -f 'bytecoding.c'; then $(CYGPATH_W) 'bytecoding.c'; else $(CYGPATH_W) '$(srcdir)/bytecoding.c'; fi`
+
+gsnap_sse42-univdiag.o: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-univdiag.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-univdiag.Tpo -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '$(srcdir)/'`univdiag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-univdiag.Tpo $(DEPDIR)/gsnap_sse42-univdiag.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '$(srcdir)/'`univdiag.c
+
+gsnap_sse42-univdiag.obj: univdiag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-univdiag.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-univdiag.Tpo -c -o gsnap_sse42-univdiag.obj `if test -f 'univdiag.c'; then $(CYGPATH_W) 'univdiag.c'; else $(CYGPATH_W) '$(srcdir)/univdiag.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-univdiag.Tpo $(DEPDIR)/gsnap_sse42-univdiag.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-univdiag.obj `if test -f 'univdiag.c'; then $(CYGPATH_W) 'univdiag.c'; else $(CYGPATH_W) '$(srcdir)/univdiag.c'; fi`
+
+gsnap_sse42-sarray-read.o: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-sarray-read.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-sarray-read.Tpo -c -o gsnap_sse42-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-sarray-read.Tpo $(DEPDIR)/gsnap_sse42-sarray-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-sarray-read.o `test -f 'sarray-read.c' || echo '$(srcdir)/'`sarray-read.c
+
+gsnap_sse42-sarray-read.obj: sarray-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-sarray-read.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-sarray-read.Tpo -c -o gsnap_sse42-sarray-read.obj `if test -f 'sarray-read.c'; then $(CYGPATH_W) 'sarray-read.c'; else $(CYGPATH_W) '$(srcdir)/sarray-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-sarray-read.Tpo $(DEPDIR)/gsnap_sse42-sarray-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-sarray-read.obj `if test -f 'sarray-read.c'; then $(CYGPATH_W) 'sarray-read.c'; else $(CYGPATH_W) '$(srcdir)/sarray-read.c'; fi`
+
+gsnap_sse42-stage1hr.o: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage1hr.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage1hr.Tpo -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage1hr.Tpo $(DEPDIR)/gsnap_sse42-stage1hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
+
+gsnap_sse42-stage1hr.obj: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-stage1hr.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-stage1hr.Tpo -c -o gsnap_sse42-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-stage1hr.Tpo $(DEPDIR)/gsnap_sse42-stage1hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -c -o gsnap_sse42-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
+
+gsnap_sse42-request.o: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-request.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-request.Tpo -c -o gsnap_sse42-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-request.Tpo $(DEPDIR)/gsnap_sse42-request.Po
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+
+gsnap_sse42-request.obj: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-request.obj -MD -MP -MF $(DEPDIR)/gsnap_sse42-request.Tpo -c -o gsnap_sse42-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_sse42-request.Tpo $(DEPDIR)/gsnap_sse42-request.Po
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+gsnap_sse42-resulthr.o: resulthr.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-output.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-output.Tpo -c -o gsnap_sse42-output.o `test -f 'output.c' || echo '$(srcdir)/'`output.c
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+gsnap_sse42-output.obj: output.c
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+
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_sse42_CFLAGS) $(CFLAGS) -MT gsnap_sse42-samheader.o -MD -MP -MF $(DEPDIR)/gsnap_sse42-samheader.Tpo -c -o gsnap_sse42-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
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+gsnap_sse42-getopt1.o: getopt1.c
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+gsnap_sse42-getopt1.obj: getopt1.c
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+gsnap_ssse3-bzip2.obj: bzip2.c
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+gsnap_ssse3-sequence.obj: sequence.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-reader.Tpo $(DEPDIR)/gsnap_ssse3-reader.Po
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+
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+
+gsnap_ssse3-genomicpos.obj: genomicpos.c
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+
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+gsnap_ssse3-compress.obj: compress.c
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+gsnap_ssse3-genome.o: genome.c
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+
+gsnap_ssse3-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-indexdb_hr.Tpo -c -o gsnap_ssse3-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-indexdb_hr.Tpo $(DEPDIR)/gsnap_ssse3-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnap_ssse3-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+
+gsnap_ssse3-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-indexdb_hr.Tpo -c -o gsnap_ssse3-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-indexdb_hr.Tpo $(DEPDIR)/gsnap_ssse3-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnap_ssse3-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+
+gsnap_ssse3-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-oligo.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-oligo.Tpo -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-oligo.Tpo $(DEPDIR)/gsnap_ssse3-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnap_ssse3-oligo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gsnap_ssse3-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-oligo.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-oligo.Tpo -c -o gsnap_ssse3-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-oligo.Tpo $(DEPDIR)/gsnap_ssse3-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnap_ssse3-oligo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+
+gsnap_ssse3-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-chrom.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-chrom.Tpo -c -o gsnap_ssse3-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-chrom.Tpo $(DEPDIR)/gsnap_ssse3-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnap_ssse3-chrom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+
+gsnap_ssse3-chrom.obj: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-chrom.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-chrom.Tpo -c -o gsnap_ssse3-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-chrom.Tpo $(DEPDIR)/gsnap_ssse3-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnap_ssse3-chrom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+
+gsnap_ssse3-segmentpos.o: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-segmentpos.Tpo -c -o gsnap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-segmentpos.Tpo $(DEPDIR)/gsnap_ssse3-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap_ssse3-segmentpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+
+gsnap_ssse3-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-segmentpos.Tpo -c -o gsnap_ssse3-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-segmentpos.Tpo $(DEPDIR)/gsnap_ssse3-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnap_ssse3-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gsnap_ssse3-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-chrnum.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-chrnum.Tpo -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-chrnum.Tpo $(DEPDIR)/gsnap_ssse3-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_ssse3-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnap_ssse3-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-chrnum.Tpo -c -o gsnap_ssse3-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-chrnum.Tpo $(DEPDIR)/gsnap_ssse3-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnap_ssse3-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnap_ssse3-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-maxent_hr.Tpo -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-maxent_hr.Tpo $(DEPDIR)/gsnap_ssse3-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_ssse3-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnap_ssse3-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-maxent_hr.Tpo -c -o gsnap_ssse3-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-maxent_hr.Tpo $(DEPDIR)/gsnap_ssse3-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnap_ssse3-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnap_ssse3-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-samprint.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-samprint.Tpo -c -o gsnap_ssse3-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-samprint.Tpo $(DEPDIR)/gsnap_ssse3-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_ssse3-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnap_ssse3-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-samprint.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-samprint.Tpo -c -o gsnap_ssse3-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-samprint.Tpo $(DEPDIR)/gsnap_ssse3-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnap_ssse3-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnap_ssse3-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-mapq.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-mapq.Tpo -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-mapq.Tpo $(DEPDIR)/gsnap_ssse3-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_ssse3-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnap_ssse3-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-mapq.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-mapq.Tpo -c -o gsnap_ssse3-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-mapq.Tpo $(DEPDIR)/gsnap_ssse3-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnap_ssse3-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnap_ssse3-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-shortread.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-shortread.Tpo -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-shortread.Tpo $(DEPDIR)/gsnap_ssse3-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_ssse3-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnap_ssse3-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-shortread.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-shortread.Tpo -c -o gsnap_ssse3-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-shortread.Tpo $(DEPDIR)/gsnap_ssse3-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnap_ssse3-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnap_ssse3-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-substring.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-substring.Tpo -c -o gsnap_ssse3-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-substring.Tpo $(DEPDIR)/gsnap_ssse3-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_ssse3-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnap_ssse3-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-substring.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-substring.Tpo -c -o gsnap_ssse3-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-substring.Tpo $(DEPDIR)/gsnap_ssse3-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnap_ssse3-substring.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-dynprog_simd.Tpo $(DEPDIR)/gsnap_ssse3-dynprog_simd.Po
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-dynprog_simd.Tpo $(DEPDIR)/gsnap_ssse3-dynprog_simd.Po
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+
+gsnap_ssse3-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-dynprog_single.Tpo -c -o gsnap_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
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+
+gsnap_ssse3-dynprog_single.obj: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-dynprog_single.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-dynprog_single.Tpo -c -o gsnap_ssse3-dynprog_single.obj `if test -f 'dynprog_single.c'; then $(CYGPATH_W) 'dynprog_single.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_single.c'; fi`
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+
+gsnap_ssse3-dynprog_genome.o: dynprog_genome.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-dynprog_genome.Tpo $(DEPDIR)/gsnap_ssse3-dynprog_genome.Po
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+
+gsnap_ssse3-dynprog_genome.obj: dynprog_genome.c
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+
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+gsnap_ssse3-dynprog_end.obj: dynprog_end.c
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+gsnap_ssse3-translation.obj: translation.c
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+gsnap_ssse3-doublelist.obj: doublelist.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-chimera.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-chimera.Tpo -c -o gsnap_ssse3-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-chimera.Tpo $(DEPDIR)/gsnap_ssse3-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnap_ssse3-chimera.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnap_ssse3-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-stage3.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-stage3.Tpo -c -o gsnap_ssse3-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-stage3.Tpo $(DEPDIR)/gsnap_ssse3-stage3.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnap_ssse3-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-stage3.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-stage3.Tpo -c -o gsnap_ssse3-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-stage3.Tpo $(DEPDIR)/gsnap_ssse3-stage3.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnap_ssse3-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splicestringpool.Tpo -c -o gsnap_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splicestringpool.Tpo $(DEPDIR)/gsnap_ssse3-splicestringpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnap_ssse3-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splicestringpool.Tpo -c -o gsnap_ssse3-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splicestringpool.Tpo $(DEPDIR)/gsnap_ssse3-splicestringpool.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnap_ssse3-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splicetrie_build.Tpo -c -o gsnap_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splicetrie_build.Tpo $(DEPDIR)/gsnap_ssse3-splicetrie_build.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnap_ssse3-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splicetrie_build.Tpo -c -o gsnap_ssse3-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splicetrie_build.Tpo $(DEPDIR)/gsnap_ssse3-splicetrie_build.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnap_ssse3-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splicetrie.Tpo -c -o gsnap_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
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+
+gsnap_ssse3-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splicetrie.Tpo -c -o gsnap_ssse3-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splicetrie.Tpo $(DEPDIR)/gsnap_ssse3-splicetrie.Po
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+
+gsnap_ssse3-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splice.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splice.Tpo -c -o gsnap_ssse3-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splice.Tpo $(DEPDIR)/gsnap_ssse3-splice.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnap_ssse3-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-splice.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-splice.Tpo -c -o gsnap_ssse3-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-splice.Tpo $(DEPDIR)/gsnap_ssse3-splice.Po
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-indel.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-indel.Tpo -c -o gsnap_ssse3-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-indel.Tpo $(DEPDIR)/gsnap_ssse3-indel.Po
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+
+gsnap_ssse3-indel.obj: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-indel.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-indel.Tpo -c -o gsnap_ssse3-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-indel.Tpo $(DEPDIR)/gsnap_ssse3-indel.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+
+gsnap_ssse3-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-bitpack64-access.Tpo -c -o gsnap_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-bitpack64-access.Tpo $(DEPDIR)/gsnap_ssse3-bitpack64-access.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+gsnap_ssse3-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-bitpack64-access.Tpo -c -o gsnap_ssse3-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-bitpack64-access.Tpo $(DEPDIR)/gsnap_ssse3-bitpack64-access.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
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+gsnap_ssse3-bytecoding.o: bytecoding.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-bytecoding.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-bytecoding.Tpo -c -o gsnap_ssse3-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-bytecoding.o `test -f 'bytecoding.c' || echo '$(srcdir)/'`bytecoding.c
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+gsnap_ssse3-bytecoding.obj: bytecoding.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-bytecoding.Tpo $(DEPDIR)/gsnap_ssse3-bytecoding.Po
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+gsnap_ssse3-univdiag.o: univdiag.c
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+gsnap_ssse3-univdiag.obj: univdiag.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-parserange.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-parserange.Tpo -c -o gsnap_ssse3-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-parserange.Tpo $(DEPDIR)/gsnap_ssse3-parserange.Po
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+
+gsnap_ssse3-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-getopt.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-getopt.Tpo -c -o gsnap_ssse3-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-getopt.Tpo $(DEPDIR)/gsnap_ssse3-getopt.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -c -o gsnap_ssse3-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
+
+gsnap_ssse3-getopt.obj: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-getopt.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-getopt.Tpo -c -o gsnap_ssse3-getopt.obj `if test -f 'getopt.c'; then $(CYGPATH_W) 'getopt.c'; else $(CYGPATH_W) '$(srcdir)/getopt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-getopt.Tpo $(DEPDIR)/gsnap_ssse3-getopt.Po
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+
+gsnap_ssse3-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-getopt1.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-getopt1.Tpo -c -o gsnap_ssse3-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-getopt1.Tpo $(DEPDIR)/gsnap_ssse3-getopt1.Po
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+
+gsnap_ssse3-getopt1.obj: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-getopt1.obj -MD -MP -MF $(DEPDIR)/gsnap_ssse3-getopt1.Tpo -c -o gsnap_ssse3-getopt1.obj `if test -f 'getopt1.c'; then $(CYGPATH_W) 'getopt1.c'; else $(CYGPATH_W) '$(srcdir)/getopt1.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-getopt1.Tpo $(DEPDIR)/gsnap_ssse3-getopt1.Po
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+
+gsnap_ssse3-gsnap.o: gsnap.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_ssse3_CFLAGS) $(CFLAGS) -MT gsnap_ssse3-gsnap.o -MD -MP -MF $(DEPDIR)/gsnap_ssse3-gsnap.Tpo -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '$(srcdir)/'`gsnap.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnap_ssse3-gsnap.Tpo $(DEPDIR)/gsnap_ssse3-gsnap.Po
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+gsnap_ssse3-gsnap.obj: gsnap.c
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+gsnapl-cpuid.o: cpuid.c
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+gsnapl-cpuid.obj: cpuid.c
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+
+gsnapl-gsnapl_select.o: gsnapl_select.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-gsnapl_select.o -MD -MP -MF $(DEPDIR)/gsnapl-gsnapl_select.Tpo -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '$(srcdir)/'`gsnapl_select.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-gsnapl_select.Tpo $(DEPDIR)/gsnapl-gsnapl_select.Po
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+
+gsnapl-gsnapl_select.obj: gsnapl_select.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_CFLAGS) $(CFLAGS) -MT gsnapl-gsnapl_select.obj -MD -MP -MF $(DEPDIR)/gsnapl-gsnapl_select.Tpo -c -o gsnapl-gsnapl_select.obj `if test -f 'gsnapl_select.c'; then $(CYGPATH_W) 'gsnapl_select.c'; else $(CYGPATH_W) '$(srcdir)/gsnapl_select.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl-gsnapl_select.Tpo $(DEPDIR)/gsnapl-gsnapl_select.Po
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+
+gsnapl_avx2-except.o: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-except.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-except.Tpo -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
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+
+gsnapl_avx2-except.obj: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-except.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-except.Tpo -c -o gsnapl_avx2-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-assert.Tpo $(DEPDIR)/gsnapl_avx2-assert.Po
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+
+gsnapl_avx2-assert.obj: assert.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-assert.Tpo $(DEPDIR)/gsnapl_avx2-assert.Po
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+gsnapl_avx2-mem.o: mem.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-mem.Tpo $(DEPDIR)/gsnapl_avx2-mem.Po
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+
+gsnapl_avx2-mem.obj: mem.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-mem.Tpo $(DEPDIR)/gsnapl_avx2-mem.Po
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+gsnapl_avx2-intlist.obj: intlist.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-list.Tpo $(DEPDIR)/gsnapl_avx2-list.Po
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-iit-read-univ.Tpo $(DEPDIR)/gsnapl_avx2-iit-read-univ.Po
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+gsnapl_avx2-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-iit-read.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-iit-read.Tpo -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
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+gsnapl_avx2-iit-read.obj: iit-read.c
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+gsnapl_avx2-md5.o: md5.c
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+gsnapl_avx2-md5.obj: md5.c
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+gsnapl_avx2-bzip2.o: bzip2.c
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+gsnapl_avx2-bzip2.obj: bzip2.c
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+gsnapl_avx2-sequence.obj: sequence.c
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+gsnapl_avx2-reader.o: reader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-reader.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-reader.Tpo -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo '$(srcdir)/'`reader.c
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+gsnapl_avx2-reader.obj: reader.c
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+gsnapl_avx2-genomicpos.o: genomicpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genomicpos.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genomicpos.Tpo -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '$(srcdir)/'`genomicpos.c
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+gsnapl_avx2-genomicpos.obj: genomicpos.c
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+gsnapl_avx2-compress.obj: compress.c
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+
+gsnapl_avx2-genome.o: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genome.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genome.Tpo -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-genome.Tpo $(DEPDIR)/gsnapl_avx2-genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnapl_avx2-genome.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '$(srcdir)/'`genome.c
+
+gsnapl_avx2-genome.obj: genome.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genome.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genome.Tpo -c -o gsnapl_avx2-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-genome.Tpo $(DEPDIR)/gsnapl_avx2-genome.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome.c' object='gsnapl_avx2-genome.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-genome.obj `if test -f 'genome.c'; then $(CYGPATH_W) 'genome.c'; else $(CYGPATH_W) '$(srcdir)/genome.c'; fi`
+
+gsnapl_avx2-popcount.o: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-popcount.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-popcount.Tpo -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-popcount.Tpo $(DEPDIR)/gsnapl_avx2-popcount.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnapl_avx2-popcount.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo '$(srcdir)/'`popcount.c
+
+gsnapl_avx2-popcount.obj: popcount.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-popcount.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-popcount.Tpo -c -o gsnapl_avx2-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-popcount.Tpo $(DEPDIR)/gsnapl_avx2-popcount.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='popcount.c' object='gsnapl_avx2-popcount.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-popcount.obj `if test -f 'popcount.c'; then $(CYGPATH_W) 'popcount.c'; else $(CYGPATH_W) '$(srcdir)/popcount.c'; fi`
+
+gsnapl_avx2-genome128_hr.o: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genome128_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genome128_hr.Tpo -c -o gsnapl_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-genome128_hr.Tpo $(DEPDIR)/gsnapl_avx2-genome128_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnapl_avx2-genome128_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-genome128_hr.o `test -f 'genome128_hr.c' || echo '$(srcdir)/'`genome128_hr.c
+
+gsnapl_avx2-genome128_hr.obj: genome128_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genome128_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genome128_hr.Tpo -c -o gsnapl_avx2-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-genome128_hr.Tpo $(DEPDIR)/gsnapl_avx2-genome128_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome128_hr.c' object='gsnapl_avx2-genome128_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-genome128_hr.obj `if test -f 'genome128_hr.c'; then $(CYGPATH_W) 'genome128_hr.c'; else $(CYGPATH_W) '$(srcdir)/genome128_hr.c'; fi`
+
+gsnapl_avx2-genome_sites.o: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genome_sites.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genome_sites.Tpo -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-genome_sites.Tpo $(DEPDIR)/gsnapl_avx2-genome_sites.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='genome_sites.c' object='gsnapl_avx2-genome_sites.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '$(srcdir)/'`genome_sites.c
+
+gsnapl_avx2-genome_sites.obj: genome_sites.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-genome_sites.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-genome_sites.Tpo -c -o gsnapl_avx2-genome_sites.obj `if test -f 'genome_sites.c'; then $(CYGPATH_W) 'genome_sites.c'; else $(CYGPATH_W) '$(srcdir)/genome_sites.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-genome_sites.Tpo $(DEPDIR)/gsnapl_avx2-genome_sites.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+
+gsnapl_avx2-bitpack64-read.o: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-bitpack64-read.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-bitpack64-read.Tpo -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-bitpack64-read.Tpo $(DEPDIR)/gsnapl_avx2-bitpack64-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '$(srcdir)/'`bitpack64-read.c
+
+gsnapl_avx2-bitpack64-read.obj: bitpack64-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-bitpack64-read.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-bitpack64-read.Tpo -c -o gsnapl_avx2-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-bitpack64-read.Tpo $(DEPDIR)/gsnapl_avx2-bitpack64-read.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-bitpack64-read.obj `if test -f 'bitpack64-read.c'; then $(CYGPATH_W) 'bitpack64-read.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-read.c'; fi`
+
+gsnapl_avx2-bitpack64-readtwo.o: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-bitpack64-readtwo.Tpo -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl_avx2-bitpack64-readtwo.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+
+gsnapl_avx2-bitpack64-readtwo.obj: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-bitpack64-readtwo.Tpo -c -o gsnapl_avx2-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl_avx2-bitpack64-readtwo.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+
+gsnapl_avx2-indexdb.o: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-indexdb.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-indexdb.Tpo -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-indexdb.Tpo $(DEPDIR)/gsnapl_avx2-indexdb.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+
+gsnapl_avx2-indexdb.obj: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-indexdb.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-indexdb.Tpo -c -o gsnapl_avx2-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-indexdb.Tpo $(DEPDIR)/gsnapl_avx2-indexdb.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+
+gsnapl_avx2-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-indexdb_hr.Tpo -c -o gsnapl_avx2-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-indexdb_hr.Tpo $(DEPDIR)/gsnapl_avx2-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl_avx2-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+
+gsnapl_avx2-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-indexdb_hr.Tpo -c -o gsnapl_avx2-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-indexdb_hr.Tpo $(DEPDIR)/gsnapl_avx2-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl_avx2-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+
+gsnapl_avx2-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-oligo.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-oligo.Tpo -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-oligo.Tpo $(DEPDIR)/gsnapl_avx2-oligo.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gsnapl_avx2-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-oligo.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-oligo.Tpo -c -o gsnapl_avx2-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-oligo.Tpo $(DEPDIR)/gsnapl_avx2-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl_avx2-oligo.obj' libtool=no @AMDEPBACKSLASH@
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+
+gsnapl_avx2-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-chrom.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-chrom.Tpo -c -o gsnapl_avx2-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-chrom.Tpo $(DEPDIR)/gsnapl_avx2-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl_avx2-chrom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+
+gsnapl_avx2-chrom.obj: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-chrom.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-chrom.Tpo -c -o gsnapl_avx2-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-chrom.Tpo $(DEPDIR)/gsnapl_avx2-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl_avx2-chrom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+
+gsnapl_avx2-segmentpos.o: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-segmentpos.Tpo -c -o gsnapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-segmentpos.Tpo $(DEPDIR)/gsnapl_avx2-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl_avx2-segmentpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+
+gsnapl_avx2-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-segmentpos.Tpo -c -o gsnapl_avx2-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-segmentpos.Tpo $(DEPDIR)/gsnapl_avx2-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl_avx2-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gsnapl_avx2-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-chrnum.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-chrnum.Tpo -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-chrnum.Tpo $(DEPDIR)/gsnapl_avx2-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl_avx2-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnapl_avx2-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-chrnum.Tpo -c -o gsnapl_avx2-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-chrnum.Tpo $(DEPDIR)/gsnapl_avx2-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl_avx2-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnapl_avx2-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-maxent_hr.Tpo -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-maxent_hr.Tpo $(DEPDIR)/gsnapl_avx2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl_avx2-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnapl_avx2-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-maxent_hr.Tpo -c -o gsnapl_avx2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-maxent_hr.Tpo $(DEPDIR)/gsnapl_avx2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl_avx2-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnapl_avx2-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-samprint.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-samprint.Tpo -c -o gsnapl_avx2-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-samprint.Tpo $(DEPDIR)/gsnapl_avx2-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl_avx2-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnapl_avx2-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-samprint.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-samprint.Tpo -c -o gsnapl_avx2-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-samprint.Tpo $(DEPDIR)/gsnapl_avx2-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl_avx2-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnapl_avx2-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-mapq.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-mapq.Tpo -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-mapq.Tpo $(DEPDIR)/gsnapl_avx2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl_avx2-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnapl_avx2-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-mapq.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-mapq.Tpo -c -o gsnapl_avx2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-mapq.Tpo $(DEPDIR)/gsnapl_avx2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl_avx2-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnapl_avx2-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-shortread.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-shortread.Tpo -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-shortread.Tpo $(DEPDIR)/gsnapl_avx2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnapl_avx2-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnapl_avx2-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-shortread.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-shortread.Tpo -c -o gsnapl_avx2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-shortread.Tpo $(DEPDIR)/gsnapl_avx2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnapl_avx2-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnapl_avx2-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-substring.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-substring.Tpo -c -o gsnapl_avx2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-substring.Tpo $(DEPDIR)/gsnapl_avx2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnapl_avx2-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnapl_avx2-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-substring.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-substring.Tpo -c -o gsnapl_avx2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-substring.Tpo $(DEPDIR)/gsnapl_avx2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnapl_avx2-substring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnapl_avx2-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-junction.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-junction.Tpo -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-junction.Tpo $(DEPDIR)/gsnapl_avx2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnapl_avx2-junction.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+
+gsnapl_avx2-junction.obj: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-junction.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-junction.Tpo -c -o gsnapl_avx2-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-junction.Tpo $(DEPDIR)/gsnapl_avx2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnapl_avx2-junction.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+
+gsnapl_avx2-stage3hr.o: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage3hr.Tpo -c -o gsnapl_avx2-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage3hr.Tpo $(DEPDIR)/gsnapl_avx2-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnapl_avx2-stage3hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+
+gsnapl_avx2-stage3hr.obj: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage3hr.Tpo -c -o gsnapl_avx2-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage3hr.Tpo $(DEPDIR)/gsnapl_avx2-stage3hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+
+gsnapl_avx2-spanningelt.o: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-spanningelt.Tpo -c -o gsnapl_avx2-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-spanningelt.Tpo $(DEPDIR)/gsnapl_avx2-spanningelt.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+
+gsnapl_avx2-spanningelt.obj: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-spanningelt.Tpo -c -o gsnapl_avx2-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-spanningelt.Tpo $(DEPDIR)/gsnapl_avx2-spanningelt.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+
+gsnapl_avx2-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-cmet.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-cmet.Tpo -c -o gsnapl_avx2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-cmet.Tpo $(DEPDIR)/gsnapl_avx2-cmet.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gsnapl_avx2-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-cmet.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-cmet.Tpo -c -o gsnapl_avx2-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-cmet.Tpo $(DEPDIR)/gsnapl_avx2-cmet.Po
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+
+gsnapl_avx2-atoi.o: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-atoi.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-atoi.Tpo -c -o gsnapl_avx2-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-atoi.Tpo $(DEPDIR)/gsnapl_avx2-atoi.Po
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+
+gsnapl_avx2-atoi.obj: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-atoi.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-atoi.Tpo -c -o gsnapl_avx2-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-atoi.Tpo $(DEPDIR)/gsnapl_avx2-atoi.Po
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+
+gsnapl_avx2-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-maxent.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-maxent.Tpo -c -o gsnapl_avx2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-maxent.Tpo $(DEPDIR)/gsnapl_avx2-maxent.Po
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+
+gsnapl_avx2-maxent.obj: maxent.c
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+
+gsnapl_avx2-pair.o: pair.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-pair.Tpo $(DEPDIR)/gsnapl_avx2-pair.Po
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+
+gsnapl_avx2-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-pair.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-pair.Tpo -c -o gsnapl_avx2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-pair.Tpo $(DEPDIR)/gsnapl_avx2-pair.Po
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+
+gsnapl_avx2-pairpool.o: pairpool.c
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+gsnapl_avx2-pairpool.obj: pairpool.c
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+gsnapl_avx2-diag.o: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-diag.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-diag.Tpo -c -o gsnapl_avx2-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
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+
+gsnapl_avx2-diag.obj: diag.c
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+gsnapl_avx2-diagpool.o: diagpool.c
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+gsnapl_avx2-diagpool.obj: diagpool.c
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+gsnapl_avx2-orderstat.obj: orderstat.c
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+
+gsnapl_avx2-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-oligoindex_hr.Tpo -c -o gsnapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-oligoindex_hr.Tpo $(DEPDIR)/gsnapl_avx2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnapl_avx2-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gsnapl_avx2-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-oligoindex_hr.Tpo -c -o gsnapl_avx2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-oligoindex_hr.Tpo $(DEPDIR)/gsnapl_avx2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnapl_avx2-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gsnapl_avx2-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-cellpool.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-cellpool.Tpo -c -o gsnapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-cellpool.Tpo $(DEPDIR)/gsnapl_avx2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnapl_avx2-cellpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gsnapl_avx2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-cellpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-cellpool.Tpo -c -o gsnapl_avx2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-cellpool.Tpo $(DEPDIR)/gsnapl_avx2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnapl_avx2-cellpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+
+gsnapl_avx2-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage2.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage2.Tpo -c -o gsnapl_avx2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage2.Tpo $(DEPDIR)/gsnapl_avx2-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnapl_avx2-stage2.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gsnapl_avx2-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage2.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage2.Tpo -c -o gsnapl_avx2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage2.Tpo $(DEPDIR)/gsnapl_avx2-stage2.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage2.c' object='gsnapl_avx2-stage2.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+
+gsnapl_avx2-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-intron.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-intron.Tpo -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-intron.Tpo $(DEPDIR)/gsnapl_avx2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnapl_avx2-intron.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gsnapl_avx2-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-intron.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-intron.Tpo -c -o gsnapl_avx2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-intron.Tpo $(DEPDIR)/gsnapl_avx2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnapl_avx2-intron.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gsnapl_avx2-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-boyer-moore.Tpo -c -o gsnapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-boyer-moore.Tpo $(DEPDIR)/gsnapl_avx2-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnapl_avx2-boyer-moore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gsnapl_avx2-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-boyer-moore.Tpo -c -o gsnapl_avx2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-boyer-moore.Tpo $(DEPDIR)/gsnapl_avx2-boyer-moore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='boyer-moore.c' object='gsnapl_avx2-boyer-moore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gsnapl_avx2-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-changepoint.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-changepoint.Tpo -c -o gsnapl_avx2-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-changepoint.Tpo $(DEPDIR)/gsnapl_avx2-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnapl_avx2-changepoint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+
+gsnapl_avx2-changepoint.obj: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-changepoint.Tpo -c -o gsnapl_avx2-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-changepoint.Tpo $(DEPDIR)/gsnapl_avx2-changepoint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='changepoint.c' object='gsnapl_avx2-changepoint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+
+gsnapl_avx2-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-pbinom.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-pbinom.Tpo -c -o gsnapl_avx2-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-pbinom.Tpo $(DEPDIR)/gsnapl_avx2-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnapl_avx2-pbinom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+
+gsnapl_avx2-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-pbinom.Tpo -c -o gsnapl_avx2-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-pbinom.Tpo $(DEPDIR)/gsnapl_avx2-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnapl_avx2-pbinom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+
+gsnapl_avx2-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-dynprog.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-dynprog.Tpo -c -o gsnapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-dynprog.Tpo $(DEPDIR)/gsnapl_avx2-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnapl_avx2-dynprog.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
+
+gsnapl_avx2-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-dynprog.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-dynprog.Tpo -c -o gsnapl_avx2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-dynprog.Tpo $(DEPDIR)/gsnapl_avx2-dynprog.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='dynprog.c' object='gsnapl_avx2-dynprog.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+
+gsnapl_avx2-dynprog_simd.o: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-dynprog_simd.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-dynprog_simd.Tpo -c -o gsnapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-dynprog_simd.Tpo $(DEPDIR)/gsnapl_avx2-dynprog_simd.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '$(srcdir)/'`dynprog_simd.c
+
+gsnapl_avx2-dynprog_simd.obj: dynprog_simd.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-dynprog_simd.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-dynprog_simd.Tpo -c -o gsnapl_avx2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-dynprog_simd.Tpo $(DEPDIR)/gsnapl_avx2-dynprog_simd.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-dynprog_simd.obj `if test -f 'dynprog_simd.c'; then $(CYGPATH_W) 'dynprog_simd.c'; else $(CYGPATH_W) '$(srcdir)/dynprog_simd.c'; fi`
+
+gsnapl_avx2-dynprog_single.o: dynprog_single.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-dynprog_single.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-dynprog_single.Tpo -c -o gsnapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '$(srcdir)/'`dynprog_single.c
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+gsnapl_avx2-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage3.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage3.Tpo -c -o gsnapl_avx2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage3.Tpo $(DEPDIR)/gsnapl_avx2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl_avx2-stage3.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnapl_avx2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splicestringpool.Tpo -c -o gsnapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splicestringpool.Tpo $(DEPDIR)/gsnapl_avx2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl_avx2-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnapl_avx2-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splicestringpool.Tpo -c -o gsnapl_avx2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splicestringpool.Tpo $(DEPDIR)/gsnapl_avx2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl_avx2-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnapl_avx2-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splicetrie_build.Tpo -c -o gsnapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splicetrie_build.Tpo $(DEPDIR)/gsnapl_avx2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl_avx2-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnapl_avx2-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splicetrie_build.Tpo -c -o gsnapl_avx2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splicetrie_build.Tpo $(DEPDIR)/gsnapl_avx2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl_avx2-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnapl_avx2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splicetrie.Tpo -c -o gsnapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splicetrie.Tpo $(DEPDIR)/gsnapl_avx2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnapl_avx2-splicetrie.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gsnapl_avx2-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splicetrie.Tpo -c -o gsnapl_avx2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splicetrie.Tpo $(DEPDIR)/gsnapl_avx2-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnapl_avx2-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gsnapl_avx2-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splice.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splice.Tpo -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splice.Tpo $(DEPDIR)/gsnapl_avx2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl_avx2-splice.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnapl_avx2-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-splice.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-splice.Tpo -c -o gsnapl_avx2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-splice.Tpo $(DEPDIR)/gsnapl_avx2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl_avx2-splice.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+
+gsnapl_avx2-indel.o: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-indel.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-indel.Tpo -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-indel.Tpo $(DEPDIR)/gsnapl_avx2-indel.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnapl_avx2-indel.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+
+gsnapl_avx2-indel.obj: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-indel.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-indel.Tpo -c -o gsnapl_avx2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-indel.Tpo $(DEPDIR)/gsnapl_avx2-indel.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnapl_avx2-indel.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+
+gsnapl_avx2-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-bitpack64-access.Tpo -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-bitpack64-access.Tpo $(DEPDIR)/gsnapl_avx2-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnapl_avx2-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+gsnapl_avx2-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-bitpack64-access.Tpo -c -o gsnapl_avx2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-bitpack64-access.Tpo $(DEPDIR)/gsnapl_avx2-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='gsnapl_avx2-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+
+gsnapl_avx2-stage1hr.o: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage1hr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage1hr.Tpo -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage1hr.Tpo $(DEPDIR)/gsnapl_avx2-stage1hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='gsnapl_avx2-stage1hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '$(srcdir)/'`stage1hr.c
+
+gsnapl_avx2-stage1hr.obj: stage1hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-stage1hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-stage1hr.Tpo -c -o gsnapl_avx2-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-stage1hr.Tpo $(DEPDIR)/gsnapl_avx2-stage1hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage1hr.c' object='gsnapl_avx2-stage1hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-stage1hr.obj `if test -f 'stage1hr.c'; then $(CYGPATH_W) 'stage1hr.c'; else $(CYGPATH_W) '$(srcdir)/stage1hr.c'; fi`
+
+gsnapl_avx2-request.o: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-request.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-request.Tpo -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-request.Tpo $(DEPDIR)/gsnapl_avx2-request.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gsnapl_avx2-request.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo '$(srcdir)/'`request.c
+
+gsnapl_avx2-request.obj: request.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-request.obj -MD -MP -MF $(DEPDIR)/gsnapl_avx2-request.Tpo -c -o gsnapl_avx2-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-request.Tpo $(DEPDIR)/gsnapl_avx2-request.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='request.c' object='gsnapl_avx2-request.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-request.obj `if test -f 'request.c'; then $(CYGPATH_W) 'request.c'; else $(CYGPATH_W) '$(srcdir)/request.c'; fi`
+
+gsnapl_avx2-resulthr.o: resulthr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-resulthr.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-resulthr.Tpo -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-resulthr.Tpo $(DEPDIR)/gsnapl_avx2-resulthr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='resulthr.c' object='gsnapl_avx2-resulthr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo '$(srcdir)/'`resulthr.c
+
+gsnapl_avx2-resulthr.obj: resulthr.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-resulthr.Tpo $(DEPDIR)/gsnapl_avx2-resulthr.Po
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+
+gsnapl_avx2-output.o: output.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-output.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-output.Tpo -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo '$(srcdir)/'`output.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-output.Tpo $(DEPDIR)/gsnapl_avx2-output.Po
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+
+gsnapl_avx2-output.obj: output.c
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+
+gsnapl_avx2-inbuffer.o: inbuffer.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-inbuffer.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-inbuffer.Tpo -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '$(srcdir)/'`inbuffer.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-inbuffer.Tpo $(DEPDIR)/gsnapl_avx2-inbuffer.Po
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+
+gsnapl_avx2-inbuffer.obj: inbuffer.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-inbuffer.Tpo $(DEPDIR)/gsnapl_avx2-inbuffer.Po
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+
+gsnapl_avx2-samheader.o: samheader.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-samheader.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-samheader.Tpo -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo '$(srcdir)/'`samheader.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-samheader.Tpo $(DEPDIR)/gsnapl_avx2-samheader.Po
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+
+gsnapl_avx2-samheader.obj: samheader.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-samheader.Tpo $(DEPDIR)/gsnapl_avx2-samheader.Po
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+
+gsnapl_avx2-outbuffer.o: outbuffer.c
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+gsnapl_avx2-outbuffer.obj: outbuffer.c
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+
+gsnapl_avx2-datadir.o: datadir.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-datadir.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-datadir.Tpo -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo '$(srcdir)/'`datadir.c
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+
+gsnapl_avx2-datadir.obj: datadir.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_avx2-datadir.Tpo $(DEPDIR)/gsnapl_avx2-datadir.Po
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+
+gsnapl_avx2-parserange.o: parserange.c
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+gsnapl_avx2-parserange.obj: parserange.c
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+gsnapl_avx2-getopt.o: getopt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-getopt.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-getopt.Tpo -c -o gsnapl_avx2-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
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+gsnapl_avx2-getopt.obj: getopt.c
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+
+gsnapl_avx2-getopt1.o: getopt1.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_avx2_CFLAGS) $(CFLAGS) -MT gsnapl_avx2-getopt1.o -MD -MP -MF $(DEPDIR)/gsnapl_avx2-getopt1.Tpo -c -o gsnapl_avx2-getopt1.o `test -f 'getopt1.c' || echo '$(srcdir)/'`getopt1.c
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+gsnapl_avx2-getopt1.obj: getopt1.c
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+gsnapl_nosimd-except.o: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-except.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-except.Tpo -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-except.Tpo $(DEPDIR)/gsnapl_nosimd-except.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '$(srcdir)/'`except.c
+
+gsnapl_nosimd-except.obj: except.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-except.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-except.Tpo -c -o gsnapl_nosimd-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-except.Tpo $(DEPDIR)/gsnapl_nosimd-except.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-except.obj `if test -f 'except.c'; then $(CYGPATH_W) 'except.c'; else $(CYGPATH_W) '$(srcdir)/except.c'; fi`
+
+gsnapl_nosimd-assert.o: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-assert.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-assert.Tpo -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-assert.Tpo $(DEPDIR)/gsnapl_nosimd-assert.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '$(srcdir)/'`assert.c
+
+gsnapl_nosimd-assert.obj: assert.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-assert.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-assert.Tpo -c -o gsnapl_nosimd-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-assert.Tpo $(DEPDIR)/gsnapl_nosimd-assert.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-assert.obj `if test -f 'assert.c'; then $(CYGPATH_W) 'assert.c'; else $(CYGPATH_W) '$(srcdir)/assert.c'; fi`
+
+gsnapl_nosimd-mem.o: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-mem.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-mem.Tpo -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-mem.Tpo $(DEPDIR)/gsnapl_nosimd-mem.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '$(srcdir)/'`mem.c
+
+gsnapl_nosimd-mem.obj: mem.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-mem.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-mem.Tpo -c -o gsnapl_nosimd-mem.obj `if test -f 'mem.c'; then $(CYGPATH_W) 'mem.c'; else $(CYGPATH_W) '$(srcdir)/mem.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-mem.Tpo $(DEPDIR)/gsnapl_nosimd-mem.Po
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+
+gsnapl_nosimd-intlist.o: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-intlist.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-intlist.Tpo -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-intlist.Tpo $(DEPDIR)/gsnapl_nosimd-intlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intlist.c' object='gsnapl_nosimd-intlist.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '$(srcdir)/'`intlist.c
+
+gsnapl_nosimd-intlist.obj: intlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-intlist.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-intlist.Tpo -c -o gsnapl_nosimd-intlist.obj `if test -f 'intlist.c'; then $(CYGPATH_W) 'intlist.c'; else $(CYGPATH_W) '$(srcdir)/intlist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-intlist.Tpo $(DEPDIR)/gsnapl_nosimd-intlist.Po
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+
+gsnapl_nosimd-list.o: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-list.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-list.Tpo -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-list.Tpo $(DEPDIR)/gsnapl_nosimd-list.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '$(srcdir)/'`list.c
+
+gsnapl_nosimd-list.obj: list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-list.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-list.Tpo -c -o gsnapl_nosimd-list.obj `if test -f 'list.c'; then $(CYGPATH_W) 'list.c'; else $(CYGPATH_W) '$(srcdir)/list.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-list.Tpo $(DEPDIR)/gsnapl_nosimd-list.Po
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+
+gsnapl_nosimd-littleendian.o: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-littleendian.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-littleendian.Tpo -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-littleendian.Tpo $(DEPDIR)/gsnapl_nosimd-littleendian.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '$(srcdir)/'`littleendian.c
+
+gsnapl_nosimd-littleendian.obj: littleendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-littleendian.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-littleendian.Tpo -c -o gsnapl_nosimd-littleendian.obj `if test -f 'littleendian.c'; then $(CYGPATH_W) 'littleendian.c'; else $(CYGPATH_W) '$(srcdir)/littleendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-littleendian.Tpo $(DEPDIR)/gsnapl_nosimd-littleendian.Po
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+
+gsnapl_nosimd-bigendian.o: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-bigendian.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-bigendian.Tpo -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-bigendian.Tpo $(DEPDIR)/gsnapl_nosimd-bigendian.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '$(srcdir)/'`bigendian.c
+
+gsnapl_nosimd-bigendian.obj: bigendian.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-bigendian.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-bigendian.Tpo -c -o gsnapl_nosimd-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-bigendian.Tpo $(DEPDIR)/gsnapl_nosimd-bigendian.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-bigendian.obj `if test -f 'bigendian.c'; then $(CYGPATH_W) 'bigendian.c'; else $(CYGPATH_W) '$(srcdir)/bigendian.c'; fi`
+
+gsnapl_nosimd-univinterval.o: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-univinterval.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-univinterval.Tpo -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-univinterval.Tpo $(DEPDIR)/gsnapl_nosimd-univinterval.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '$(srcdir)/'`univinterval.c
+
+gsnapl_nosimd-univinterval.obj: univinterval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-univinterval.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-univinterval.Tpo -c -o gsnapl_nosimd-univinterval.obj `if test -f 'univinterval.c'; then $(CYGPATH_W) 'univinterval.c'; else $(CYGPATH_W) '$(srcdir)/univinterval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-univinterval.Tpo $(DEPDIR)/gsnapl_nosimd-univinterval.Po
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+
+gsnapl_nosimd-interval.o: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-interval.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-interval.Tpo -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '$(srcdir)/'`interval.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-interval.Tpo $(DEPDIR)/gsnapl_nosimd-interval.Po
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+
+gsnapl_nosimd-interval.obj: interval.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-interval.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-interval.Tpo -c -o gsnapl_nosimd-interval.obj `if test -f 'interval.c'; then $(CYGPATH_W) 'interval.c'; else $(CYGPATH_W) '$(srcdir)/interval.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-interval.Tpo $(DEPDIR)/gsnapl_nosimd-interval.Po
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+
+gsnapl_nosimd-uintlist.o: uintlist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-uintlist.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-uintlist.Tpo -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-uintlist.Tpo $(DEPDIR)/gsnapl_nosimd-uintlist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='uintlist.c' object='gsnapl_nosimd-uintlist.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '$(srcdir)/'`uintlist.c
+
+gsnapl_nosimd-uintlist.obj: uintlist.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-uintlist.Tpo $(DEPDIR)/gsnapl_nosimd-uintlist.Po
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+
+gsnapl_nosimd-uint8list.o: uint8list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-uint8list.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-uint8list.Tpo -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '$(srcdir)/'`uint8list.c
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+
+gsnapl_nosimd-uint8list.obj: uint8list.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-uint8list.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-uint8list.Tpo -c -o gsnapl_nosimd-uint8list.obj `if test -f 'uint8list.c'; then $(CYGPATH_W) 'uint8list.c'; else $(CYGPATH_W) '$(srcdir)/uint8list.c'; fi`
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+
+gsnapl_nosimd-stopwatch.o: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stopwatch.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stopwatch.Tpo -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '$(srcdir)/'`stopwatch.c
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+
+gsnapl_nosimd-stopwatch.obj: stopwatch.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stopwatch.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stopwatch.Tpo -c -o gsnapl_nosimd-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-stopwatch.Tpo $(DEPDIR)/gsnapl_nosimd-stopwatch.Po
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+
+gsnapl_nosimd-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-semaphore.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-semaphore.Tpo -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
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+
+gsnapl_nosimd-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-semaphore.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-semaphore.Tpo -c -o gsnapl_nosimd-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
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+
+gsnapl_nosimd-access.o: access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-access.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-access.Tpo -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
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+
+gsnapl_nosimd-access.obj: access.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-access.Tpo $(DEPDIR)/gsnapl_nosimd-access.Po
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+
+gsnapl_nosimd-filestring.o: filestring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-filestring.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-filestring.Tpo -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '$(srcdir)/'`filestring.c
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+gsnapl_nosimd-filestring.obj: filestring.c
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+
+gsnapl_nosimd-iit-read-univ.o: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-iit-read-univ.Tpo -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-iit-read-univ.Tpo $(DEPDIR)/gsnapl_nosimd-iit-read-univ.Po
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+
+gsnapl_nosimd-iit-read-univ.obj: iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-iit-read-univ.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-iit-read-univ.Tpo -c -o gsnapl_nosimd-iit-read-univ.obj `if test -f 'iit-read-univ.c'; then $(CYGPATH_W) 'iit-read-univ.c'; else $(CYGPATH_W) '$(srcdir)/iit-read-univ.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-iit-read-univ.Tpo $(DEPDIR)/gsnapl_nosimd-iit-read-univ.Po
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+
+gsnapl_nosimd-iit-read.o: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-iit-read.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-iit-read.Tpo -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '$(srcdir)/'`iit-read.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-iit-read.Tpo $(DEPDIR)/gsnapl_nosimd-iit-read.Po
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+
+gsnapl_nosimd-iit-read.obj: iit-read.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-iit-read.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-iit-read.Tpo -c -o gsnapl_nosimd-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-iit-read.Tpo $(DEPDIR)/gsnapl_nosimd-iit-read.Po
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+
+gsnapl_nosimd-md5.o: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-md5.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-md5.Tpo -c -o gsnapl_nosimd-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-md5.o `test -f 'md5.c' || echo '$(srcdir)/'`md5.c
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+gsnapl_nosimd-md5.obj: md5.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-md5.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-md5.Tpo -c -o gsnapl_nosimd-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-md5.Tpo $(DEPDIR)/gsnapl_nosimd-md5.Po
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+gsnapl_nosimd-bzip2.o: bzip2.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '$(srcdir)/'`bzip2.c
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+gsnapl_nosimd-bzip2.obj: bzip2.c
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+gsnapl_nosimd-genomicpos.o: genomicpos.c
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+gsnapl_nosimd-genomicpos.obj: genomicpos.c
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+gsnapl_nosimd-genome128_hr.o: genome128_hr.c
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+gsnapl_nosimd-genome128_hr.obj: genome128_hr.c
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+gsnapl_nosimd-genome_sites.o: genome_sites.c
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+gsnapl_nosimd-genome_sites.obj: genome_sites.c
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+
+gsnapl_nosimd-bitpack64-readtwo.o: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-bitpack64-readtwo.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-bitpack64-readtwo.Tpo -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl_nosimd-bitpack64-readtwo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gsnapl_nosimd-bitpack64-readtwo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '$(srcdir)/'`bitpack64-readtwo.c
+
+gsnapl_nosimd-bitpack64-readtwo.obj: bitpack64-readtwo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-bitpack64-readtwo.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-bitpack64-readtwo.Tpo -c -o gsnapl_nosimd-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-bitpack64-readtwo.Tpo $(DEPDIR)/gsnapl_nosimd-bitpack64-readtwo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-readtwo.c' object='gsnapl_nosimd-bitpack64-readtwo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+
+gsnapl_nosimd-indexdb.o: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-indexdb.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-indexdb.Tpo -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-indexdb.Tpo $(DEPDIR)/gsnapl_nosimd-indexdb.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gsnapl_nosimd-indexdb.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '$(srcdir)/'`indexdb.c
+
+gsnapl_nosimd-indexdb.obj: indexdb.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-indexdb.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-indexdb.Tpo -c -o gsnapl_nosimd-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-indexdb.Tpo $(DEPDIR)/gsnapl_nosimd-indexdb.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb.c' object='gsnapl_nosimd-indexdb.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-indexdb.obj `if test -f 'indexdb.c'; then $(CYGPATH_W) 'indexdb.c'; else $(CYGPATH_W) '$(srcdir)/indexdb.c'; fi`
+
+gsnapl_nosimd-indexdb_hr.o: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-indexdb_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-indexdb_hr.Tpo -c -o gsnapl_nosimd-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-indexdb_hr.Tpo $(DEPDIR)/gsnapl_nosimd-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl_nosimd-indexdb_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-indexdb_hr.o `test -f 'indexdb_hr.c' || echo '$(srcdir)/'`indexdb_hr.c
+
+gsnapl_nosimd-indexdb_hr.obj: indexdb_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-indexdb_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-indexdb_hr.Tpo -c -o gsnapl_nosimd-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-indexdb_hr.Tpo $(DEPDIR)/gsnapl_nosimd-indexdb_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl_nosimd-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+
+gsnapl_nosimd-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-oligo.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-oligo.Tpo -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-oligo.Tpo $(DEPDIR)/gsnapl_nosimd-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl_nosimd-oligo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gsnapl_nosimd-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-oligo.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-oligo.Tpo -c -o gsnapl_nosimd-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-oligo.Tpo $(DEPDIR)/gsnapl_nosimd-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl_nosimd-oligo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+
+gsnapl_nosimd-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-chrom.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-chrom.Tpo -c -o gsnapl_nosimd-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-chrom.Tpo $(DEPDIR)/gsnapl_nosimd-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl_nosimd-chrom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+
+gsnapl_nosimd-chrom.obj: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-chrom.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-chrom.Tpo -c -o gsnapl_nosimd-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-chrom.Tpo $(DEPDIR)/gsnapl_nosimd-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl_nosimd-chrom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+
+gsnapl_nosimd-segmentpos.o: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-segmentpos.Tpo -c -o gsnapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-segmentpos.Tpo $(DEPDIR)/gsnapl_nosimd-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl_nosimd-segmentpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+
+gsnapl_nosimd-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-segmentpos.Tpo -c -o gsnapl_nosimd-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-segmentpos.Tpo $(DEPDIR)/gsnapl_nosimd-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl_nosimd-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gsnapl_nosimd-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-chrnum.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-chrnum.Tpo -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-chrnum.Tpo $(DEPDIR)/gsnapl_nosimd-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl_nosimd-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnapl_nosimd-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-chrnum.Tpo -c -o gsnapl_nosimd-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-chrnum.Tpo $(DEPDIR)/gsnapl_nosimd-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl_nosimd-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnapl_nosimd-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-maxent_hr.Tpo -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-maxent_hr.Tpo $(DEPDIR)/gsnapl_nosimd-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl_nosimd-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnapl_nosimd-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-maxent_hr.Tpo -c -o gsnapl_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-maxent_hr.Tpo $(DEPDIR)/gsnapl_nosimd-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl_nosimd-maxent_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnapl_nosimd-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-samprint.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-samprint.Tpo -c -o gsnapl_nosimd-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-samprint.Tpo $(DEPDIR)/gsnapl_nosimd-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl_nosimd-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnapl_nosimd-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-samprint.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-samprint.Tpo -c -o gsnapl_nosimd-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-samprint.Tpo $(DEPDIR)/gsnapl_nosimd-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl_nosimd-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnapl_nosimd-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-mapq.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-mapq.Tpo -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-mapq.Tpo $(DEPDIR)/gsnapl_nosimd-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl_nosimd-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnapl_nosimd-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-mapq.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-mapq.Tpo -c -o gsnapl_nosimd-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-mapq.Tpo $(DEPDIR)/gsnapl_nosimd-mapq.Po
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+
+gsnapl_nosimd-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-shortread.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-shortread.Tpo -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-shortread.Tpo $(DEPDIR)/gsnapl_nosimd-shortread.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnapl_nosimd-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-shortread.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-shortread.Tpo -c -o gsnapl_nosimd-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-shortread.Tpo $(DEPDIR)/gsnapl_nosimd-shortread.Po
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+
+gsnapl_nosimd-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-substring.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-substring.Tpo -c -o gsnapl_nosimd-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-substring.Tpo $(DEPDIR)/gsnapl_nosimd-substring.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnapl_nosimd-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-substring.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-substring.Tpo -c -o gsnapl_nosimd-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-substring.Tpo $(DEPDIR)/gsnapl_nosimd-substring.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnapl_nosimd-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-junction.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-junction.Tpo -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-junction.Tpo $(DEPDIR)/gsnapl_nosimd-junction.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+
+gsnapl_nosimd-junction.obj: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-junction.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-junction.Tpo -c -o gsnapl_nosimd-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-junction.Tpo $(DEPDIR)/gsnapl_nosimd-junction.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+
+gsnapl_nosimd-stage3hr.o: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stage3hr.Tpo -c -o gsnapl_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-stage3hr.Tpo $(DEPDIR)/gsnapl_nosimd-stage3hr.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+
+gsnapl_nosimd-stage3hr.obj: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stage3hr.Tpo -c -o gsnapl_nosimd-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-stage3hr.Tpo $(DEPDIR)/gsnapl_nosimd-stage3hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+
+gsnapl_nosimd-spanningelt.o: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-spanningelt.Tpo -c -o gsnapl_nosimd-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-spanningelt.Tpo $(DEPDIR)/gsnapl_nosimd-spanningelt.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+
+gsnapl_nosimd-spanningelt.obj: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-spanningelt.Tpo -c -o gsnapl_nosimd-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-spanningelt.Tpo $(DEPDIR)/gsnapl_nosimd-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnapl_nosimd-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+
+gsnapl_nosimd-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-cmet.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-cmet.Tpo -c -o gsnapl_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-cmet.Tpo $(DEPDIR)/gsnapl_nosimd-cmet.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gsnapl_nosimd-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-cmet.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-cmet.Tpo -c -o gsnapl_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-cmet.Tpo $(DEPDIR)/gsnapl_nosimd-cmet.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+
+gsnapl_nosimd-atoi.o: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-atoi.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-atoi.Tpo -c -o gsnapl_nosimd-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-atoi.Tpo $(DEPDIR)/gsnapl_nosimd-atoi.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='atoi.c' object='gsnapl_nosimd-atoi.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+
+gsnapl_nosimd-atoi.obj: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-atoi.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-atoi.Tpo -c -o gsnapl_nosimd-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-atoi.Tpo $(DEPDIR)/gsnapl_nosimd-atoi.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+
+gsnapl_nosimd-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-maxent.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-maxent.Tpo -c -o gsnapl_nosimd-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-maxent.Tpo $(DEPDIR)/gsnapl_nosimd-maxent.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent.c' object='gsnapl_nosimd-maxent.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+
+gsnapl_nosimd-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-maxent.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-maxent.Tpo -c -o gsnapl_nosimd-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-maxent.Tpo $(DEPDIR)/gsnapl_nosimd-maxent.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+
+gsnapl_nosimd-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-pair.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-pair.Tpo -c -o gsnapl_nosimd-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-pair.Tpo $(DEPDIR)/gsnapl_nosimd-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnapl_nosimd-pair.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gsnapl_nosimd-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-pair.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-pair.Tpo -c -o gsnapl_nosimd-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-pair.Tpo $(DEPDIR)/gsnapl_nosimd-pair.Po
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+gsnapl_nosimd-pairpool.obj: pairpool.c
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+gsnapl_nosimd-diag.obj: diag.c
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+
+gsnapl_nosimd-diagpool.o: diagpool.c
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+gsnapl_nosimd-diagpool.obj: diagpool.c
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+
+gsnapl_nosimd-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-orderstat.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-orderstat.Tpo -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-orderstat.Tpo $(DEPDIR)/gsnapl_nosimd-orderstat.Po
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+
+gsnapl_nosimd-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-orderstat.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-orderstat.Tpo -c -o gsnapl_nosimd-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-orderstat.Tpo $(DEPDIR)/gsnapl_nosimd-orderstat.Po
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+
+gsnapl_nosimd-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-oligoindex_hr.Tpo -c -o gsnapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-oligoindex_hr.Tpo $(DEPDIR)/gsnapl_nosimd-oligoindex_hr.Po
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+
+gsnapl_nosimd-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-oligoindex_hr.Tpo -c -o gsnapl_nosimd-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-oligoindex_hr.Tpo $(DEPDIR)/gsnapl_nosimd-oligoindex_hr.Po
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+
+gsnapl_nosimd-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-cellpool.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-cellpool.Tpo -c -o gsnapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
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+gsnapl_nosimd-cellpool.obj: cellpool.c
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+gsnapl_nosimd-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stage2.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stage2.Tpo -c -o gsnapl_nosimd-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
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+gsnapl_nosimd-stage2.obj: stage2.c
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+
+gsnapl_nosimd-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-intron.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-intron.Tpo -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
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+
+gsnapl_nosimd-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-intron.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-intron.Tpo -c -o gsnapl_nosimd-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-intron.Tpo $(DEPDIR)/gsnapl_nosimd-intron.Po
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+gsnapl_nosimd-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-boyer-moore.Tpo -c -o gsnapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-boyer-moore.Tpo $(DEPDIR)/gsnapl_nosimd-boyer-moore.Po
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-boyer-moore.Tpo -c -o gsnapl_nosimd-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-boyer-moore.Tpo $(DEPDIR)/gsnapl_nosimd-boyer-moore.Po
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+gsnapl_nosimd-changepoint.o: changepoint.c
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+
+gsnapl_nosimd-changepoint.obj: changepoint.c
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+
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-pbinom.Tpo $(DEPDIR)/gsnapl_nosimd-pbinom.Po
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+
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+
+gsnapl_nosimd-dynprog.o: dynprog.c
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+gsnapl_nosimd-dynprog.obj: dynprog.c
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+
+gsnapl_nosimd-dynprog_simd.o: dynprog_simd.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-dynprog_simd.Tpo $(DEPDIR)/gsnapl_nosimd-dynprog_simd.Po
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+
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+
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+gsnapl_nosimd-dynprog_genome.o: dynprog_genome.c
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+gsnapl_nosimd-dynprog_genome.obj: dynprog_genome.c
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+gsnapl_nosimd-dynprog_cdna.o: dynprog_cdna.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-dynprog_cdna.Tpo $(DEPDIR)/gsnapl_nosimd-dynprog_cdna.Po
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+gsnapl_nosimd-dynprog_end.o: dynprog_end.c
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+gsnapl_nosimd-dynprog_end.obj: dynprog_end.c
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+gsnapl_nosimd-gbuffer.o: gbuffer.c
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+gsnapl_nosimd-translation.o: translation.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-translation.Tpo $(DEPDIR)/gsnapl_nosimd-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnapl_nosimd-translation.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-translation.o `test -f 'translation.c' || echo '$(srcdir)/'`translation.c
+
+gsnapl_nosimd-translation.obj: translation.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-translation.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-translation.Tpo -c -o gsnapl_nosimd-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-translation.Tpo $(DEPDIR)/gsnapl_nosimd-translation.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='translation.c' object='gsnapl_nosimd-translation.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-translation.obj `if test -f 'translation.c'; then $(CYGPATH_W) 'translation.c'; else $(CYGPATH_W) '$(srcdir)/translation.c'; fi`
+
+gsnapl_nosimd-doublelist.o: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-doublelist.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-doublelist.Tpo -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-doublelist.Tpo $(DEPDIR)/gsnapl_nosimd-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnapl_nosimd-doublelist.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '$(srcdir)/'`doublelist.c
+
+gsnapl_nosimd-doublelist.obj: doublelist.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-doublelist.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-doublelist.Tpo -c -o gsnapl_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-doublelist.Tpo $(DEPDIR)/gsnapl_nosimd-doublelist.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='doublelist.c' object='gsnapl_nosimd-doublelist.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-doublelist.obj `if test -f 'doublelist.c'; then $(CYGPATH_W) 'doublelist.c'; else $(CYGPATH_W) '$(srcdir)/doublelist.c'; fi`
+
+gsnapl_nosimd-smooth.o: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-smooth.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-smooth.Tpo -c -o gsnapl_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-smooth.Tpo $(DEPDIR)/gsnapl_nosimd-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnapl_nosimd-smooth.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-smooth.o `test -f 'smooth.c' || echo '$(srcdir)/'`smooth.c
+
+gsnapl_nosimd-smooth.obj: smooth.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-smooth.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-smooth.Tpo -c -o gsnapl_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-smooth.Tpo $(DEPDIR)/gsnapl_nosimd-smooth.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='smooth.c' object='gsnapl_nosimd-smooth.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
+
+gsnapl_nosimd-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-chimera.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-chimera.Tpo -c -o gsnapl_nosimd-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-chimera.Tpo $(DEPDIR)/gsnapl_nosimd-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnapl_nosimd-chimera.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gsnapl_nosimd-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-chimera.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-chimera.Tpo -c -o gsnapl_nosimd-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-chimera.Tpo $(DEPDIR)/gsnapl_nosimd-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnapl_nosimd-chimera.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnapl_nosimd-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stage3.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stage3.Tpo -c -o gsnapl_nosimd-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-stage3.Tpo $(DEPDIR)/gsnapl_nosimd-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl_nosimd-stage3.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnapl_nosimd-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-stage3.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-stage3.Tpo -c -o gsnapl_nosimd-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-stage3.Tpo $(DEPDIR)/gsnapl_nosimd-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl_nosimd-stage3.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnapl_nosimd-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splicestringpool.Tpo -c -o gsnapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splicestringpool.Tpo $(DEPDIR)/gsnapl_nosimd-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl_nosimd-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnapl_nosimd-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splicestringpool.Tpo -c -o gsnapl_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splicestringpool.Tpo $(DEPDIR)/gsnapl_nosimd-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl_nosimd-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnapl_nosimd-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splicetrie_build.Tpo -c -o gsnapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splicetrie_build.Tpo $(DEPDIR)/gsnapl_nosimd-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl_nosimd-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnapl_nosimd-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splicetrie_build.Tpo -c -o gsnapl_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splicetrie_build.Tpo $(DEPDIR)/gsnapl_nosimd-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl_nosimd-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnapl_nosimd-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splicetrie.Tpo -c -o gsnapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splicetrie.Tpo $(DEPDIR)/gsnapl_nosimd-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnapl_nosimd-splicetrie.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gsnapl_nosimd-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splicetrie.Tpo -c -o gsnapl_nosimd-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splicetrie.Tpo $(DEPDIR)/gsnapl_nosimd-splicetrie.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie.c' object='gsnapl_nosimd-splicetrie.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gsnapl_nosimd-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splice.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splice.Tpo -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splice.Tpo $(DEPDIR)/gsnapl_nosimd-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl_nosimd-splice.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnapl_nosimd-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-splice.obj -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-splice.Tpo -c -o gsnapl_nosimd-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-splice.Tpo $(DEPDIR)/gsnapl_nosimd-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl_nosimd-splice.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -c -o gsnapl_nosimd-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+
+gsnapl_nosimd-indel.o: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_nosimd_CFLAGS) $(CFLAGS) -MT gsnapl_nosimd-indel.o -MD -MP -MF $(DEPDIR)/gsnapl_nosimd-indel.Tpo -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_nosimd-indel.Tpo $(DEPDIR)/gsnapl_nosimd-indel.Po
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+gsnapl_nosimd-stage1hr.o: stage1hr.c
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+gsnapl_nosimd-stage1hr.obj: stage1hr.c
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+gsnapl_nosimd-request.o: request.c
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+gsnapl_nosimd-request.obj: request.c
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+
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-iit-read-univ.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-iit-read-univ.Tpo -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-iit-read-univ.Tpo $(DEPDIR)/gsnapl_sse2-iit-read-univ.Po
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-iit-read-univ.Tpo $(DEPDIR)/gsnapl_sse2-iit-read-univ.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-md5.obj `if test -f 'md5.c'; then $(CYGPATH_W) 'md5.c'; else $(CYGPATH_W) '$(srcdir)/md5.c'; fi`
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+gsnapl_sse2-bzip2.obj: bzip2.c
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+
+gsnapl_sse2-sequence.o: sequence.c
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+gsnapl_sse2-sequence.obj: sequence.c
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indexdb_hr.c' object='gsnapl_sse2-indexdb_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-indexdb_hr.obj `if test -f 'indexdb_hr.c'; then $(CYGPATH_W) 'indexdb_hr.c'; else $(CYGPATH_W) '$(srcdir)/indexdb_hr.c'; fi`
+
+gsnapl_sse2-oligo.o: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-oligo.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-oligo.Tpo -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-oligo.Tpo $(DEPDIR)/gsnapl_sse2-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl_sse2-oligo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo '$(srcdir)/'`oligo.c
+
+gsnapl_sse2-oligo.obj: oligo.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-oligo.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-oligo.Tpo -c -o gsnapl_sse2-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-oligo.Tpo $(DEPDIR)/gsnapl_sse2-oligo.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligo.c' object='gsnapl_sse2-oligo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-oligo.obj `if test -f 'oligo.c'; then $(CYGPATH_W) 'oligo.c'; else $(CYGPATH_W) '$(srcdir)/oligo.c'; fi`
+
+gsnapl_sse2-chrom.o: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-chrom.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-chrom.Tpo -c -o gsnapl_sse2-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-chrom.Tpo $(DEPDIR)/gsnapl_sse2-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl_sse2-chrom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-chrom.o `test -f 'chrom.c' || echo '$(srcdir)/'`chrom.c
+
+gsnapl_sse2-chrom.obj: chrom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-chrom.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-chrom.Tpo -c -o gsnapl_sse2-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-chrom.Tpo $(DEPDIR)/gsnapl_sse2-chrom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrom.c' object='gsnapl_sse2-chrom.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-chrom.obj `if test -f 'chrom.c'; then $(CYGPATH_W) 'chrom.c'; else $(CYGPATH_W) '$(srcdir)/chrom.c'; fi`
+
+gsnapl_sse2-segmentpos.o: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-segmentpos.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-segmentpos.Tpo -c -o gsnapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-segmentpos.Tpo $(DEPDIR)/gsnapl_sse2-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl_sse2-segmentpos.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '$(srcdir)/'`segmentpos.c
+
+gsnapl_sse2-segmentpos.obj: segmentpos.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-segmentpos.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-segmentpos.Tpo -c -o gsnapl_sse2-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-segmentpos.Tpo $(DEPDIR)/gsnapl_sse2-segmentpos.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='segmentpos.c' object='gsnapl_sse2-segmentpos.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-segmentpos.obj `if test -f 'segmentpos.c'; then $(CYGPATH_W) 'segmentpos.c'; else $(CYGPATH_W) '$(srcdir)/segmentpos.c'; fi`
+
+gsnapl_sse2-chrnum.o: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-chrnum.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-chrnum.Tpo -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-chrnum.Tpo $(DEPDIR)/gsnapl_sse2-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl_sse2-chrnum.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '$(srcdir)/'`chrnum.c
+
+gsnapl_sse2-chrnum.obj: chrnum.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-chrnum.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-chrnum.Tpo -c -o gsnapl_sse2-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-chrnum.Tpo $(DEPDIR)/gsnapl_sse2-chrnum.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chrnum.c' object='gsnapl_sse2-chrnum.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-chrnum.obj `if test -f 'chrnum.c'; then $(CYGPATH_W) 'chrnum.c'; else $(CYGPATH_W) '$(srcdir)/chrnum.c'; fi`
+
+gsnapl_sse2-maxent_hr.o: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-maxent_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-maxent_hr.Tpo -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-maxent_hr.Tpo $(DEPDIR)/gsnapl_sse2-maxent_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='maxent_hr.c' object='gsnapl_sse2-maxent_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '$(srcdir)/'`maxent_hr.c
+
+gsnapl_sse2-maxent_hr.obj: maxent_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-maxent_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-maxent_hr.Tpo -c -o gsnapl_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-maxent_hr.Tpo $(DEPDIR)/gsnapl_sse2-maxent_hr.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-maxent_hr.obj `if test -f 'maxent_hr.c'; then $(CYGPATH_W) 'maxent_hr.c'; else $(CYGPATH_W) '$(srcdir)/maxent_hr.c'; fi`
+
+gsnapl_sse2-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-samprint.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-samprint.Tpo -c -o gsnapl_sse2-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-samprint.Tpo $(DEPDIR)/gsnapl_sse2-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl_sse2-samprint.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+
+gsnapl_sse2-samprint.obj: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-samprint.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-samprint.Tpo -c -o gsnapl_sse2-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-samprint.Tpo $(DEPDIR)/gsnapl_sse2-samprint.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='samprint.c' object='gsnapl_sse2-samprint.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
+
+gsnapl_sse2-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-mapq.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-mapq.Tpo -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-mapq.Tpo $(DEPDIR)/gsnapl_sse2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl_sse2-mapq.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+
+gsnapl_sse2-mapq.obj: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-mapq.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-mapq.Tpo -c -o gsnapl_sse2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-mapq.Tpo $(DEPDIR)/gsnapl_sse2-mapq.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='mapq.c' object='gsnapl_sse2-mapq.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
+
+gsnapl_sse2-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-shortread.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-shortread.Tpo -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-shortread.Tpo $(DEPDIR)/gsnapl_sse2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnapl_sse2-shortread.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
+
+gsnapl_sse2-shortread.obj: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-shortread.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-shortread.Tpo -c -o gsnapl_sse2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-shortread.Tpo $(DEPDIR)/gsnapl_sse2-shortread.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='shortread.c' object='gsnapl_sse2-shortread.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
+
+gsnapl_sse2-substring.o: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-substring.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-substring.Tpo -c -o gsnapl_sse2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-substring.Tpo $(DEPDIR)/gsnapl_sse2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnapl_sse2-substring.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
+
+gsnapl_sse2-substring.obj: substring.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-substring.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-substring.Tpo -c -o gsnapl_sse2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-substring.Tpo $(DEPDIR)/gsnapl_sse2-substring.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='substring.c' object='gsnapl_sse2-substring.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
+
+gsnapl_sse2-junction.o: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-junction.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-junction.Tpo -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-junction.Tpo $(DEPDIR)/gsnapl_sse2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnapl_sse2-junction.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
+
+gsnapl_sse2-junction.obj: junction.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-junction.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-junction.Tpo -c -o gsnapl_sse2-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-junction.Tpo $(DEPDIR)/gsnapl_sse2-junction.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='junction.c' object='gsnapl_sse2-junction.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-junction.obj `if test -f 'junction.c'; then $(CYGPATH_W) 'junction.c'; else $(CYGPATH_W) '$(srcdir)/junction.c'; fi`
+
+gsnapl_sse2-stage3hr.o: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-stage3hr.Tpo -c -o gsnapl_sse2-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-stage3hr.Tpo $(DEPDIR)/gsnapl_sse2-stage3hr.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
+
+gsnapl_sse2-stage3hr.obj: stage3hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-stage3hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-stage3hr.Tpo -c -o gsnapl_sse2-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-stage3hr.Tpo $(DEPDIR)/gsnapl_sse2-stage3hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3hr.c' object='gsnapl_sse2-stage3hr.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-stage3hr.obj `if test -f 'stage3hr.c'; then $(CYGPATH_W) 'stage3hr.c'; else $(CYGPATH_W) '$(srcdir)/stage3hr.c'; fi`
+
+gsnapl_sse2-spanningelt.o: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-spanningelt.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-spanningelt.Tpo -c -o gsnapl_sse2-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-spanningelt.Tpo $(DEPDIR)/gsnapl_sse2-spanningelt.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-spanningelt.o `test -f 'spanningelt.c' || echo '$(srcdir)/'`spanningelt.c
+
+gsnapl_sse2-spanningelt.obj: spanningelt.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-spanningelt.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-spanningelt.Tpo -c -o gsnapl_sse2-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-spanningelt.Tpo $(DEPDIR)/gsnapl_sse2-spanningelt.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='spanningelt.c' object='gsnapl_sse2-spanningelt.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-spanningelt.obj `if test -f 'spanningelt.c'; then $(CYGPATH_W) 'spanningelt.c'; else $(CYGPATH_W) '$(srcdir)/spanningelt.c'; fi`
+
+gsnapl_sse2-cmet.o: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-cmet.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-cmet.Tpo -c -o gsnapl_sse2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-cmet.Tpo $(DEPDIR)/gsnapl_sse2-cmet.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-cmet.o `test -f 'cmet.c' || echo '$(srcdir)/'`cmet.c
+
+gsnapl_sse2-cmet.obj: cmet.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-cmet.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-cmet.Tpo -c -o gsnapl_sse2-cmet.obj `if test -f 'cmet.c'; then $(CYGPATH_W) 'cmet.c'; else $(CYGPATH_W) '$(srcdir)/cmet.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-cmet.Tpo $(DEPDIR)/gsnapl_sse2-cmet.Po
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+
+gsnapl_sse2-atoi.o: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-atoi.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-atoi.Tpo -c -o gsnapl_sse2-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-atoi.Tpo $(DEPDIR)/gsnapl_sse2-atoi.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-atoi.o `test -f 'atoi.c' || echo '$(srcdir)/'`atoi.c
+
+gsnapl_sse2-atoi.obj: atoi.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-atoi.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-atoi.Tpo -c -o gsnapl_sse2-atoi.obj `if test -f 'atoi.c'; then $(CYGPATH_W) 'atoi.c'; else $(CYGPATH_W) '$(srcdir)/atoi.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-atoi.Tpo $(DEPDIR)/gsnapl_sse2-atoi.Po
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+
+gsnapl_sse2-maxent.o: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-maxent.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-maxent.Tpo -c -o gsnapl_sse2-maxent.o `test -f 'maxent.c' || echo '$(srcdir)/'`maxent.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-maxent.Tpo $(DEPDIR)/gsnapl_sse2-maxent.Po
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+
+gsnapl_sse2-maxent.obj: maxent.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-maxent.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-maxent.Tpo -c -o gsnapl_sse2-maxent.obj `if test -f 'maxent.c'; then $(CYGPATH_W) 'maxent.c'; else $(CYGPATH_W) '$(srcdir)/maxent.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-maxent.Tpo $(DEPDIR)/gsnapl_sse2-maxent.Po
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+
+gsnapl_sse2-pair.o: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-pair.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-pair.Tpo -c -o gsnapl_sse2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-pair.Tpo $(DEPDIR)/gsnapl_sse2-pair.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pair.c' object='gsnapl_sse2-pair.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-pair.o `test -f 'pair.c' || echo '$(srcdir)/'`pair.c
+
+gsnapl_sse2-pair.obj: pair.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-pair.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-pair.Tpo -c -o gsnapl_sse2-pair.obj `if test -f 'pair.c'; then $(CYGPATH_W) 'pair.c'; else $(CYGPATH_W) '$(srcdir)/pair.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-pair.Tpo $(DEPDIR)/gsnapl_sse2-pair.Po
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+
+gsnapl_sse2-pairpool.o: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-pairpool.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-pairpool.Tpo -c -o gsnapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-pairpool.Tpo $(DEPDIR)/gsnapl_sse2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnapl_sse2-pairpool.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '$(srcdir)/'`pairpool.c
+
+gsnapl_sse2-pairpool.obj: pairpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-pairpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-pairpool.Tpo -c -o gsnapl_sse2-pairpool.obj `if test -f 'pairpool.c'; then $(CYGPATH_W) 'pairpool.c'; else $(CYGPATH_W) '$(srcdir)/pairpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-pairpool.Tpo $(DEPDIR)/gsnapl_sse2-pairpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pairpool.c' object='gsnapl_sse2-pairpool.obj' libtool=no @AMDEPBACKSLASH@
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+
+gsnapl_sse2-diag.o: diag.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-diag.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-diag.Tpo -c -o gsnapl_sse2-diag.o `test -f 'diag.c' || echo '$(srcdir)/'`diag.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-diag.Tpo $(DEPDIR)/gsnapl_sse2-diag.Po
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+
+gsnapl_sse2-diag.obj: diag.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-diag.Tpo $(DEPDIR)/gsnapl_sse2-diag.Po
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+
+gsnapl_sse2-diagpool.o: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-diagpool.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-diagpool.Tpo -c -o gsnapl_sse2-diagpool.o `test -f 'diagpool.c' || echo '$(srcdir)/'`diagpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-diagpool.Tpo $(DEPDIR)/gsnapl_sse2-diagpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gsnapl_sse2-diagpool.o' libtool=no @AMDEPBACKSLASH@
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+
+gsnapl_sse2-diagpool.obj: diagpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-diagpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-diagpool.Tpo -c -o gsnapl_sse2-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-diagpool.Tpo $(DEPDIR)/gsnapl_sse2-diagpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='diagpool.c' object='gsnapl_sse2-diagpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-diagpool.obj `if test -f 'diagpool.c'; then $(CYGPATH_W) 'diagpool.c'; else $(CYGPATH_W) '$(srcdir)/diagpool.c'; fi`
+
+gsnapl_sse2-orderstat.o: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-orderstat.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-orderstat.Tpo -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-orderstat.Tpo $(DEPDIR)/gsnapl_sse2-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gsnapl_sse2-orderstat.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '$(srcdir)/'`orderstat.c
+
+gsnapl_sse2-orderstat.obj: orderstat.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-orderstat.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-orderstat.Tpo -c -o gsnapl_sse2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-orderstat.Tpo $(DEPDIR)/gsnapl_sse2-orderstat.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='orderstat.c' object='gsnapl_sse2-orderstat.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-orderstat.obj `if test -f 'orderstat.c'; then $(CYGPATH_W) 'orderstat.c'; else $(CYGPATH_W) '$(srcdir)/orderstat.c'; fi`
+
+gsnapl_sse2-oligoindex_hr.o: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-oligoindex_hr.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-oligoindex_hr.Tpo -c -o gsnapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-oligoindex_hr.Tpo $(DEPDIR)/gsnapl_sse2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnapl_sse2-oligoindex_hr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '$(srcdir)/'`oligoindex_hr.c
+
+gsnapl_sse2-oligoindex_hr.obj: oligoindex_hr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-oligoindex_hr.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-oligoindex_hr.Tpo -c -o gsnapl_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-oligoindex_hr.Tpo $(DEPDIR)/gsnapl_sse2-oligoindex_hr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='oligoindex_hr.c' object='gsnapl_sse2-oligoindex_hr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-oligoindex_hr.obj `if test -f 'oligoindex_hr.c'; then $(CYGPATH_W) 'oligoindex_hr.c'; else $(CYGPATH_W) '$(srcdir)/oligoindex_hr.c'; fi`
+
+gsnapl_sse2-cellpool.o: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-cellpool.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-cellpool.Tpo -c -o gsnapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-cellpool.Tpo $(DEPDIR)/gsnapl_sse2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnapl_sse2-cellpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '$(srcdir)/'`cellpool.c
+
+gsnapl_sse2-cellpool.obj: cellpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-cellpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-cellpool.Tpo -c -o gsnapl_sse2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-cellpool.Tpo $(DEPDIR)/gsnapl_sse2-cellpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='cellpool.c' object='gsnapl_sse2-cellpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-cellpool.obj `if test -f 'cellpool.c'; then $(CYGPATH_W) 'cellpool.c'; else $(CYGPATH_W) '$(srcdir)/cellpool.c'; fi`
+
+gsnapl_sse2-stage2.o: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-stage2.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-stage2.Tpo -c -o gsnapl_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-stage2.Tpo $(DEPDIR)/gsnapl_sse2-stage2.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-stage2.o `test -f 'stage2.c' || echo '$(srcdir)/'`stage2.c
+
+gsnapl_sse2-stage2.obj: stage2.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-stage2.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-stage2.Tpo -c -o gsnapl_sse2-stage2.obj `if test -f 'stage2.c'; then $(CYGPATH_W) 'stage2.c'; else $(CYGPATH_W) '$(srcdir)/stage2.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-stage2.Tpo $(DEPDIR)/gsnapl_sse2-stage2.Po
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+
+gsnapl_sse2-intron.o: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-intron.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-intron.Tpo -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-intron.Tpo $(DEPDIR)/gsnapl_sse2-intron.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='intron.c' object='gsnapl_sse2-intron.o' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo '$(srcdir)/'`intron.c
+
+gsnapl_sse2-intron.obj: intron.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-intron.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-intron.Tpo -c -o gsnapl_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-intron.Tpo $(DEPDIR)/gsnapl_sse2-intron.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-intron.obj `if test -f 'intron.c'; then $(CYGPATH_W) 'intron.c'; else $(CYGPATH_W) '$(srcdir)/intron.c'; fi`
+
+gsnapl_sse2-boyer-moore.o: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-boyer-moore.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-boyer-moore.Tpo -c -o gsnapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-boyer-moore.Tpo $(DEPDIR)/gsnapl_sse2-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '$(srcdir)/'`boyer-moore.c
+
+gsnapl_sse2-boyer-moore.obj: boyer-moore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-boyer-moore.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-boyer-moore.Tpo -c -o gsnapl_sse2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-boyer-moore.Tpo $(DEPDIR)/gsnapl_sse2-boyer-moore.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-boyer-moore.obj `if test -f 'boyer-moore.c'; then $(CYGPATH_W) 'boyer-moore.c'; else $(CYGPATH_W) '$(srcdir)/boyer-moore.c'; fi`
+
+gsnapl_sse2-changepoint.o: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-changepoint.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-changepoint.Tpo -c -o gsnapl_sse2-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-changepoint.Tpo $(DEPDIR)/gsnapl_sse2-changepoint.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-changepoint.o `test -f 'changepoint.c' || echo '$(srcdir)/'`changepoint.c
+
+gsnapl_sse2-changepoint.obj: changepoint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-changepoint.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-changepoint.Tpo -c -o gsnapl_sse2-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-changepoint.Tpo $(DEPDIR)/gsnapl_sse2-changepoint.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-changepoint.obj `if test -f 'changepoint.c'; then $(CYGPATH_W) 'changepoint.c'; else $(CYGPATH_W) '$(srcdir)/changepoint.c'; fi`
+
+gsnapl_sse2-pbinom.o: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-pbinom.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-pbinom.Tpo -c -o gsnapl_sse2-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-pbinom.Tpo $(DEPDIR)/gsnapl_sse2-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnapl_sse2-pbinom.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-pbinom.o `test -f 'pbinom.c' || echo '$(srcdir)/'`pbinom.c
+
+gsnapl_sse2-pbinom.obj: pbinom.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-pbinom.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-pbinom.Tpo -c -o gsnapl_sse2-pbinom.obj `if test -f 'pbinom.c'; then $(CYGPATH_W) 'pbinom.c'; else $(CYGPATH_W) '$(srcdir)/pbinom.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-pbinom.Tpo $(DEPDIR)/gsnapl_sse2-pbinom.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='pbinom.c' object='gsnapl_sse2-pbinom.obj' libtool=no @AMDEPBACKSLASH@
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+
+gsnapl_sse2-dynprog.o: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-dynprog.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-dynprog.Tpo -c -o gsnapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '$(srcdir)/'`dynprog.c
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+gsnapl_sse2-dynprog.obj: dynprog.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-dynprog.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-dynprog.Tpo -c -o gsnapl_sse2-dynprog.obj `if test -f 'dynprog.c'; then $(CYGPATH_W) 'dynprog.c'; else $(CYGPATH_W) '$(srcdir)/dynprog.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-dynprog.Tpo $(DEPDIR)/gsnapl_sse2-dynprog.Po
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+gsnapl_sse2-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-chimera.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-chimera.Tpo -c -o gsnapl_sse2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-chimera.Tpo $(DEPDIR)/gsnapl_sse2-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnapl_sse2-chimera.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+
+gsnapl_sse2-chimera.obj: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-chimera.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-chimera.Tpo -c -o gsnapl_sse2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-chimera.Tpo $(DEPDIR)/gsnapl_sse2-chimera.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='chimera.c' object='gsnapl_sse2-chimera.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
+
+gsnapl_sse2-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-stage3.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-stage3.Tpo -c -o gsnapl_sse2-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-stage3.Tpo $(DEPDIR)/gsnapl_sse2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl_sse2-stage3.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+
+gsnapl_sse2-stage3.obj: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-stage3.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-stage3.Tpo -c -o gsnapl_sse2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-stage3.Tpo $(DEPDIR)/gsnapl_sse2-stage3.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='stage3.c' object='gsnapl_sse2-stage3.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
+
+gsnapl_sse2-splicestringpool.o: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splicestringpool.Tpo -c -o gsnapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splicestringpool.Tpo $(DEPDIR)/gsnapl_sse2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl_sse2-splicestringpool.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
+
+gsnapl_sse2-splicestringpool.obj: splicestringpool.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splicestringpool.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splicestringpool.Tpo -c -o gsnapl_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splicestringpool.Tpo $(DEPDIR)/gsnapl_sse2-splicestringpool.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicestringpool.c' object='gsnapl_sse2-splicestringpool.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splicestringpool.obj `if test -f 'splicestringpool.c'; then $(CYGPATH_W) 'splicestringpool.c'; else $(CYGPATH_W) '$(srcdir)/splicestringpool.c'; fi`
+
+gsnapl_sse2-splicetrie_build.o: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splicetrie_build.Tpo -c -o gsnapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splicetrie_build.Tpo $(DEPDIR)/gsnapl_sse2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl_sse2-splicetrie_build.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
+
+gsnapl_sse2-splicetrie_build.obj: splicetrie_build.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splicetrie_build.Tpo -c -o gsnapl_sse2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splicetrie_build.Tpo $(DEPDIR)/gsnapl_sse2-splicetrie_build.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splicetrie_build.c' object='gsnapl_sse2-splicetrie_build.obj' libtool=no @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
+
+gsnapl_sse2-splicetrie.o: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splicetrie.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splicetrie.Tpo -c -o gsnapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splicetrie.Tpo $(DEPDIR)/gsnapl_sse2-splicetrie.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '$(srcdir)/'`splicetrie.c
+
+gsnapl_sse2-splicetrie.obj: splicetrie.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splicetrie.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splicetrie.Tpo -c -o gsnapl_sse2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splicetrie.Tpo $(DEPDIR)/gsnapl_sse2-splicetrie.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splicetrie.obj `if test -f 'splicetrie.c'; then $(CYGPATH_W) 'splicetrie.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie.c'; fi`
+
+gsnapl_sse2-splice.o: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splice.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splice.Tpo -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splice.Tpo $(DEPDIR)/gsnapl_sse2-splice.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='splice.c' object='gsnapl_sse2-splice.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo '$(srcdir)/'`splice.c
+
+gsnapl_sse2-splice.obj: splice.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-splice.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-splice.Tpo -c -o gsnapl_sse2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-splice.Tpo $(DEPDIR)/gsnapl_sse2-splice.Po
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-splice.obj `if test -f 'splice.c'; then $(CYGPATH_W) 'splice.c'; else $(CYGPATH_W) '$(srcdir)/splice.c'; fi`
+
+gsnapl_sse2-indel.o: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-indel.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-indel.Tpo -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-indel.Tpo $(DEPDIR)/gsnapl_sse2-indel.Po
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+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo '$(srcdir)/'`indel.c
+
+gsnapl_sse2-indel.obj: indel.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-indel.obj -MD -MP -MF $(DEPDIR)/gsnapl_sse2-indel.Tpo -c -o gsnapl_sse2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-indel.Tpo $(DEPDIR)/gsnapl_sse2-indel.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='indel.c' object='gsnapl_sse2-indel.obj' libtool=no @AMDEPBACKSLASH@
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-indel.obj `if test -f 'indel.c'; then $(CYGPATH_W) 'indel.c'; else $(CYGPATH_W) '$(srcdir)/indel.c'; fi`
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+gsnapl_sse2-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -MT gsnapl_sse2-bitpack64-access.o -MD -MP -MF $(DEPDIR)/gsnapl_sse2-bitpack64-access.Tpo -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gmapindex_CFLAGS) $(CFLAGS) -MT gmapindex-compress.o -MD -MP -MF $(DEPDIR)/gmapindex-compress.Tpo -c -o gmapindex-compress.o `test -f 'compress.c' || echo '$(srcdir)/'`compress.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse2-bitpack64-access.Tpo $(DEPDIR)/gsnapl_sse2-bitpack64-access.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse2_CFLAGS) $(CFLAGS) -c -o gsnapl_sse2-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+gsnapl_sse42-samprint.o: samprint.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-samprint.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-samprint.Tpo -c -o gsnapl_sse42-samprint.o `test -f 'samprint.c' || echo '$(srcdir)/'`samprint.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-samprint.Tpo $(DEPDIR)/gsnapl_sse42-samprint.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-samprint.Tpo $(DEPDIR)/gsnapl_sse42-samprint.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-samprint.obj `if test -f 'samprint.c'; then $(CYGPATH_W) 'samprint.c'; else $(CYGPATH_W) '$(srcdir)/samprint.c'; fi`
-gsnap-mapq.o: mapq.c
- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-mapq.o -MD -MP -MF $(DEPDIR)/gsnap-mapq.Tpo -c -o gsnap-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
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+gsnapl_sse42-mapq.o: mapq.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-mapq.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-mapq.Tpo -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '$(srcdir)/'`mapq.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-mapq.Tpo $(DEPDIR)/gsnapl_sse42-mapq.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-mapq.obj -MD -MP -MF $(DEPDIR)/gsnap-mapq.Tpo -c -o gsnap-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-mapq.Tpo $(DEPDIR)/gsnapl_sse42-mapq.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-mapq.obj `if test -f 'mapq.c'; then $(CYGPATH_W) 'mapq.c'; else $(CYGPATH_W) '$(srcdir)/mapq.c'; fi`
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-shortread.o -MD -MP -MF $(DEPDIR)/gsnap-shortread.Tpo -c -o gsnap-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
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+gsnapl_sse42-shortread.o: shortread.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-shortread.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-shortread.Tpo -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '$(srcdir)/'`shortread.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-shortread.obj `if test -f 'shortread.c'; then $(CYGPATH_W) 'shortread.c'; else $(CYGPATH_W) '$(srcdir)/shortread.c'; fi`
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-substring.o -MD -MP -MF $(DEPDIR)/gsnap-substring.Tpo -c -o gsnap-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-substring.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-substring.Tpo -c -o gsnapl_sse42-substring.o `test -f 'substring.c' || echo '$(srcdir)/'`substring.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-substring.obj -MD -MP -MF $(DEPDIR)/gsnap-substring.Tpo -c -o gsnap-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-substring.obj `if test -f 'substring.c'; then $(CYGPATH_W) 'substring.c'; else $(CYGPATH_W) '$(srcdir)/substring.c'; fi`
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-junction.o -MD -MP -MF $(DEPDIR)/gsnap-junction.Tpo -c -o gsnap-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
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+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-junction.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-junction.Tpo -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '$(srcdir)/'`junction.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage3hr.o -MD -MP -MF $(DEPDIR)/gsnap-stage3hr.Tpo -c -o gsnap-stage3hr.o `test -f 'stage3hr.c' || echo '$(srcdir)/'`stage3hr.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-smooth.Tpo $(DEPDIR)/gsnapl_sse42-smooth.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-smooth.obj `if test -f 'smooth.c'; then $(CYGPATH_W) 'smooth.c'; else $(CYGPATH_W) '$(srcdir)/smooth.c'; fi`
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-chimera.o -MD -MP -MF $(DEPDIR)/gsnap-chimera.Tpo -c -o gsnap-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
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+gsnapl_sse42-chimera.o: chimera.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-chimera.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-chimera.Tpo -c -o gsnapl_sse42-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-chimera.Tpo $(DEPDIR)/gsnapl_sse42-chimera.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-chimera.o `test -f 'chimera.c' || echo '$(srcdir)/'`chimera.c
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+gsnapl_sse42-chimera.obj: chimera.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-chimera.Tpo $(DEPDIR)/gsnapl_sse42-chimera.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-chimera.obj `if test -f 'chimera.c'; then $(CYGPATH_W) 'chimera.c'; else $(CYGPATH_W) '$(srcdir)/chimera.c'; fi`
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-stage3.o -MD -MP -MF $(DEPDIR)/gsnap-stage3.Tpo -c -o gsnap-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
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+gsnapl_sse42-stage3.o: stage3.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -MT gsnapl_sse42-stage3.o -MD -MP -MF $(DEPDIR)/gsnapl_sse42-stage3.Tpo -c -o gsnapl_sse42-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-stage3.Tpo $(DEPDIR)/gsnapl_sse42-stage3.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-stage3.o `test -f 'stage3.c' || echo '$(srcdir)/'`stage3.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-stage3.obj `if test -f 'stage3.c'; then $(CYGPATH_W) 'stage3.c'; else $(CYGPATH_W) '$(srcdir)/stage3.c'; fi`
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splicestringpool.o -MD -MP -MF $(DEPDIR)/gsnap-splicestringpool.Tpo -c -o gsnap-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-splicestringpool.Tpo $(DEPDIR)/gsnapl_sse42-splicestringpool.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnapl_sse42_CFLAGS) $(CFLAGS) -c -o gsnapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '$(srcdir)/'`splicestringpool.c
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splicetrie_build.o -MD -MP -MF $(DEPDIR)/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '$(srcdir)/'`splicetrie_build.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/gsnapl_sse42-splicetrie_build.Tpo $(DEPDIR)/gsnapl_sse42-splicetrie_build.Po
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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-gsnap-splicetrie_build.obj: splicetrie_build.c
- at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(gsnap_CFLAGS) $(CFLAGS) -MT gsnap-splicetrie_build.obj -MD -MP -MF $(DEPDIR)/gsnap-splicetrie_build.Tpo -c -o gsnap-splicetrie_build.obj `if test -f 'splicetrie_build.c'; then $(CYGPATH_W) 'splicetrie_build.c'; else $(CYGPATH_W) '$(srcdir)/splicetrie_build.c'; fi`
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
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@@ -9062,6 +37300,20 @@ iit_dump-stopwatch.obj: stopwatch.c
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+iit_dump-semaphore.obj: semaphore.c
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+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-semaphore.Tpo $(DEPDIR)/iit_dump-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='iit_dump-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -c -o iit_dump-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
iit_dump-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-access.o -MD -MP -MF $(DEPDIR)/iit_dump-access.Tpo -c -o iit_dump-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-access.Tpo $(DEPDIR)/iit_dump-access.Po
@@ -9118,6 +37370,20 @@ iit_dump-iit-read.obj: iit-read.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -c -o iit_dump-iit-read.obj `if test -f 'iit-read.c'; then $(CYGPATH_W) 'iit-read.c'; else $(CYGPATH_W) '$(srcdir)/iit-read.c'; fi`
+iit_dump-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-parserange.o -MD -MP -MF $(DEPDIR)/iit_dump-parserange.Tpo -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-parserange.Tpo $(DEPDIR)/iit_dump-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='iit_dump-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+iit_dump-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-parserange.obj -MD -MP -MF $(DEPDIR)/iit_dump-parserange.Tpo -c -o iit_dump-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-parserange.Tpo $(DEPDIR)/iit_dump-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='iit_dump-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -c -o iit_dump-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
iit_dump-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_dump_CFLAGS) $(CFLAGS) -MT iit_dump-getopt.o -MD -MP -MF $(DEPDIR)/iit_dump-getopt.Tpo -c -o iit_dump-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_dump-getopt.Tpo $(DEPDIR)/iit_dump-getopt.Po
@@ -9314,6 +37580,20 @@ iit_get-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -c -o iit_get-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+iit_get-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-semaphore.o -MD -MP -MF $(DEPDIR)/iit_get-semaphore.Tpo -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-semaphore.Tpo $(DEPDIR)/iit_get-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='iit_get-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+iit_get-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-semaphore.obj -MD -MP -MF $(DEPDIR)/iit_get-semaphore.Tpo -c -o iit_get-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-semaphore.Tpo $(DEPDIR)/iit_get-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='iit_get-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -c -o iit_get-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
iit_get-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_get_CFLAGS) $(CFLAGS) -MT iit_get-access.o -MD -MP -MF $(DEPDIR)/iit_get-access.Tpo -c -o iit_get-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_get-access.Tpo $(DEPDIR)/iit_get-access.Po
@@ -9580,6 +37860,20 @@ iit_store-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -c -o iit_store-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+iit_store-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-semaphore.o -MD -MP -MF $(DEPDIR)/iit_store-semaphore.Tpo -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-semaphore.Tpo $(DEPDIR)/iit_store-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='iit_store-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+iit_store-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-semaphore.obj -MD -MP -MF $(DEPDIR)/iit_store-semaphore.Tpo -c -o iit_store-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-semaphore.Tpo $(DEPDIR)/iit_store-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='iit_store-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -c -o iit_store-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
iit_store-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(iit_store_CFLAGS) $(CFLAGS) -MT iit_store-access.o -MD -MP -MF $(DEPDIR)/iit_store-access.Tpo -c -o iit_store-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/iit_store-access.Tpo $(DEPDIR)/iit_store-access.Po
@@ -9832,6 +38126,20 @@ sam_sort-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+sam_sort-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-semaphore.o -MD -MP -MF $(DEPDIR)/sam_sort-semaphore.Tpo -c -o sam_sort-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-semaphore.Tpo $(DEPDIR)/sam_sort-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='sam_sort-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+sam_sort-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-semaphore.obj -MD -MP -MF $(DEPDIR)/sam_sort-semaphore.Tpo -c -o sam_sort-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-semaphore.Tpo $(DEPDIR)/sam_sort-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='sam_sort-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
sam_sort-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-access.o -MD -MP -MF $(DEPDIR)/sam_sort-access.Tpo -c -o sam_sort-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-access.Tpo $(DEPDIR)/sam_sort-access.Po
@@ -9902,6 +38210,20 @@ sam_sort-filestring.obj: filestring.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-filestring.obj `if test -f 'filestring.c'; then $(CYGPATH_W) 'filestring.c'; else $(CYGPATH_W) '$(srcdir)/filestring.c'; fi`
+sam_sort-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-parserange.o -MD -MP -MF $(DEPDIR)/sam_sort-parserange.Tpo -c -o sam_sort-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-parserange.Tpo $(DEPDIR)/sam_sort-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='sam_sort-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+sam_sort-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-parserange.obj -MD -MP -MF $(DEPDIR)/sam_sort-parserange.Tpo -c -o sam_sort-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-parserange.Tpo $(DEPDIR)/sam_sort-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='sam_sort-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -c -o sam_sort-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
sam_sort-iit-read-univ.o: iit-read-univ.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sam_sort_CFLAGS) $(CFLAGS) -MT sam_sort-iit-read-univ.o -MD -MP -MF $(DEPDIR)/sam_sort-iit-read-univ.Tpo -c -o sam_sort-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '$(srcdir)/'`iit-read-univ.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/sam_sort-iit-read-univ.Tpo $(DEPDIR)/sam_sort-iit-read-univ.Po
@@ -10168,6 +38490,20 @@ snpindex-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+snpindex-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-semaphore.o -MD -MP -MF $(DEPDIR)/snpindex-semaphore.Tpo -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-semaphore.Tpo $(DEPDIR)/snpindex-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='snpindex-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+snpindex-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-semaphore.obj -MD -MP -MF $(DEPDIR)/snpindex-semaphore.Tpo -c -o snpindex-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-semaphore.Tpo $(DEPDIR)/snpindex-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='snpindex-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
snpindex-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-access.o -MD -MP -MF $(DEPDIR)/snpindex-access.Tpo -c -o snpindex-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-access.Tpo $(DEPDIR)/snpindex-access.Po
@@ -10322,6 +38658,34 @@ snpindex-bitpack64-readtwo.obj: bitpack64-readtwo.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-bitpack64-readtwo.obj `if test -f 'bitpack64-readtwo.c'; then $(CYGPATH_W) 'bitpack64-readtwo.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-readtwo.c'; fi`
+snpindex-bitpack64-access.o: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-access.o -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-access.Tpo -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-access.Tpo $(DEPDIR)/snpindex-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='snpindex-bitpack64-access.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '$(srcdir)/'`bitpack64-access.c
+
+snpindex-bitpack64-access.obj: bitpack64-access.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-access.obj -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-access.Tpo -c -o snpindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-access.Tpo $(DEPDIR)/snpindex-bitpack64-access.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-access.c' object='snpindex-bitpack64-access.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-bitpack64-access.obj `if test -f 'bitpack64-access.c'; then $(CYGPATH_W) 'bitpack64-access.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-access.c'; fi`
+
+snpindex-bitpack64-incr.o: bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-incr.o -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-incr.Tpo -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '$(srcdir)/'`bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-incr.Tpo $(DEPDIR)/snpindex-bitpack64-incr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-incr.c' object='snpindex-bitpack64-incr.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '$(srcdir)/'`bitpack64-incr.c
+
+snpindex-bitpack64-incr.obj: bitpack64-incr.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-incr.obj -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-incr.Tpo -c -o snpindex-bitpack64-incr.obj `if test -f 'bitpack64-incr.c'; then $(CYGPATH_W) 'bitpack64-incr.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-incr.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-incr.Tpo $(DEPDIR)/snpindex-bitpack64-incr.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='bitpack64-incr.c' object='snpindex-bitpack64-incr.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-bitpack64-incr.obj `if test -f 'bitpack64-incr.c'; then $(CYGPATH_W) 'bitpack64-incr.c'; else $(CYGPATH_W) '$(srcdir)/bitpack64-incr.c'; fi`
+
snpindex-bitpack64-write.o: bitpack64-write.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-bitpack64-write.o -MD -MP -MF $(DEPDIR)/snpindex-bitpack64-write.Tpo -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '$(srcdir)/'`bitpack64-write.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-bitpack64-write.Tpo $(DEPDIR)/snpindex-bitpack64-write.Po
@@ -10448,6 +38812,20 @@ snpindex-datadir.obj: datadir.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+snpindex-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-parserange.o -MD -MP -MF $(DEPDIR)/snpindex-parserange.Tpo -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-parserange.Tpo $(DEPDIR)/snpindex-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='snpindex-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+snpindex-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-parserange.obj -MD -MP -MF $(DEPDIR)/snpindex-parserange.Tpo -c -o snpindex-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-parserange.Tpo $(DEPDIR)/snpindex-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='snpindex-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -c -o snpindex-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
snpindex-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(snpindex_CFLAGS) $(CFLAGS) -MT snpindex-getopt.o -MD -MP -MF $(DEPDIR)/snpindex-getopt.Tpo -c -o snpindex-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/snpindex-getopt.Tpo $(DEPDIR)/snpindex-getopt.Po
@@ -10644,6 +39022,20 @@ uniqscan-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -c -o uniqscan-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+uniqscan-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-semaphore.o -MD -MP -MF $(DEPDIR)/uniqscan-semaphore.Tpo -c -o uniqscan-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-semaphore.Tpo $(DEPDIR)/uniqscan-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='uniqscan-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -c -o uniqscan-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+uniqscan-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-semaphore.obj -MD -MP -MF $(DEPDIR)/uniqscan-semaphore.Tpo -c -o uniqscan-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-semaphore.Tpo $(DEPDIR)/uniqscan-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='uniqscan-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -c -o uniqscan-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
uniqscan-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-access.o -MD -MP -MF $(DEPDIR)/uniqscan-access.Tpo -c -o uniqscan-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-access.Tpo $(DEPDIR)/uniqscan-access.Po
@@ -11582,6 +39974,20 @@ uniqscan-datadir.obj: datadir.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -c -o uniqscan-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+uniqscan-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-parserange.o -MD -MP -MF $(DEPDIR)/uniqscan-parserange.Tpo -c -o uniqscan-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-parserange.Tpo $(DEPDIR)/uniqscan-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='uniqscan-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -c -o uniqscan-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+uniqscan-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-parserange.obj -MD -MP -MF $(DEPDIR)/uniqscan-parserange.Tpo -c -o uniqscan-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-parserange.Tpo $(DEPDIR)/uniqscan-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='uniqscan-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -c -o uniqscan-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
uniqscan-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscan_CFLAGS) $(CFLAGS) -MT uniqscan-getopt.o -MD -MP -MF $(DEPDIR)/uniqscan-getopt.Tpo -c -o uniqscan-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscan-getopt.Tpo $(DEPDIR)/uniqscan-getopt.Po
@@ -11792,6 +40198,20 @@ uniqscanl-stopwatch.obj: stopwatch.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -c -o uniqscanl-stopwatch.obj `if test -f 'stopwatch.c'; then $(CYGPATH_W) 'stopwatch.c'; else $(CYGPATH_W) '$(srcdir)/stopwatch.c'; fi`
+uniqscanl-semaphore.o: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-semaphore.o -MD -MP -MF $(DEPDIR)/uniqscanl-semaphore.Tpo -c -o uniqscanl-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-semaphore.Tpo $(DEPDIR)/uniqscanl-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='uniqscanl-semaphore.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -c -o uniqscanl-semaphore.o `test -f 'semaphore.c' || echo '$(srcdir)/'`semaphore.c
+
+uniqscanl-semaphore.obj: semaphore.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-semaphore.obj -MD -MP -MF $(DEPDIR)/uniqscanl-semaphore.Tpo -c -o uniqscanl-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-semaphore.Tpo $(DEPDIR)/uniqscanl-semaphore.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='semaphore.c' object='uniqscanl-semaphore.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -c -o uniqscanl-semaphore.obj `if test -f 'semaphore.c'; then $(CYGPATH_W) 'semaphore.c'; else $(CYGPATH_W) '$(srcdir)/semaphore.c'; fi`
+
uniqscanl-access.o: access.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-access.o -MD -MP -MF $(DEPDIR)/uniqscanl-access.Tpo -c -o uniqscanl-access.o `test -f 'access.c' || echo '$(srcdir)/'`access.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-access.Tpo $(DEPDIR)/uniqscanl-access.Po
@@ -12688,6 +41108,20 @@ uniqscanl-datadir.obj: datadir.c
@AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
@am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -c -o uniqscanl-datadir.obj `if test -f 'datadir.c'; then $(CYGPATH_W) 'datadir.c'; else $(CYGPATH_W) '$(srcdir)/datadir.c'; fi`
+uniqscanl-parserange.o: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-parserange.o -MD -MP -MF $(DEPDIR)/uniqscanl-parserange.Tpo -c -o uniqscanl-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-parserange.Tpo $(DEPDIR)/uniqscanl-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='uniqscanl-parserange.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -c -o uniqscanl-parserange.o `test -f 'parserange.c' || echo '$(srcdir)/'`parserange.c
+
+uniqscanl-parserange.obj: parserange.c
+ at am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-parserange.obj -MD -MP -MF $(DEPDIR)/uniqscanl-parserange.Tpo -c -o uniqscanl-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+ at am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-parserange.Tpo $(DEPDIR)/uniqscanl-parserange.Po
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ source='parserange.c' object='uniqscanl-parserange.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCC_FALSE@ DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCC_FALSE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -c -o uniqscanl-parserange.obj `if test -f 'parserange.c'; then $(CYGPATH_W) 'parserange.c'; else $(CYGPATH_W) '$(srcdir)/parserange.c'; fi`
+
uniqscanl-getopt.o: getopt.c
@am__fastdepCC_TRUE@ $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(uniqscanl_CFLAGS) $(CFLAGS) -MT uniqscanl-getopt.o -MD -MP -MF $(DEPDIR)/uniqscanl-getopt.Tpo -c -o uniqscanl-getopt.o `test -f 'getopt.c' || echo '$(srcdir)/'`getopt.c
@am__fastdepCC_TRUE@ $(am__mv) $(DEPDIR)/uniqscanl-getopt.Tpo $(DEPDIR)/uniqscanl-getopt.Po
@@ -12938,6 +41372,28 @@ uninstall-am: uninstall-binPROGRAMS
tags uninstall uninstall-am uninstall-binPROGRAMS
+#SPLICING_SCORE_FILES = fopen.h bool.h types.h \
+# except.c except.h assert.c assert.h mem.c mem.h \
+# intlistdef.h intlist.c intlist.h listdef.h list.c list.h \
+# univinterval.c univinterval.h interval.c interval.h \
+# uintlist.c uintlist.h \
+# chrom.c chrom.h stopwatch.c stopwatch.h access.c access.h \
+# iit-read-univ.c iit-read-univ.h iitdef.h iit-read.c iit-read.h \
+# filestring.c filestring.h \
+# md5.c md5.h complement.h bzip2.c bzip2.h sequence.c sequence.h \
+# genome.c genome.h \
+# genomicpos.c genomicpos.h \
+# chrnum.c chrnum.h chrsubset.c chrsubset.h \
+# maxent.c maxent.h \
+# branchpoint.c branchpoint.h \
+# parserange.c parserange.h datadir.c datadir.h getopt.c getopt1.c getopt.h splicing-score.c
+#
+#splicing_score_CFLAGS = $(AM_CFLAGS) $(PTHREAD_CFLAGS) -DGMAPDB=\"$(GMAPDB)\"
+#splicing_score_LDFLAGS = $(AM_LDFLAGS) $(STATIC_LDFLAG) $(PTHREAD_CFLAGS)
+#splicing_score_LDADD = $(PTHREAD_LIBS) $(ZLIB_LIBS) $(BZLIB_LIBS)
+#dist_splicing_score_SOURCES =
+#nodist_splicing_score_SOURCES = $(SPLICING_SCORE_FILES)
+
# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT:
diff --git a/src/access.c b/src/access.c
index e819902..2d379e6 100644
--- a/src/access.c
+++ b/src/access.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: access.c 170327 2015-07-22 17:50:11Z twu $";
+static char rcsid[] = "$Id: access.c 184162 2016-02-12 18:54:56Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -12,6 +12,7 @@ static char rcsid[] = "$Id: access.c 170327 2015-07-22 17:50:11Z twu $";
#include <stdlib.h>
#include <string.h> /* For strerror */
#include <errno.h>
+#include <sys/stat.h> /* For fstat */
/* <unistd.h> and <sys/types.h> included in access.h */
#include <sys/mman.h> /* For mmap */
@@ -19,7 +20,8 @@ static char rcsid[] = "$Id: access.c 170327 2015-07-22 17:50:11Z twu $";
#define PROJECT_ID 42
#include <sys/ipc.h>
#include <sys/shm.h> /* For shmat and shmdt */
-#include <sys/sem.h> /* For semaphores */
+#include "semaphore.h"
+
#ifdef USE_MPI
#include <mpi.h>
@@ -58,17 +60,30 @@ static char rcsid[] = "$Id: access.c 170327 2015-07-22 17:50:11Z twu $";
#define debug(x)
#endif
+static bool preload_shared_memory_p = false;
+static bool unload_shared_memory_p = false;
+
+void
+Access_setup (bool preload_shared_memory_p_in, bool unload_shared_memory_p_in) {
+ preload_shared_memory_p = preload_shared_memory_p_in;
+ unload_shared_memory_p = unload_shared_memory_p_in;
+ return;
+}
+
+
bool
Access_file_exists_p (char *filename) {
#ifdef HAVE_STRUCT_STAT64
- struct stat64 sb;
+ /* struct stat64 is now deprecated */
+ struct stat sb;
#else
struct stat sb;
#endif
#ifdef HAVE_STAT64
- if (stat64(filename,&sb) == 0) {
+ /* stat64 is now deprecated */
+ if (stat(filename,&sb) == 0) {
return true;
} else {
return false;
@@ -83,21 +98,23 @@ Access_file_exists_p (char *filename) {
}
-off_t
+size_t
Access_filesize (char *filename) {
#ifdef HAVE_STRUCT_STAT64
- struct stat64 sb;
+ /* struct stat64 is now deprecated */
+ struct stat sb;
#else
struct stat sb;
#endif
#ifdef HAVE_STAT64
- stat64(filename,&sb);
+ /* stat64 is now deprecated */
+ stat(filename,&sb);
#else
stat(filename,&sb);
#endif
- debug(printf("filesize is %zu\n",sb.st_size));
- return sb.st_size;
+ debug(printf("filesize is %zu\n",(size_t) sb.st_size));
+ return (size_t) sb.st_size;
}
@@ -189,8 +206,9 @@ Access_fileio_rw (char *filename) {
}
+#if 0
#ifndef WORDS_BIGENDIAN
-/* Needed as a test on Macintosh machines */
+/* Previously needed as a test on Macintosh machines */
static unsigned char
first_nonzero_char (size_t *i, char *filename) {
size_t len;
@@ -198,7 +216,7 @@ first_nonzero_char (size_t *i, char *filename) {
unsigned char value = 0;
void *p;
- len = (size_t) Access_filesize(filename);
+ len = Access_filesize(filename);
if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
fprintf(stderr,"Error: can't open file %s with fopen\n",filename);
@@ -225,7 +243,7 @@ first_nonzero_uint (size_t *i, char *filename) {
UINT4 value = 0;
void *p;
- len = (size_t) Access_filesize(filename);
+ len = Access_filesize(filename);
if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
fprintf(stderr,"Error: can't open file %s with fopen\n",filename);
@@ -252,8 +270,7 @@ first_nonzero_uint8 (size_t *i, char *filename) {
UINT8 value = 0;
void *p;
- len = (size_t) Access_filesize(filename);
-
+ len = Access_filesize(filename);
if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
fprintf(stderr,"Error: can't open file %s with fopen\n",filename);
exit(9);
@@ -272,7 +289,7 @@ first_nonzero_uint8 (size_t *i, char *filename) {
}
}
#endif
-
+#endif
/************************************************************************
@@ -284,10 +301,7 @@ static Intlist_T shmem_ids = NULL;
static Intlist_T semaphore_ids = NULL;
-#define SEMAPHORE_NA 0 /* For commands, like removal, where semnum
- argument is ignored */
-#define SEMAPHORE_CREATION 0 /* -1 to lock, +1 to unlock */
-
+#if 0
/* See if item is already in shared memory */
static bool
shmem_exists_p (int *shmid, key_t key) {
@@ -297,6 +311,7 @@ shmem_exists_p (int *shmid, key_t key) {
return true;
}
}
+#endif
static short
@@ -315,6 +330,7 @@ shmem_nattached (int shmid) {
}
+#if 0
void
Access_shmem_remove (char *filename) {
key_t key;
@@ -334,89 +350,13 @@ Access_shmem_remove (char *filename) {
/* Nothing to do */
} else {
fprintf(stderr,"Removing semaphore set %d\n",semid);
- semctl(semid,SEMAPHORE_NA,IPC_RMID,NULL);
+ semctl(semid,SEMNO_NA,IPC_RMID,NULL);
}
return;
}
-
-static void
-semaphore_init (int semid, int sem_i, int value) {
- union semun {
- int val;
- struct semid_ds *buf;
- ushort *array;
- } argument;
-
- argument.val = value;
- semctl(semid,sem_i,SETVAL,argument);
- return;
-}
-
-#if 0
-static int
-semaphore_value (int semid, int sem_i) {
- return semctl(semid,sem_i,GETVAL,NULL);
-}
-#endif
-
-#if 0
-static int
-semaphore_nwaiting (int semid, int sem_i) {
- printf("nwaiting = %d\n",semctl(semid,sem_i,GETNCNT,NULL));
- return semctl(semid,sem_i,GETNCNT,NULL);
-}
-#endif
-
-#if 0
-/* If already locked, then puts process to sleep */
-static void
-semaphore_lock (int semid) {
- struct sembuf op;
-
- /* printf("Process %d locking semaphore %d\n",getpid(),semid); */
- op.sem_num = SEMAPHORE_CREATION;
- op.sem_op = -1;
- op.sem_flg = SEM_UNDO;
- semop(semid,&op,1);
-
- return;
-}
#endif
-#if 0
-static int
-semaphore_unlock (int semid) {
- struct sembuf op;
-
- /* printf("Process %d unlocking semaphore %d\n",getpid(),semid); */
- op.sem_num = SEMAPHORE_CREATION;
- op.sem_op = +1;
- op.sem_flg = SEM_UNDO;
- semop(semid,&op,1);
-
- /* printf("%d processes still waiting\n",semctl(semid,SEMAPHORE_CREATION,GETNCNT,NULL)); */
-
- return semctl(semid,SEMAPHORE_CREATION,GETNCNT,NULL);
-}
-#endif
-
-
-/* Same as semaphore_lock */
-static void
-semaphore_wait (int semid) {
- struct sembuf op;
-
- /* printf("Process %d locking semaphore %d\n",getpid(),semid); */
- op.sem_num = SEMAPHORE_CREATION;
- op.sem_op = -1;
- op.sem_flg = SEM_UNDO;
- semop(semid,&op,1);
-
- return;
-}
-
-
void
Access_controlled_cleanup () {
List_free(&shmem_memory);
@@ -429,17 +369,17 @@ Access_controlled_cleanup () {
void
Access_emergency_cleanup () {
List_T p;
- Intlist_T q;
+ Intlist_T r, q;
void *memory;
int shmid, semid;
int nattached;
struct shmid_ds *buf = NULL;
fprintf(stderr,"Calling Access_emergency_cleanup\n");
- for (p = shmem_memory, q = shmem_ids; p != NULL; p = List_next(p), q = Intlist_next(q)) {
- memory = List_head(p);
- shmid = Intlist_head(q);
+ /* First, detach all memory */
+ for (p = shmem_memory; p != NULL; p = List_next(p)) {
+ memory = List_head(p);
if (shmdt(memory) == -1) {
#if 0
/* Somehow, shmdt forks and prints the error message and continues with the rest of the code */
@@ -447,63 +387,83 @@ Access_emergency_cleanup () {
memory,shmid,errno,strerror(errno));
#endif
}
+ }
- if ((nattached = shmem_nattached(shmid)) > 0) {
- fprintf(stderr,"For shmid %d, %d other processes still attached\n",shmid,(int) nattached);
+ if (unload_shared_memory_p == true) {
+ /* Don't try to fix */
- } else if (shmctl(shmid,IPC_RMID,buf) == -1) {
-#if 0
- fprintf(stderr,"Error in Access_emergency_cleanup with shmctl. Error %d: %s\n",
- errno,strerror(errno));
-#endif
- } else {
- fprintf(stderr,"Removed existing memory for shmid %d\n",shmid);
+ } else if (preload_shared_memory_p == true) {
+ /* Don't try to fix */
+
+ } else {
+ /* Delete memory and semaphores */
+ for (r = semaphore_ids, q = shmem_ids; r != NULL; r = Intlist_next(r), q = Intlist_next(q)) {
+ semid = Intlist_head(r);
+ shmid = Intlist_head(q);
+
+ if (Semaphore_get_value(semid,SEMNO_KEEP) == SEMAPHORE_RESIDENT) {
+ /* Keep memory resident */
+ } else if ((nattached = shmem_nattached(shmid)) > 0) {
+ /* Keep memory resident */
+ } else if (shmctl(shmid,IPC_RMID,buf) == -1) {
+ /* Error in deleting memory, possibly with multiple threads trying to delete */
+ /* fprintf(stderr,"Error in Access_emergency_cleanup with shmctl. Error %d: %s\n",
+ errno,strerror(errno)); */
+ /* Semaphore_delete(semid); */
+ } else {
+ fprintf(stderr,"Removed existing memory for shmid %d\n",shmid);
+ Semaphore_delete(semid);
+ }
}
}
- for (q = semaphore_ids; q != NULL; q = Intlist_next(q)) {
- /* Many of these removals will be for semaphores that don't exist */
- semid = Intlist_head(q);
- semctl(semid,/*semnum*/0,IPC_RMID,NULL);
- }
- Intlist_free(&semaphore_ids);
-
if (shmem_memory != NULL) {
fprintf(stderr,"\n");
fprintf(stderr,"You may want to run 'ipcs -m' to see if any shared memory segments are still in use\n");
fprintf(stderr,"You can remove a shared memory segment manually by doing 'ipcrm -m <shmid>'\n");
fprintf(stderr,"\n");
- List_free(&shmem_memory);
- Intlist_free(&shmem_ids);
}
+ List_free(&shmem_memory);
+ Intlist_free(&shmem_ids);
+ Intlist_free(&semaphore_ids);
+
return;
}
void
-Access_deallocate (void *memory, int shmid) {
+Access_deallocate (void *memory, int shmid, key_t key) {
struct shmid_ds *buf = NULL;
short nattached;
+ int semid;
+ /* First, detach memory */
if (shmdt(memory) == -1) {
#if 0
- /* Somehow, shmdt forks and prints the error message and continues with the rest of the code */
- fprintf(stderr,"Error in Access_emergency_cleanup with shmdt on memory %p, shmid %d. Error %d: %s\n",
- memory,shmid,errno,strerror(errno));
+ /* Somehow, shmdt forks and prints the error message and continues with the rest of the code */
+ fprintf(stderr,"Error in Access_emergency_cleanup with shmdt on memory %p, shmid %d. Error %d: %s\n",
+ memory,shmid,errno,strerror(errno));
#endif
}
- if ((nattached = shmem_nattached(shmid)) > 0) {
- fprintf(stderr,"For shmid %d, %d processes still attached\n",shmid,(int) nattached);
+ /* Then, delete memory and semaphores, if applicable */
+ if ((semid = Semaphore_find(key)) != -1 && Semaphore_get_value(semid,SEMNO_KEEP) == SEMAPHORE_RESIDENT) {
+ fprintf(stderr,"Keeping memory for shmid %d resident, because it was pre-loaded. To remove, run gsnap on this genome index with --unload-shared-memory\n",
+ shmid);
+
+ } else if ((nattached = shmem_nattached(shmid)) > 0) {
+ fprintf(stderr,"Keeping memory for shmid %d resident, because it is being used by %d processes\n",
+ shmid,nattached);
+
} else if (shmctl(shmid,IPC_RMID,buf) == -1) {
-#if 0
/* Somehow, shmctl forks and prints the error message and continues with the rest of the code */
- fprintf(stderr,"Error in Access_deallocate with shmctl. Error %d: %s\n",
- errno,strerror(errno));
-#endif
+ /* fprintf(stderr,"Error in Access_deallocate with shmctl. Error %d: %s\n",errno,strerror(errno)); */
+ /* Semaphore_delete(semid); */
+
} else {
fprintf(stderr,"Removed existing memory for shmid %d\n",shmid);
+ Semaphore_delete(semid);
}
return;
@@ -567,32 +527,95 @@ copy_memory_from_file (void *memory, char *filename, size_t filesize, size_t elt
}
+static void
+copy_limited_from_file (void *memory, char *filename, size_t filesize, size_t eltsize) {
+ FILE *fp;
+ void *p;
+
+ if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
+ fprintf(stderr,"Error: can't open file %s with fopen\n",filename);
+ exit(9);
+ }
+
+ if (eltsize == 1) {
+ p = (void *) &(((unsigned char *) memory)[0]);
+ if (FREAD_BATCH < filesize/eltsize) {
+ fread(p,sizeof(unsigned char),FREAD_BATCH,fp);
+ } else {
+ fread(p,sizeof(unsigned char),filesize/eltsize,fp);
+ }
+
+ } else if (eltsize == 4) {
+ p = (void *) &(((UINT4 *) memory)[0]);
+ if (FREAD_BATCH < filesize/eltsize) {
+ fread(p,sizeof(UINT4),FREAD_BATCH,fp);
+ } else {
+ fread(p,sizeof(UINT4),filesize/eltsize,fp);
+ }
+
+ } else if (eltsize == 8) {
+ p = (void *) &(((UINT8 *) memory)[0]);
+ if (FREAD_BATCH < filesize/eltsize) {
+ fread(p,sizeof(UINT8),FREAD_BATCH,fp);
+ } else {
+ fread(p,sizeof(UINT8),filesize/eltsize,fp);
+ }
+
+ } else {
+ fprintf(stderr,"Access_allocated called with an element size of %d, which is not handled\n",(int) eltsize);
+ exit(9);
+ }
+ fclose(fp);
+
+ return;
+}
+
static void *
-shmem_attach (int *shmid, char *filename, off_t filesize, size_t eltsize) {
+shmem_attach (int *shmid, key_t *key, char *filename, size_t filesize, size_t eltsize) {
void *memory = NULL;
- key_t key;
- int semid;
+ int semid = -1;
+ ushort values[NSEMAPHORES];
- key = ftok(filename,PROJECT_ID);
- if ((semid = semget(key,/*nsems*/1,IPC_CREAT | IPC_EXCL | 0666)) != -1) {
- /* Usually, we would set the value to be 1. However, we can set
- the value to 0, because this process won't perform semaphore_wait */
- semaphore_init(semid,SEMAPHORE_CREATION,/*value*/0);
-
- /* Store semid in case we abort in the middle of this procedure */
- semaphore_ids = Intlist_push(semaphore_ids,semid);
- } else if ((semid = semget(key,0,0)) == -1) {
- fprintf(stderr,"Error in getting semaphore\n");
- abort();
+ values[SEMNO_LOCK] = -1;
+ /* For some reason, these values are not being set, so using Semaphore_set_value below */
+ if (preload_shared_memory_p == true) {
+ values[SEMNO_KEEP] = SEMAPHORE_RESIDENT;
} else {
- semaphore_wait(semid);
+ values[SEMNO_KEEP] = SEMAPHORE_FREEABLE;
}
- /* The process tha created the semaphore will proceed, while the
+ *key = ftok(filename,PROJECT_ID);
+ while (semid == -1) {
+ if ((semid = Semaphore_create(*key,/*nsems*/NSEMAPHORES,values)) != -1) {
+ /* Created a new semaphore */
+ if (preload_shared_memory_p == true) {
+ Semaphore_set_value(semid,SEMNO_KEEP,SEMAPHORE_RESIDENT);
+ }
+
+ } else if ((semid = Semaphore_find(*key)) != -1) {
+ /* Got existing semaphore */
+ if (unload_shared_memory_p == true) {
+ Semaphore_set_value(semid,SEMNO_KEEP,SEMAPHORE_FREEABLE);
+ }
+
+#if 0
+ if (Semaphore_get_value(semid,SEMNO_KEEP) == SEMNO_RESIDENT) {
+ /* Semaphore exists only to keep memory resident */
+ fprintf(stderr,"Using shared memory already resident in system\n");
+
+ } else {
+ /* Semaphore being created */
+ semaphore_wait_for_creation(semid);
+ }
+#endif
+ }
+ }
+
+ /* The process that created the semaphore will proceed, while the
others wait. They will be woken up when the semaphore is
removed. */
- if ((*shmid = shmget(key,filesize,IPC_CREAT | IPC_EXCL |
+ if ((*shmid = shmget(*key,filesize,IPC_CREAT | IPC_EXCL |
#ifdef HAVE_SHM_NORESERVE
SHM_NORESERVE |
#endif
@@ -600,18 +623,25 @@ shmem_attach (int *shmid, char *filename, off_t filesize, size_t eltsize) {
/* Created new shared memory */
if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
fprintf(stderr,"Error with shmat. Error %d: %s\n",errno,strerror(errno));
+ } else if (unload_shared_memory_p == true) {
+ semaphore_ids = Intlist_push(semaphore_ids,semid);
+ shmem_memory = List_push(shmem_memory,memory);
+ shmem_ids = Intlist_push(shmem_ids,*shmid);
+ copy_limited_from_file(memory,filename,filesize,eltsize);
} else {
+ semaphore_ids = Intlist_push(semaphore_ids,semid);
shmem_memory = List_push(shmem_memory,memory);
shmem_ids = Intlist_push(shmem_ids,*shmid);
copy_memory_from_file(memory,filename,filesize,eltsize);
fprintf(stderr,"Attached new memory for %s...",filename);
}
- } else if ((*shmid = shmget(key,0,0)) != -1) {
+ } else if ((*shmid = shmget(*key,0,0)) != -1) {
/* Found existing shared memory */
if ((memory = shmat(*shmid,NULL,0)) == (void *) -1) {
fprintf(stderr,"Error with shmat. Error %d: %s\n",errno,strerror(errno));
} else {
+ semaphore_ids = Intlist_push(semaphore_ids,semid);
shmem_memory = List_push(shmem_memory,memory);
shmem_ids = Intlist_push(shmem_ids,*shmid);
fprintf(stderr,"Attached existing memory for %s...",filename);
@@ -622,11 +652,31 @@ shmem_attach (int *shmid, char *filename, off_t filesize, size_t eltsize) {
memory = (void *) NULL;
}
+#if 0
/* The process that proceeded removes the semaphore here, allowing
the other processes to continue after their waits. The other
processes will try to remove the semaphore too, yielding an
error, which we simply ignore. */
- semctl(semid,SEMAPHORE_NA,IPC_RMID,NULL);
+ if (unload_shared_memory_p == true) {
+ /* Deleting semaphore will allow Access_deallocate to remove the shared memory */
+ Semaphore_delete(semid);
+
+ } else if (Semaphore_get_value(semid,SEMNO_KEEP) == SEMAPHORE_RESIDENT) {
+ /* Exists to keep memory resident */
+ fprintf(stderr,"Semaphore %d intended to keep memory resident\n",semid);
+
+ } else if (preload_shared_memory_p == false) {
+ Semaphore_delete(semid);
+
+ } else {
+ /* Keep semaphore in system, but indicate we are done with creation */
+ /* fprintf(stderr,"Forcing memory for %d to stay resident in system\n",*shmid); */
+#if 0
+ semaphore_set_value(semid,SEMAPHORE_KEEP_RESIDENT,/*value*/0);
+#endif
+ }
+#endif
+
return memory;
}
@@ -634,7 +684,72 @@ shmem_attach (int *shmid, char *filename, off_t filesize, size_t eltsize) {
/* Bigendian conversion not needed after this */
void *
-Access_allocate (int *shmid, size_t *len, double *seconds, char *filename, size_t eltsize, bool sharedp) {
+Access_allocate_private (Access_T *access, size_t *len, double *seconds, char *filename, size_t eltsize) {
+ void *memory;
+#ifdef CHECK
+ void *memory2;
+#endif
+#if 0 && defined (USE_MPI)
+ /* Does not work. Gets ftruncate error */
+ MPI_Comm comm;
+ MPI_Win win;
+#endif
+ Stopwatch_T stopwatch;
+
+ *len = Access_filesize(filename);
+ if (*len == 0) {
+ *seconds = 0.0;
+ return (void *) NULL;
+ }
+
+ Stopwatch_start(stopwatch = Stopwatch_new());
+
+#ifdef CHECK
+ memory2 = (void *) MALLOC(*len);
+ if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
+ fprintf(stderr,"Error: can't open file %s with fopen\n",filename);
+ exit(9);
+ }
+
+ if (eltsize == 1) {
+ FREAD_CHARS(memory2,(*len)/eltsize,fp);
+ } else if (eltsize == 4) {
+ FREAD_UINTS(memory2,(*len)/eltsize,fp);
+ } else if (eltsize == 8) {
+ FREAD_UINT8S(memory2,(*len)/eltsize,fp);
+ } else {
+ fprintf(stderr,"Access_allocated called with an element size of %d, which is not handled\n",(int) eltsize);
+ exit(9);
+ }
+ fclose(fp);
+#endif
+
+ memory = (void *) MALLOC(*len);
+ copy_memory_from_file(memory,filename,/*filesize*/*len,eltsize);
+ *access = ALLOCATED_PRIVATE;
+
+ /* Note: the following (old non-batch mode) requires conversion to bigendian later, as needed */
+ /* fread(new->offsets,eltsize,sb.st_size/eltsize,fp); */
+
+#ifdef CHECK
+ for (i = 0; i < *len; i++) {
+ if (((unsigned char *) memory)[i] != ((unsigned char *) memory2)[i]) {
+ abort();
+ }
+ }
+ FREE(memory2);
+#endif
+
+ *seconds = Stopwatch_stop(stopwatch);
+ Stopwatch_free(&stopwatch);
+
+ return memory;
+}
+
+
+/* Bigendian conversion not needed after this */
+void *
+Access_allocate_shared (Access_T *access, int *shmid, key_t *key, int *fd, size_t *len, double *seconds, char *filename, size_t eltsize) {
void *memory;
#ifdef CHECK
void *memory2;
@@ -674,26 +789,34 @@ Access_allocate (int *shmid, size_t *len, double *seconds, char *filename, size_
fclose(fp);
#endif
- if (sharedp == true) {
#if 0 && defined(USE_MPI)
- /* Does not work. Gives ftruncate error */
- MPI_Comm_split_type(MPI_COMM_WORLD,MPI_COMM_TYPE_SHARED,0,MPI_INFO_NULL,&comm);
- MPI_Win_allocate_shared(*len,/*disp_unit*/1,MPI_INFO_NULL,comm,&memory,&win);
- MPI_Win_free(&win);
+ /* Does not work. Gives ftruncate error */
+ MPI_Comm_split_type(MPI_COMM_WORLD,MPI_COMM_TYPE_SHARED,0,MPI_INFO_NULL,&comm);
+ MPI_Win_allocate_shared(*len,/*disp_unit*/1,MPI_INFO_NULL,comm,&memory,&win);
+ MPI_Win_free(&win);
+#elif defined(HAVE_MMAP)
+ if ((memory = shmem_attach(&(*shmid),&(*key),filename,/*filesize*/*len,eltsize)) != NULL) {
+ *access = ALLOCATED_SHARED;
+ } else {
+ fprintf(stderr,"shm_attach not working on file %s, so using memory mapping instead on %lu bytes\n",
+ filename,*len);
+ *shmid = 0;
+ memory = Access_mmap(&(*fd),&(*len),filename,/*randomp*/true);
+ copy_memory_from_file(memory,filename,/*filesize*/*len,eltsize);
+ *access = MMAPPED;
+ }
#else
- if ((memory = shmem_attach(&(*shmid),filename,/*filesize*/*len,eltsize)) == NULL) {
- fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n",
- filename,*len);
- *shmid = 0;
- memory = (void *) MALLOC(*len);
- copy_memory_from_file(memory,filename,/*filesize*/*len,eltsize);
- }
-#endif
+ if ((memory = shmem_attach(&(*shmid),&(*key),filename,/*filesize*/*len,eltsize)) != NULL) {
+ *access = ALLOCATED_SHARED;
} else {
+ fprintf(stderr,"shm_attach not working on file %s, so using malloc instead on %lu bytes\n",
+ filename,*len);
*shmid = 0;
memory = (void *) MALLOC(*len);
copy_memory_from_file(memory,filename,/*filesize*/*len,eltsize);
+ *access = ALLOCATED_PRIVATE;
}
+#endif
/* Note: the following (old non-batch mode) requires conversion to bigendian later, as needed */
/* fread(new->offsets,eltsize,sb.st_size/eltsize,fp); */
@@ -751,8 +874,8 @@ caddr_t
#else
void *
#endif
-Access_mmap (int *fd, size_t *len, char *filename, size_t eltsize, bool randomp) {
- off_t length;
+Access_mmap (int *fd, size_t *len, char *filename, bool randomp) {
+ size_t length;
#ifdef HAVE_CADDR_T
caddr_t memory;
#else
@@ -774,7 +897,7 @@ Access_mmap (int *fd, size_t *len, char *filename, size_t eltsize, bool randomp)
memory = (void *) NULL;
} else {
- *len = (size_t) length;
+ *len = length;
memory = mmap(NULL,length,PROT_READ,0
#ifdef HAVE_MMAP_MAP_SHARED
|MAP_SHARED
@@ -825,7 +948,7 @@ caddr_t
#else
void *
#endif
-Access_mmap_offset (int *remainder, int fd, off_t offset, size_t length, size_t eltsize, bool randomp) {
+Access_mmap_offset (int *remainder, int fd, size_t offset, size_t length, bool randomp) {
#ifdef HAVE_CADDR_T
caddr_t memory;
#else
@@ -837,7 +960,7 @@ Access_mmap_offset (int *remainder, int fd, off_t offset, size_t length, size_t
}
*remainder = offset % get_pagesize();
- offset -= (off_t) *remainder;
+ offset -= (size_t) *remainder;
length += (size_t) *remainder;
if (sizeof(size_t) <= 4 && length > MAX32BIT) {
@@ -894,8 +1017,8 @@ caddr_t
#else
void *
#endif
-Access_mmap_rw (int *fd, size_t *len, char *filename, size_t eltsize, bool randomp) {
- off_t length;
+Access_mmap_rw (int *fd, size_t *len, char *filename, bool randomp) {
+ size_t length;
#ifdef HAVE_CADDR_T
caddr_t memory;
#else
@@ -914,7 +1037,7 @@ Access_mmap_rw (int *fd, size_t *len, char *filename, size_t eltsize, bool rando
*len = 0;
memory = (void *) NULL;
} else {
- *len = (size_t) length;
+ *len = length;
memory = mmap(NULL,length,PROT_READ|PROT_WRITE,0
#ifdef HAVE_MMAP_MAP_SHARED
|MAP_SHARED
@@ -963,7 +1086,7 @@ caddr_t
#else
void *
#endif
-Access_mmap_offset_rw (int *remainder, int fd, off_t offset, size_t length, size_t eltsize, bool randomp) {
+Access_mmap_offset_rw (int *remainder, int fd, size_t offset, size_t length, bool randomp) {
#ifdef HAVE_CADDR_T
caddr_t memory;
#else
@@ -975,7 +1098,7 @@ Access_mmap_offset_rw (int *remainder, int fd, off_t offset, size_t length, size
}
*remainder = offset % get_pagesize();
- offset -= (off_t) *remainder;
+ offset -= (size_t) *remainder;
length += (size_t) *remainder;
if (sizeof(size_t) <= 4 && length > MAX32BIT) {
@@ -1034,7 +1157,7 @@ caddr_t
void *
#endif
Access_mmap_and_preload (int *fd, size_t *len, int *npages, double *seconds, char *filename, size_t eltsize) {
- off_t length;
+ size_t length;
#ifdef HAVE_CADDR_T
caddr_t memory;
#else
@@ -1099,18 +1222,23 @@ Access_mmap_and_preload (int *fd, size_t *len, int *npages, double *seconds, cha
#endif
#endif
totalindices = (*len)/eltsize;
+ fprintf(stderr,"...");
for (i = 0; i < totalindices; i += indicesperpage) {
if (((char *) memory)[i] == 0) {
nzero++;
+#if 0
if (i % 10000 == 0) {
fprintf(stderr,",");
}
+#endif
} else {
npos++;
}
+#if 0
if (i % 10000 == 0) {
fprintf(stderr,".");
}
+#endif
}
*npages = nzero + npos;
*seconds = Stopwatch_stop(stopwatch);
diff --git a/src/access.h b/src/access.h
index f9cfefe..2378b6c 100644
--- a/src/access.h
+++ b/src/access.h
@@ -1,4 +1,4 @@
-/* $Id: access.h 161940 2015-03-25 20:36:59Z twu $ */
+/* $Id: access.h 184156 2016-02-12 18:30:44Z twu $ */
#ifndef ACCESS_INCLUDED
#define ACCESS_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -18,13 +18,16 @@
/* ALLOCATED implies bigendian conversion already done */
typedef enum {USE_ALLOCATE, USE_MMAP_ONLY, USE_MMAP_PRELOAD, USE_FILEIO} Access_mode_T;
-typedef enum {ALLOCATED_PRIVATE, ALLOCATED_SHARED, MMAPPED, FILEIO} Access_T;
+typedef enum {ALLOCATED_PRIVATE, ALLOCATED_SHARED, MMAPPED, LOADED, FILEIO} Access_T;
#define MAX32BIT 4294967295U /* 2^32 - 1 */
+extern void
+Access_setup (bool preload_shared_memory_p_in, bool unload_shared_memory_p_in);
+
extern bool
Access_file_exists_p (char *filename);
-extern off_t
+extern size_t
Access_filesize (char *filename);
extern size_t
@@ -49,38 +52,40 @@ extern void
Access_shmem_remove (char *filename);
extern void
-Access_deallocate (void *memory, int shmid);
+Access_deallocate (void *memory, int shmid, key_t key);
extern void *
-Access_allocate (int *shmid, size_t *len, double *seconds, char *filename, size_t eltsize, bool sharedp);
+Access_allocate_private (Access_T *access, size_t *len, double *seconds, char *filename, size_t eltsize);
+extern void *
+Access_allocate_shared (Access_T *access, int *shmid, key_t *key, int *fd, size_t *len, double *seconds, char *filename, size_t eltsize);
#ifdef HAVE_CADDR_T
extern caddr_t
#else
extern void *
#endif
-Access_mmap (int *fd, size_t *len, char *filename, size_t eltsize, bool randomp);
+Access_mmap (int *fd, size_t *len, char *filename, bool randomp);
#ifdef HAVE_CADDR_T
extern caddr_t
#else
extern void *
#endif
-Access_mmap_offset (int *remainder, int fd, off_t offset, size_t length, size_t eltsize, bool randomp);
+Access_mmap_offset (int *remainder, int fd, size_t offset, size_t length, bool randomp);
#ifdef HAVE_CADDR_T
extern caddr_t
#else
extern void *
#endif
-Access_mmap_rw (int *fd, size_t *len, char *filename, size_t eltsize, bool randomp);
+Access_mmap_rw (int *fd, size_t *len, char *filename, bool randomp);
#ifdef HAVE_CADDR_T
extern caddr_t
#else
extern void *
#endif
-Access_mmap_offset_rw (int *remainder, int fd, off_t offset, size_t length, size_t eltsize, bool randomp);
+Access_mmap_offset_rw (int *remainder, int fd, size_t offset, size_t length, bool randomp);
#ifdef HAVE_CADDR_T
extern caddr_t
diff --git a/src/atoi.c b/src/atoi.c
index 9aefbd9..c5fce58 100644
--- a/src/atoi.c
+++ b/src/atoi.c
@@ -1,13 +1,12 @@
-static char rcsid[] = "$Id: atoi.c 99737 2013-06-27 19:33:03Z twu $";
+static char rcsid[] = "$Id: atoi.c 181327 2015-12-19 13:07:25Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "atoi.h"
-#include "types.h"
-static const Storedoligomer_T convert_ag[] =
+static const UINT4 convert_ag[] =
{0xAAAA,0xAAA9,0xAAAA,0xAAAB,0xAAA6,0xAAA5,0xAAA6,0xAAA7,
0xAAAA,0xAAA9,0xAAAA,0xAAAB,0xAAAE,0xAAAD,0xAAAE,0xAAAF,
0xAA9A,0xAA99,0xAA9A,0xAA9B,0xAA96,0xAA95,0xAA96,0xAA97,
@@ -8202,7 +8201,7 @@ static const Storedoligomer_T convert_ag[] =
0xFFFA,0xFFF9,0xFFFA,0xFFFB,0xFFFE,0xFFFD,0xFFFE,0xFFFF,
};
-static const Storedoligomer_T convert_tc[] =
+static const UINT4 convert_tc[] =
{0x0000,0x0001,0x0002,0x0001,0x0004,0x0005,0x0006,0x0005,
0x0008,0x0009,0x000A,0x0009,0x0004,0x0005,0x0006,0x0005,
0x0010,0x0011,0x0012,0x0011,0x0014,0x0015,0x0016,0x0015,
@@ -16398,21 +16397,41 @@ static const Storedoligomer_T convert_tc[] =
};
-Storedoligomer_T
-Atoi_reduce_tc (Storedoligomer_T oligo) {
- Storedoligomer_T reduced;
+Oligospace_T
+Atoi_reduce_tc (Oligospace_T oligo) {
+ Oligospace_T reduced;
+#ifdef HAVE_64_BIT
+ /* Handles 48 bits, or k-mer up to 24 */
+ reduced = (Oligospace_T) convert_tc[oligo >> 32];
+ reduced <<= 32; /* Put in separate line to make it clear we want 64 bits */
+ reduced |= (Oligospace_T) (convert_tc[oligo >> 16 & 0xFFFF] << 16);
+ reduced |= (Oligospace_T) convert_tc[oligo & 0xFFFF];
+
+#else
+ /* Handles 32 bits, or k-mer up to 16 */
reduced = convert_tc[oligo >> 16] << 16;
- reduced |= convert_tc[oligo & 0x0000FFFF];
+ reduced |= convert_tc[oligo & 0xFFFF];
+#endif
+
return reduced;
}
-Storedoligomer_T
-Atoi_reduce_ag (Storedoligomer_T oligo) {
- Storedoligomer_T reduced;
+Oligospace_T
+Atoi_reduce_ag (Oligospace_T oligo) {
+ Oligospace_T reduced;
+#ifdef HAVE_64_BIT
+ /* Handles 48 bits, or k-mer up to 24 */
+ reduced = (Oligospace_T) convert_ag[oligo >> 32];
+ reduced <<= 32; /* Put in separate line to make it clear we want 64 bits */
+ reduced |= (Oligospace_T) (convert_ag[oligo >> 16 & 0xFFFF] << 16);
+ reduced |= (Oligospace_T) convert_ag[oligo & 0xFFFF];
+#else
+ /* Handles 32 bits, or k-mer up to 16 */
reduced = convert_ag[oligo >> 16] << 16;
- reduced |= convert_ag[oligo & 0x0000FFFF];
+ reduced |= convert_ag[oligo & 0xFFFF];
+#endif
return reduced;
}
diff --git a/src/atoi.h b/src/atoi.h
index b19fbc7..8e9cba5 100644
--- a/src/atoi.h
+++ b/src/atoi.h
@@ -1,13 +1,13 @@
-/* $Id: atoi.h 157222 2015-01-22 18:40:00Z twu $ */
+/* $Id: atoi.h 180699 2015-12-10 19:10:10Z twu $ */
#ifndef ATOI_INCLUDED
#define ATOI_INCLUDED
-#include "indexdb.h" /* For Storedoligomer_T */
+#include "types.h"
-extern Storedoligomer_T
-Atoi_reduce_ag (Storedoligomer_T oligo);
-extern Storedoligomer_T
-Atoi_reduce_tc (Storedoligomer_T oligo);
+extern Oligospace_T
+Atoi_reduce_ag (Oligospace_T oligo);
+extern Oligospace_T
+Atoi_reduce_tc (Oligospace_T oligo);
#endif
diff --git a/src/atoiindex.c b/src/atoiindex.c
index 13344fa..17e62cf 100644
--- a/src/atoiindex.c
+++ b/src/atoiindex.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: atoiindex.c 167263 2015-06-10 23:59:15Z twu $";
+static char rcsid[] = "$Id: atoiindex.c 184156 2016-02-12 18:30:44Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -48,7 +48,7 @@ static char rcsid[] = "$Id: atoiindex.c 167263 2015-06-10 23:59:15Z twu $";
#include "mem.h"
#include "fopen.h"
#include "access.h"
-#include "types.h" /* For Positionsptr_T, Oligospace_T, and Storedoligomer_T */
+#include "types.h" /* For Positionsptr_T and Oligospace_T */
#include "mode.h"
#include "atoi.h"
@@ -63,6 +63,10 @@ static char rcsid[] = "$Id: atoiindex.c 167263 2015-06-10 23:59:15Z twu $";
#include "bytecoding.h"
#include "sarray-write.h"
#include "bitpack64-write.h"
+#include "bitpack64-read.h"
+#include "bitpack64-readtwo.h"
+#include "bitpack64-access.h"
+#include "bitpack64-incr.h"
#include "datadir.h"
#include "getopt.h"
@@ -70,13 +74,20 @@ static char rcsid[] = "$Id: atoiindex.c 167263 2015-06-10 23:59:15Z twu $";
#define POSITIONS8_HIGH_SHIFT 32
#define POSITIONS8_LOW_MASK 0xFFFFFFFF
+#define DIFFERENTIAL_METAINFO_SIZE 2
+#define BLOCKSIZE 64
+#define BUFFER_SIZE 1000000
+
+#define MONITOR_INTERVAL 10000000
+
+
#ifdef DEBUG
#define debug(x) x
#else
#define debug(x)
#endif
-#define MONITOR_INTERVAL 10000000
+
static char *user_sourcedir = NULL;
static char *user_destdir = NULL;
@@ -137,25 +148,14 @@ power (int base, int exponent) {
}
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
-/* 87654321 */
-#define LEFT_A 0x00000000
-#define LEFT_C 0x40000000
-#define LEFT_G 0x80000000
-#define LEFT_T 0xC0000000
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
-static Storedoligomer_T
-reduce_oligo_old (Storedoligomer_T oligo, int oligosize) {
- Storedoligomer_T reduced = 0U, lowbits;
+#if 0
+static Oligospace_T
+reduce_oligo_old (Oligospace_T oligo, int oligosize) {
+ Oligospace_T reduced = 0U, lowbits;
int i;
for (i = 0; i < oligosize; i++) {
@@ -176,13 +176,15 @@ reduce_oligo_old (Storedoligomer_T oligo, int oligosize) {
return reduced;
}
+#endif
+#if 0
static char *
-shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
+shortoligo_nt (Oligospace_T oligo, int oligosize) {
char *nt;
int i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -200,10 +202,13 @@ shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
return nt;
}
+#endif
+#if 0
+/* Old method */
static Positionsptr_T *
-compute_offsets_ag (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedoligomer_T mask) {
+compute_offsets_ag_using_array (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Oligospace_T mask) {
Positionsptr_T *offsets;
Oligospace_T oligoi, reduced;
#ifdef DEBUG
@@ -247,10 +252,14 @@ compute_offsets_ag (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedo
return offsets;
}
+#endif
+
+#if 0
+/* Old method */
static Positionsptr_T *
-compute_offsets_tc (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedoligomer_T mask) {
+compute_offsets_tc (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Oligospace_T mask) {
Positionsptr_T *offsets;
Oligospace_T oligoi, reduced;
#ifdef DEBUG
@@ -273,7 +282,7 @@ compute_offsets_tc (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedo
/*size*/offsets[reduced+1] += (oldoffsets[oligoi+1] - oldoffsets[oligoi]);
#endif
debug(
- printf(" to %d\n",offsets[reduced+1]);
+ printf(" to %u\n",offsets[reduced+1]);
FREE(nt2);
FREE(nt1);
);
@@ -289,6 +298,106 @@ compute_offsets_tc (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedo
return offsets;
}
+#endif
+
+
+static void
+compute_offsets_ag_using_bitpack (char *new_pointers_filename, char *new_offsets_filename,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm,
+ Oligospace_T oligospace, Oligospace_T mask) {
+ Oligospace_T bmerspace;
+ char *packsizes;
+ UINT4 **bitpacks;
+ UINT4 increment;
+ int new_packsize;
+ UINT4 offsets[BLOCKSIZE+1];
+ Oligospace_T oligoi, reduced, bmer;
+ int ii;
+#ifdef DEBUG
+ char *nt1, *nt2;
+#endif
+
+ /* Fill with sizes */
+ bmerspace = oligospace/BLOCKSIZE;
+ packsizes = (char *) CALLOC(bmerspace,sizeof(char));
+ bitpacks = (UINT4 **) CALLOC(bmerspace,sizeof(UINT4 *));
+
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(offsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((increment = offsets[ii+1] - offsets[ii]) > 0) {
+ reduced = Atoi_reduce_ag(oligoi + ii) & mask;
+ bmer = reduced/BLOCKSIZE;
+ if ((new_packsize = Bitpack64_access_new_packsize(reduced,/*old_packsize*/(int) packsizes[bmer],
+ bitpacks[bmer],increment)) != (int) packsizes[bmer]) {
+ bitpacks[bmer] = Bitpack64_realloc_multiple((int) packsizes[bmer],new_packsize,bitpacks[bmer]);
+ packsizes[bmer] = (char) new_packsize;
+ }
+ Bitpack64_add_bitpack(reduced,(int) packsizes[bmer],bitpacks[bmer],increment);
+ }
+ }
+ }
+
+ Bitpack64_write_differential_bitpacks(new_pointers_filename,new_offsets_filename,packsizes,bitpacks,oligospace);
+
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
+ }
+ FREE(bitpacks);
+ FREE(packsizes);
+
+ return;
+}
+
+
+static void
+compute_offsets_tc_using_bitpack (char *new_pointers_filename, char *new_offsets_filename,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm,
+ Oligospace_T oligospace, Oligospace_T mask) {
+ Oligospace_T bmerspace;
+ char *packsizes;
+ UINT4 **bitpacks;
+ UINT4 increment;
+ int new_packsize;
+ UINT4 offsets[BLOCKSIZE+1];
+ Oligospace_T oligoi, reduced, bmer;
+ int ii;
+#ifdef DEBUG
+ char *nt1, *nt2;
+#endif
+
+ /* Fill with sizes */
+ bmerspace = oligospace/BLOCKSIZE;
+ packsizes = (char *) CALLOC(bmerspace,sizeof(char));
+ bitpacks = (UINT4 **) CALLOC(bmerspace,sizeof(UINT4 *));
+
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(offsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((increment = offsets[ii+1] - offsets[ii]) > 0) {
+ reduced = Atoi_reduce_tc(oligoi + ii) & mask;
+ bmer = reduced/BLOCKSIZE;
+ if ((new_packsize = Bitpack64_access_new_packsize(reduced,/*old_packsize*/(int) packsizes[bmer],
+ bitpacks[bmer],increment)) != (int) packsizes[bmer]) {
+ bitpacks[bmer] = Bitpack64_realloc_multiple((int) packsizes[bmer],new_packsize,bitpacks[bmer]);
+ packsizes[bmer] = (char) new_packsize;
+ }
+ Bitpack64_add_bitpack(reduced,(int) packsizes[bmer],bitpacks[bmer],increment);
+ }
+ }
+ }
+
+ Bitpack64_write_differential_bitpacks(new_pointers_filename,new_offsets_filename,packsizes,bitpacks,oligospace);
+
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
+ }
+ FREE(bitpacks);
+ FREE(packsizes);
+
+ return;
+}
+
static void
@@ -309,30 +418,229 @@ sort_8mers (unsigned char *positions8_high, UINT4 *positions8_low, Positionsptr_
}
+static void
+sort_positions (char *ptrsfile, char *compfile, FILE *positions_high_fp, FILE *positions_low_fp,
+ unsigned char *positions8_high, UINT4 *positions8_low, UINT4 *positions4,
+ UINT4 *newoffsetsmeta, UINT4 *newoffsetsstrm, Oligospace_T oligospace, bool coord_values_8p) {
+ Oligospace_T oligoi;
+ Positionsptr_T block_start, block_end, j, npositions;
+
+ FILE *ptrs_fp, *comp_fp;
+ UINT4 *ptrs, nregisters;
+ UINT4 ptri;
+ int ii;
+
+ /* Buffer is used to avoid frequent writes to the file */
+ UINT4 *buffer;
+ int buffer_size = BUFFER_SIZE;
+ int buffer_i;
+
+ UINT4 newoffsets[BLOCKSIZE+1];
+ UINT4 diffs[BLOCKSIZE], ascending[BLOCKSIZE+1];
+ UINT4 totalcount;
+ int packsize;
+
+
+ /* Sort positions in each block. For snps_root, use code from Bitpack64_write_differential */
+ if (snps_root) {
+ ptrs = (UINT4 *) CALLOC(((oligospace + BLOCKSIZE)/BLOCKSIZE + 1) * DIFFERENTIAL_METAINFO_SIZE,sizeof(UINT4));
+ ptri = 0;
+
+ if ((comp_fp = FOPEN_WRITE_BINARY(compfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",compfile);
+ exit(9);
+ }
+ buffer = (UINT4 *) CALLOC(buffer_size,sizeof(UINT4));
+ buffer_i = 0;
+ nregisters = 0;
+ }
+
+ totalcount = 0;
+ for (oligoi = 0; oligoi + BLOCKSIZE <= oligospace; oligoi += BLOCKSIZE) {
+ if (snps_root) {
+ ptrs[ptri++] = nregisters;
+ ptrs[ptri++] = totalcount;
+ }
+ ascending[0] = totalcount;
+ Bitpack64_block_offsets(newoffsets,oligoi,newoffsetsmeta,newoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ block_start = newoffsets[ii];
+ block_end = newoffsets[ii+1];
+ if ((npositions = block_end - block_start) > 0) {
+ if (coord_values_8p == true) {
+ sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
+ if (snps_root == NULL) {
+ /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
+ FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
+ FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
+ } else {
+ /* FWRITE_UINT8(positions8[block_start],positions_fp); */
+ FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
+ FWRITE_UINT(positions8_low[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
+ npositions--;
+ } else {
+ /* FWRITE_UINT8(positions8[j],positions_fp); */
+ FWRITE_CHAR(positions8_high[j],positions_high_fp);
+ FWRITE_UINT(positions8_low[j],positions_low_fp);
+ }
+ }
+ }
+
+ } else {
+ qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
+ if (snps_root == NULL) {
+ FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+ } else {
+ FWRITE_UINT(positions4[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions4[j] == positions4[j-1]) {
+ npositions--;
+ } else {
+ FWRITE_UINT(positions4[j],positions_low_fp);
+ }
+ }
+ }
+ }
+ totalcount += npositions;
+ }
+ ascending[ii+1] = totalcount;
+ }
+ if (snps_root) {
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ nregisters += packsize / 2;
+ }
+ }
+
+ if (oligoi <= oligospace) {
+ /* Finish last block (containing 1 entry, but expand to 64) */
+ if (snps_root) {
+ ptrs[ptri++] = nregisters;
+ ptrs[ptri++] = totalcount;
+ }
+ ascending[0] = totalcount;
+ for (ii = 0; ii <= (int) (oligospace - oligoi); ii++) {
+ block_start = Bitpack64_read_two(&block_end,oligoi+ii,newoffsetsmeta,newoffsetsstrm);
+ if ((npositions = block_end - block_start) > 0) {
+ if (coord_values_8p == true) {
+ sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
+ if (snps_root == NULL) {
+ /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
+ FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
+ FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
+ } else {
+ /* FWRITE_UINT8(positions8[block_start],positions_fp); */
+ FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
+ FWRITE_UINT(positions8_low[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
+ npositions--;
+ } else {
+ /* FWRITE_UINT8(positions8[j],positions_fp); */
+ FWRITE_CHAR(positions8_high[j],positions_high_fp);
+ FWRITE_UINT(positions8_low[j],positions_low_fp);
+ }
+ }
+ }
+
+ } else {
+ qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
+ if (snps_root == NULL) {
+ FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+ } else {
+ FWRITE_UINT(positions4[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions4[j] == positions4[j-1]) {
+ npositions--;
+ } else {
+ FWRITE_UINT(positions4[j],positions_low_fp);
+ }
+ }
+ }
+ }
+ totalcount += npositions;
+ }
+ ascending[ii+1] = totalcount;
+ }
+ if (snps_root) {
+ for ( ; ii < BLOCKSIZE; ii++) {
+ ascending[ii+1] = totalcount;
+ }
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ nregisters += packsize / 2;
+ }
+ }
+
+ if (snps_root) {
+ /* Write the final pointer, which will point after the end of the file */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for end of block */
+ ptrs[ptri++] = totalcount;
+
+ if ((ptrs_fp = FOPEN_WRITE_BINARY(ptrsfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",ptrsfile);
+ exit(9);
+ } else {
+ FWRITE_UINTS(ptrs,ptri,ptrs_fp);
+ FREE(ptrs);
+ fclose(ptrs_fp);
+ }
+
+ /* Empty buffer */
+ if (buffer_i > 0) {
+ FWRITE_UINTS(buffer,buffer_i,comp_fp);
+ buffer_i = 0;
+ }
+ FREE(buffer);
+ fclose(comp_fp);
+ }
+
+ return;
+}
+
+
/* G C G T */
static unsigned char ag_conversion[4] = {2, 1, 2, 3};
static char AG_CHARTABLE[4] = {'G','C','G','T'};
static void
-compute_ag (char *pointers_filename, char *offsets_filename,
- FILE *positions_high_fp, FILE *positions_low_fp, Positionsptr_T *oldoffsets,
- UINT8 *oldpositions8, UINT4 *oldpositions4,
- Oligospace_T oligospace, Storedoligomer_T mask,
- bool coord_values_8p) {
+compute_ag (char *new_pointers_filename, char *new_offsets_filename,
+ FILE *positions_high_fp, FILE *positions_low_fp,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm, UINT8 *oldpositions8, UINT4 *oldpositions4,
+ Oligospace_T oligospace, Oligospace_T mask, bool coord_values_8p) {
+ char *ptrsfile, *compfile;
unsigned char *positions8_high;
UINT4 *positions8_low;
UINT4 *positions4;
- Positionsptr_T *snpoffsets, j;
- Oligospace_T oligoi, oligok, reduced;
- Positionsptr_T *pointers, *offsets, preunique_totalcounts, block_start, block_end, npositions, offsets_ptr;
+ Oligospace_T oligoi, reduced;
+ UINT4 oldoffsets[BLOCKSIZE+1];
+ UINT4 *newoffsetsmeta, *newoffsetsstrm, *countermeta, *counterstrm;
+ Positionsptr_T preunique_totalcounts, block_start, block_end, j, offset;
+ size_t offsetsmeta_len, offsetsstrm_len;
+ int ii;
+#ifdef HAVE_MMAP
+ int offsetsmeta_fd, offsetsstrm_fd;
+#else
+ double seconds;
+#endif
#ifdef DEBUG
char *nt1, *nt2;
#endif
- offsets = compute_offsets_ag(oldoffsets,oligospace,mask);
- preunique_totalcounts = offsets[oligospace];
+ /* offsets = compute_offsets_ag_using_array(oldoffsets,oligospace,mask); */
+ compute_offsets_ag_using_bitpack(new_pointers_filename,new_offsets_filename,oldoffsetsmeta,oldoffsetsstrm,
+ oligospace,mask);
+
+ preunique_totalcounts = Bitpack64_read_one(oligospace,oldoffsetsmeta,oldoffsetsstrm);
if (preunique_totalcounts == 0) {
fprintf(stderr,"Something is wrong with the offsets. Total counts is zero.\n");
exit(9);
@@ -363,162 +671,118 @@ compute_ag (char *pointers_filename, char *offsets_filename,
}
}
- /* Point to offsets and revise (previously copied) */
- pointers = offsets;
+ /* Point to offsets and revise */
fprintf(stderr,"Rearranging AG positions...");
-
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
- reduced = Atoi_reduce_ag(oligoi) & mask;
-#ifdef WORDS_BIGENDIAN
- if (coord_values_8p == true) {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
- }
- }
+#ifdef HAVE_MMAP
+ newoffsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,new_pointers_filename,/*randomp*/false);
+ newoffsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,new_offsets_filename,/*randomp*/false);
#else
- if (coord_values_8p == true) {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = oldpositions8[j] & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = oldpositions4[j];
- }
- }
+ newoffsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,new_pointers_filename,sizeof(UINT4));
+ newoffsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,new_offsets_filename,sizeof(UINT4));
#endif
- }
- FREE(offsets);
- fprintf(stderr,"done\n");
-
-
- fprintf(stderr,"Sorting AG positions...");
- offsets = compute_offsets_ag(oldoffsets,oligospace,mask);
+ countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,newoffsetsstrm,index1part);
- /* Sort positions in each block */
- if (snps_root) {
- oligok = 0;
- snpoffsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
- offsets_ptr = 0U;
- snpoffsets[oligok++] = offsets_ptr;
- }
- if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(oldoffsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
fprintf(stderr,".");
}
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- /* qsort(&(positions8[block_start]),npositions,sizeof(UINT8),UINT8_compare); */
- sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
- if (snps_root == NULL) {
- /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
- FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
- FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
-
- } else {
- /* FWRITE_UINT8(positions8[block_start],positions_fp); */
- FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
- FWRITE_UINT(positions8_low[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
- npositions--;
- } else {
- /* FWRITE_UINT8(positions8[j],positions_fp); */
- FWRITE_CHAR(positions8_high[j],positions_high_fp);
- FWRITE_UINT(positions8_low[j],positions_low_fp);
- }
- }
- offsets_ptr += npositions;
+ block_start = oldoffsets[ii];
+ block_end = oldoffsets[ii+1];
+#ifdef WORDS_BIGENDIAN
+ reduced = Atoi_reduce_ag(oligoi) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = Bigendian_convert_uint(block_start); j < Bigendian_convert_uint(block_end); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
+ }
+ } else {
+ for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
}
}
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
- }
- }
- } else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
- if (snps_root == NULL) {
- FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+#else
+ if (block_end > block_start) {
+ reduced = Atoi_reduce_ag(oligoi) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[offset] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[offset] = oldpositions8[j] & POSITIONS8_LOW_MASK;
+ offset++;
+ }
} else {
- FWRITE_UINT(positions4[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions4[j] == positions4[j-1]) {
- npositions--;
- } else {
- FWRITE_UINT(positions4[j],positions_low_fp);
- }
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[offset] = oldpositions4[j];
+ offset++;
}
- offsets_ptr += npositions;
}
- }
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
+ Bitpack64_add(reduced,countermeta,counterstrm,block_end - block_start);
}
}
+#endif
}
+
+ FREE(counterstrm);
+ FREE(countermeta);
fprintf(stderr,"done\n");
+
+ fprintf(stderr,"Sorting AG positions...");
if (snps_root == NULL) {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,offsets,oligospace);
- } else {
- abort();
- }
+ ptrsfile = compfile = (char *) NULL;
} else {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,snpoffsets,oligospace);
- } else {
- abort();
- }
- FREE(snpoffsets);
+ ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(ptrsfile,"%s.temp",new_pointers_filename);
+ compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(compfile,"%s.temp",new_offsets_filename);
}
- FREE(offsets);
+ sort_positions(ptrsfile,compfile,positions_high_fp,positions_low_fp,
+ positions8_high,positions8_low,positions4,
+ newoffsetsmeta,newoffsetsstrm,oligospace,coord_values_8p);
+
+ /* Clean up */
+#ifdef HAVE_MMAP
+ munmap((void *) newoffsetsmeta,offsetsmeta_len);
+ munmap((void *) newoffsetsstrm,offsetsstrm_len);
+ close(offsetsmeta_fd);
+ close(offsetsstrm_fd);
+#else
+ FREE(newoffsetsmeta);
+ FREE(newoffsetsstrm);
+#endif
+
if (coord_values_8p == true) {
FREE(positions8_high);
FREE(positions8_low);
@@ -526,6 +790,16 @@ compute_ag (char *pointers_filename, char *offsets_filename,
FREE(positions4);
}
+ if (snps_root) {
+ rename(ptrsfile,new_pointers_filename);
+ rename(compfile,new_offsets_filename);
+ FREE(ptrsfile);
+ FREE(compfile);
+ }
+
+ fprintf(stderr,"done\n");
+
+
return;
}
@@ -535,24 +809,35 @@ static unsigned char tc_conversion[4] = {0, 1, 2, 1};
static char TC_CHARTABLE[4] = {'A','C','G','C'};
static void
-compute_tc (char *pointers_filename, char *offsets_filename,
- FILE *positions_high_fp, FILE *positions_low_fp, Positionsptr_T *oldoffsets,
- UINT8 *oldpositions8, UINT4 *oldpositions4,
- Oligospace_T oligospace, Storedoligomer_T mask,
- bool coord_values_8p) {
+compute_tc (char *new_pointers_filename, char *new_offsets_filename,
+ FILE *positions_high_fp, FILE *positions_low_fp,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm, UINT8 *oldpositions8, UINT4 *oldpositions4,
+ Oligospace_T oligospace, Oligospace_T mask, bool coord_values_8p) {
+ char *ptrsfile, *compfile;
unsigned char *positions8_high;
UINT4 *positions8_low;
UINT4 *positions4;
- Positionsptr_T *snpoffsets, j;
- Oligospace_T oligoi, oligok, reduced;
- Positionsptr_T *pointers, *offsets, preunique_totalcounts, block_start, block_end, npositions, offsets_ptr;
+ Oligospace_T oligoi, reduced;
+ UINT4 oldoffsets[BLOCKSIZE+1];
+ UINT4 *newoffsetsmeta, *newoffsetsstrm, *countermeta, *counterstrm;
+ Positionsptr_T preunique_totalcounts, block_start, block_end, j, offset;
+ size_t offsetsmeta_len, offsetsstrm_len;
+ int ii;
+#ifdef HAVE_MMAP
+ int offsetsmeta_fd, offsetsstrm_fd;
+#else
+ double seconds;
+#endif
#ifdef DEBUG
char *nt1, *nt2;
#endif
- offsets = compute_offsets_tc(oldoffsets,oligospace,mask);
- preunique_totalcounts = offsets[oligospace];
+ /* offsets = compute_offsets_tc_using_array(oldoffsets,oligospace,mask); */
+ compute_offsets_tc_using_bitpack(new_pointers_filename,new_offsets_filename,oldoffsetsmeta,oldoffsetsstrm,
+ oligospace,mask);
+
+ preunique_totalcounts = Bitpack64_read_one(oligospace,oldoffsetsmeta,oldoffsetsstrm);
if (preunique_totalcounts == 0) {
fprintf(stderr,"Something is wrong with the offsets. Total counts is zero.\n");
exit(9);
@@ -583,163 +868,118 @@ compute_tc (char *pointers_filename, char *offsets_filename,
}
}
- /* Point to offsets and revise (previously copied) */
- pointers = offsets;
+ /* Point to offsets and revise */
fprintf(stderr,"Rearranging TC positions...");
-
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
-
- reduced = Atoi_reduce_tc(oligoi) & mask;
-#ifdef WORDS_BIGENDIAN
- if (coord_values_8p == true) {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
- }
- }
+#ifdef HAVE_MMAP
+ newoffsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,new_pointers_filename,/*randomp*/false);
+ newoffsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,new_offsets_filename,/*randomp*/false);
#else
- if (coord_values_8p == true) {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = oldpositions8[j] & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = oldpositions4[j];
- }
- }
+ newoffsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,new_pointers_filename,sizeof(UINT4));
+ newoffsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,new_offsets_filename,sizeof(UINT4));
#endif
- }
- FREE(offsets);
- fprintf(stderr,"done\n");
+ countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,newoffsetsstrm,index1part);
-
- fprintf(stderr,"Sorting TC positions...");
- offsets = compute_offsets_tc(oldoffsets,oligospace,mask);
-
- /* Sort positions in each block */
- if (snps_root) {
- oligok = 0;
- snpoffsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
- offsets_ptr = 0U;
- snpoffsets[oligok++] = offsets_ptr;
- }
- if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(oldoffsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
fprintf(stderr,".");
}
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- /* qsort(&(positions8[block_start]),npositions,sizeof(UINT8),UINT8_compare); */
- sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
- if (snps_root == NULL) {
- /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
- FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
- FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
-
- } else {
- /* FWRITE_UINT8(positions8[block_start],positions_fp); */
- FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
- FWRITE_UINT(positions8_low[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
- npositions--;
- } else {
- /* FWRITE_UINT8(positions8[j],positions_fp); */
- FWRITE_CHAR(positions8_high[j],positions_high_fp);
- FWRITE_UINT(positions8_low[j],positions_low_fp);
- }
- }
- offsets_ptr += npositions;
+ block_start = oldoffsets[ii];
+ block_end = oldoffsets[ii+1];
+#ifdef WORDS_BIGENDIAN
+ reduced = Atoi_reduce_tc(oligoi) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = Bigendian_convert_uint(block_start); j < Bigendian_convert_uint(block_end); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
+ }
+ } else {
+ for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
}
}
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
- }
- }
- } else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
- if (snps_root == NULL) {
- FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+#else
+ if (block_end > block_start) {
+ reduced = Atoi_reduce_tc(oligoi) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[offset] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[offset] = oldpositions8[j] & POSITIONS8_LOW_MASK;
+ offset++;
+ }
} else {
- FWRITE_UINT(positions4[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions4[j] == positions4[j-1]) {
- npositions--;
- } else {
- FWRITE_UINT(positions4[j],positions_low_fp);
- }
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[offset] = oldpositions4[j];
+ offset++;
}
- offsets_ptr += npositions;
}
- }
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
+ Bitpack64_add(reduced,countermeta,counterstrm,block_end - block_start);
}
}
+#endif
}
+
+ FREE(counterstrm);
+ FREE(countermeta);
fprintf(stderr,"done\n");
+
+ fprintf(stderr,"Sorting TC positions...");
if (snps_root == NULL) {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,offsets,oligospace);
- } else {
- abort();
- }
+ ptrsfile = compfile = (char *) NULL;
} else {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,snpoffsets,oligospace);
- } else {
- abort();
- }
- FREE(snpoffsets);
+ ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(ptrsfile,"%s.temp",new_pointers_filename);
+ compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(compfile,"%s.temp",new_offsets_filename);
}
- FREE(offsets);
+ sort_positions(ptrsfile,compfile,positions_high_fp,positions_low_fp,
+ positions8_high,positions8_low,positions4,
+ newoffsetsmeta,newoffsetsstrm,oligospace,coord_values_8p);
+
+/* Clean up */
+#ifdef HAVE_MMAP
+ munmap((void *) newoffsetsmeta,offsetsmeta_len);
+ munmap((void *) newoffsetsstrm,offsetsstrm_len);
+ close(offsetsmeta_fd);
+ close(offsetsstrm_fd);
+#else
+ FREE(newoffsetsmeta);
+ FREE(newoffsetsstrm);
+#endif
+
if (coord_values_8p == true) {
FREE(positions8_high);
FREE(positions8_low);
@@ -747,6 +987,15 @@ compute_tc (char *pointers_filename, char *offsets_filename,
FREE(positions4);
}
+ if (snps_root) {
+ rename(ptrsfile,new_pointers_filename);
+ rename(compfile,new_offsets_filename);
+ FREE(ptrsfile);
+ FREE(compfile);
+ }
+
+ fprintf(stderr,"done\n");
+
return;
}
@@ -761,16 +1010,15 @@ main (int argc, char *argv[]) {
Filenames_T filenames;
char *new_pointers_filename, *new_offsets_filename;
Univ_IIT_T chromosome_iit;
- Positionsptr_T *ref_offsets;
+ UINT4 *ref_offsetsmeta, *ref_offsetsstrm;
size_t totalcounts, i;
- Storedoligomer_T mask;
+ Oligospace_T mask;
unsigned char *ref_positions8_high;
UINT4 *ref_positions8_low;
UINT8 *ref_positions8;
UINT4 *ref_positions4;
Oligospace_T oligospace;
bool coord_values_8p;
- int shmid;
/* For suffix array */
Univcoord_T genomelength;
@@ -778,21 +1026,27 @@ main (int argc, char *argv[]) {
char *childexcfile, *childguidefile;
char *lcpchilddcfile;
char *indexijptrsfile, *indexijcompfile;
- Genome_T genomecomp, genomebits;
+ Genome_T genomecomp;
unsigned char *gbuffer;
- UINT4 *SA, *lcp, *child;
+ UINT4 *SA;
UINT4 nbytes;
unsigned char *discrim_chars;
unsigned char *lcp_bytes;
- UINT4 *lcp_guide, *lcp_exceptions;
- int n_lcp_exceptions;
+ UINT4 *lcp_guide, *lcp_exceptions, n_lcp_exceptions;
+
+ unsigned char *child_bytes;
+ UINT4 *child_exceptions, n_child_exceptions;
int sa_fd;
- size_t sa_len, lcpguide_len, lcpexc_len;
+ Access_T lcpguide_access;
+ size_t sa_len, lcpguide_len;
double seconds;
+ int offsetsmeta_fd, offsetsstrm_fd;
+ size_t offsetsmeta_len, offsetsstrm_len;
+
FILE *positions_high_fp, *positions_low_fp;
int ref_positions_high_fd, ref_positions_low_fd;
size_t ref_positions_high_len, ref_positions_low_len;
@@ -876,16 +1130,13 @@ main (int argc, char *argv[]) {
required_index1part,required_interval,
/*offsets_only_p*/false);
- mask = ~(~0UL << 2*index1part);
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
+#else
+ mask = ~(~0U << 2*index1part);
+#endif
oligospace = power(4,index1part);
- /* Read offsets */
- if (compression_type == BITPACK64_COMPRESSION) {
- ref_offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part);
- } else {
- abort();
- }
-
/* Read positions */
#if 0
if ((ref_positions_fp = FOPEN_READ_BINARY(filenames->positions_low_filename)) == NULL) {
@@ -899,16 +1150,14 @@ main (int argc, char *argv[]) {
if (coord_values_8p == true) {
#ifdef HAVE_MMAP
ref_positions8_high = (unsigned char *) Access_mmap(&ref_positions_high_fd,&ref_positions_high_len,
- filenames->positions_high_filename,sizeof(unsigned char),/*randomp*/false);
+ filenames->positions_high_filename,/*randomp*/false);
ref_positions8_low = (UINT4 *) Access_mmap(&ref_positions_low_fd,&ref_positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->positions_low_filename,/*randomp*/false);
#else
- ref_positions8_high = (unsigned char *) Access_allocate(&shmid,&ref_positions_high_len,&seconds,
- filenames->positions_high_filename,sizeof(unsigned char),
- /*sharedp*/false);
- ref_positions8_low = (UINT4 *) Access_allocate(&shmid,&ref_positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),
- /*sharedp*/false);
+ ref_positions8_high = (unsigned char *) Access_allocate_private(&ref_positions_high_access,&ref_positions_high_len,&seconds,
+ filenames->positions_high_filename,sizeof(unsigned char));
+ ref_positions8_low = (UINT4 *) Access_allocate_private(&ref_positions_low_access,&ref_positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
#endif
/* Unpack */
totalcounts = ref_positions_high_len/sizeof(unsigned char);
@@ -933,11 +1182,10 @@ main (int argc, char *argv[]) {
} else {
#ifdef HAVE_MMAP
ref_positions4 = (UINT4 *) Access_mmap(&ref_positions_low_fd,&ref_positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->positions_low_filename,/*randomp*/false);
#else
- ref_positions4 = (UINT4 *) Access_allocate(&shmid,&ref_positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),
- /*sharedp*/false);
+ ref_positions4 = (UINT4 *) Access_allocate_private(&ref_positions_low_access,&ref_positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
#endif
}
@@ -1003,7 +1251,7 @@ main (int argc, char *argv[]) {
FREE(indexijcompfile);
FREE(indexijptrsfile);
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/false);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
#if 0
/* Not needed if we already have gbuffer */
@@ -1015,7 +1263,8 @@ main (int argc, char *argv[]) {
/*mode*/ATOI_STRANDED);
#endif
- lcp = Sarray_compute_lcp_from_genome(SA,gbuffer,/*n*/genomelength);
+ lcp_bytes = Sarray_compute_lcp_bytes_from_genome(&lcp_exceptions,&n_lcp_exceptions,SA,gbuffer,/*n*/genomelength);
+
munmap((void *) SA,sa_len);
close(sa_fd);
FREE(gbuffer);
@@ -1028,29 +1277,20 @@ main (int argc, char *argv[]) {
sprintf(lcpexcfile,"%s/%s.a2iag.salcpexc",destdir,fileroot);
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.a2iag.salcpguide1024",destdir,fileroot);
-
- lcp_bytes = Bytecoding_write_exceptions_only(lcpexcfile,lcpguidefile,lcp,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,lcpexcfile,lcpguidefile,lcp_bytes,lcp_exceptions,n_lcp_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(lcpguidefile);
FREE(lcpexcfile);
- FREE(lcp); /* Use lcp_bytes, which are more memory-efficient than lcp */
-
/* DC array */
- /* Assume we have lcp_bytes already in memory. Don't need to use guide for speed. */
+ /* Assume we have lcp_bytes and lcp_exceptions already in memory. Don't need to use guide for speed. */
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.a2iag.salcpguide1024",destdir,fileroot);
- lcp_guide = (UINT4 *) Access_allocate(&shmid,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4),
- /*sharedp*/false);
+ lcp_guide = (UINT4 *) Access_allocate_private(&lcpguide_access,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4));
FREE(lcpguidefile);
- lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.salcpexc")+1,sizeof(char));
- sprintf(lcpexcfile,"%s/%s.a2iag.salcpexc",destdir,fileroot);
- lcp_exceptions = (UINT4 *) Access_allocate(&shmid,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4),/*sharedp*/false);
- n_lcp_exceptions = lcpexc_len/(sizeof(UINT4) + sizeof(UINT4));
- FREE(lcpexcfile);
-
/* Compute discriminating chars (DC) array */
discrim_chars = Sarray_discriminating_chars(&nbytes,sarrayfile,genomecomp,lcp_bytes,lcp_guide,
lcp_exceptions,/*guide_interval*/1024,/*n*/genomelength,
@@ -1059,30 +1299,44 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Building child array\n");
/* Compute child array (relative values) */
- child = Sarray_compute_child(lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
+ child_bytes = Sarray_compute_child_bytes(&child_exceptions,&n_child_exceptions,lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
FREE(lcp_exceptions);
FREE(lcp_guide);
- /* Write combined lcpchilddc file */
- lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.salcpchilddc")+1,sizeof(char));
- sprintf(lcpchilddcfile,"%s/%s.a2iag.salcpchilddc",destdir,fileroot);
childexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.sachildexc")+1,sizeof(char));
sprintf(childexcfile,"%s/%s.a2iag.sachildexc",destdir,fileroot);
childguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.sachildguide1024")+1,sizeof(char));
sprintf(childguidefile,"%s/%s.a2iag.sachildguide1024",destdir,fileroot);
- Bytecoding_write_lcpchilddc(lcpchilddcfile,childexcfile,childguidefile,child,
- discrim_chars,lcp_bytes,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,childexcfile,childguidefile,child_bytes,child_exceptions,n_child_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(childguidefile);
FREE(childexcfile);
+ FREE(child_exceptions);
+
+ /* Write combined lcpchilddc file */
+ lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2iag.salcpchilddc")+1,sizeof(char));
+ sprintf(lcpchilddcfile,"%s/%s.a2iag.salcpchilddc",destdir,fileroot);
+ Bytecoding_interleave_lcpchilddc(lcpchilddcfile,child_bytes,discrim_chars,lcp_bytes,genomelength);
FREE(lcpchilddcfile);
- FREE(child);
+ FREE(child_bytes);
FREE(discrim_chars);
FREE(lcp_bytes);
}
+ /* Read offsets */
+ /* ref_offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part); */
+#ifdef HAVE_MMAP
+ ref_offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,filenames->pointers_filename,/*randomp*/false);
+ ref_offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,filenames->offsets_filename,/*randomp*/false);
+#else
+ ref_offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,filenames->pointers_filename,sizeof(UINT4));
+ ref_offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,filenames->offsets_filename,sizeof(UINT4));
+#endif
+
compute_ag(new_pointers_filename,new_offsets_filename,
- positions_high_fp,positions_low_fp,ref_offsets,ref_positions8,ref_positions4,
+ positions_high_fp,positions_low_fp,
+ ref_offsetsmeta,ref_offsetsstrm,ref_positions8,ref_positions4,
oligospace,mask,coord_values_8p);
if (coord_values_8p == true) {
fclose(positions_high_fp);
@@ -1145,7 +1399,7 @@ main (int argc, char *argv[]) {
FREE(indexijcompfile);
FREE(indexijptrsfile);
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/false);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
#if 0
/* Not needed if we already have gbuffer */
@@ -1157,7 +1411,7 @@ main (int argc, char *argv[]) {
/*mode*/ATOI_STRANDED);
#endif
- lcp = Sarray_compute_lcp_from_genome(SA,gbuffer,/*n*/genomelength);
+ lcp_bytes = Sarray_compute_lcp_bytes_from_genome(&lcp_exceptions,&n_lcp_exceptions,SA,gbuffer,/*n*/genomelength);
munmap((void *) SA,sa_len);
close(sa_fd);
FREE(gbuffer);
@@ -1170,28 +1424,20 @@ main (int argc, char *argv[]) {
sprintf(lcpexcfile,"%s/%s.a2itc.salcpexc",destdir,fileroot);
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.a2itc.salcpguide1024",destdir,fileroot);
-
- lcp_bytes = Bytecoding_write_exceptions_only(lcpexcfile,lcpguidefile,lcp,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,lcpexcfile,lcpguidefile,lcp_bytes,lcp_exceptions,n_lcp_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(lcpguidefile);
FREE(lcpexcfile);
- FREE(lcp); /* Use lcp_bytes, which are more memory-efficient than lcp */
-
/* DC array */
- /* Assume we have lcp_bytes already in memory. Don't need to use guide for speed. */
+ /* Assume we have lcp_bytes and lcp_exceptions already in memory. Don't need to use guide for speed. */
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.a2itc.salcpguide1024",destdir,fileroot);
- lcp_guide = (UINT4 *) Access_allocate(&shmid,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4),/*sharedp*/false);
+ lcp_guide = (UINT4 *) Access_allocate_private(&lcpguide_access,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4));
FREE(lcpguidefile);
- lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.salcpexc")+1,sizeof(char));
- sprintf(lcpexcfile,"%s/%s.a2itc.salcpexc",destdir,fileroot);
- lcp_exceptions = (UINT4 *) Access_allocate(&shmid,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4),/*sharedp*/false);
- n_lcp_exceptions = lcpexc_len/(sizeof(UINT4) + sizeof(UINT4));
- FREE(lcpexcfile);
-
/* Compute discriminating chars (DC) array */
discrim_chars = Sarray_discriminating_chars(&nbytes,sarrayfile,genomecomp,lcp_bytes,lcp_guide,
lcp_exceptions,/*guide_interval*/1024,/*n*/genomelength,
@@ -1200,24 +1446,27 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Building child array\n");
/* Compute child array (relative values) */
- child = Sarray_compute_child(lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
+ child_bytes = Sarray_compute_child_bytes(&child_exceptions,&n_child_exceptions,lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
FREE(lcp_exceptions);
FREE(lcp_guide);
- /* Write combined lcpchilddc file */
- lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.salcpchilddc")+1,sizeof(char));
- sprintf(lcpchilddcfile,"%s/%s.a2itc.salcpchilddc",destdir,fileroot);
childexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.sachildexc")+1,sizeof(char));
sprintf(childexcfile,"%s/%s.a2itc.sachildexc",destdir,fileroot);
childguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.sachildguide1024")+1,sizeof(char));
sprintf(childguidefile,"%s/%s.a2itc.sachildguide1024",destdir,fileroot);
- Bytecoding_write_lcpchilddc(lcpchilddcfile,childexcfile,childguidefile,child,
- discrim_chars,lcp_bytes,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,childexcfile,childguidefile,child_bytes,child_exceptions,n_child_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(childguidefile);
FREE(childexcfile);
+ FREE(child_exceptions);
+
+ /* Write combined lcpchilddc file */
+ lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".a2itc.salcpchilddc")+1,sizeof(char));
+ sprintf(lcpchilddcfile,"%s/%s.a2itc.salcpchilddc",destdir,fileroot);
+ Bytecoding_interleave_lcpchilddc(lcpchilddcfile,child_bytes,discrim_chars,lcp_bytes,genomelength);
FREE(lcpchilddcfile);
- FREE(child);
+ FREE(child_bytes);
FREE(discrim_chars);
FREE(lcp_bytes);
@@ -1225,7 +1474,8 @@ main (int argc, char *argv[]) {
}
compute_tc(new_pointers_filename,new_offsets_filename,
- positions_high_fp,positions_low_fp,ref_offsets,ref_positions8,ref_positions4,
+ positions_high_fp,positions_low_fp,
+ ref_offsetsmeta,ref_offsetsstrm,ref_positions8,ref_positions4,
oligospace,mask,coord_values_8p);
if (coord_values_8p == true) {
fclose(positions_high_fp);
@@ -1235,9 +1485,16 @@ main (int argc, char *argv[]) {
FREE(new_pointers_filename);
-
/* Clean up */
- FREE(ref_offsets);
+#ifdef HAVE_MMAP
+ munmap((void *) ref_offsetsmeta,offsetsmeta_len);
+ munmap((void *) ref_offsetsstrm,offsetsstrm_len);
+ close(offsetsmeta_fd);
+ close(offsetsstrm_fd);
+#else
+ FREE(ref_offsetsmeta);
+ FREE(ref_offsetsstrm);
+#endif
if (coord_values_8p == true) {
FREE(ref_positions8);
diff --git a/src/bitpack64-access.c b/src/bitpack64-access.c
index d69cc43..c21d45c 100644
--- a/src/bitpack64-access.c
+++ b/src/bitpack64-access.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: bitpack64-access.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: bitpack64-access.c 180341 2015-12-07 18:29:40Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -521,7 +521,7 @@ access_10_15 (const UINT4 *in) {
static UINT4
access_12_00 (const UINT4 *in) {
- return ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+ return ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
}
static UINT4
@@ -679,8 +679,8 @@ access_14_05 (const UINT4 *in) {
static UINT4
access_14_06 (const UINT4 *in) {
UINT4 out;
- in += 2 * WORD_INCR;
+ in += 2 * WORD_INCR;
out = ( CONVERT(*in) >> 20 ) % (1U << 14 ) ;
in += 1 * WORD_INCR;
out |= (CONVERT(*in) % (1U<< 2 ))<<( 14 - 2 );
@@ -989,7 +989,7 @@ access_18_15 (const UINT4 *in) {
static UINT4
access_20_00 (const UINT4 *in) {
- return ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+ return ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
}
static UINT4
@@ -2072,7 +2072,7 @@ static Accessor_T accessor_table[272] =
#ifdef HORIZONTAL
UINT4
-Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
+Bitpack64_access (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp) {
UINT4 *info, start;
int nwritten, remainder;
UINT4 *bitpack;
@@ -2081,7 +2081,7 @@ Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
int packsize, i;
#endif
- info = &(ptrs[position/BLOCKSIZE * DIRECT_METAINFO_SIZE]);
+ info = &(ptrs[oligo/BLOCKSIZE * DIRECT_METAINFO_SIZE]);
#ifdef WORDS_BIGENDIAN
start = Bigendian_convert_uint(info[0]);
@@ -2093,14 +2093,14 @@ Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
nwritten = info[1] - start; /* In 128-bit registers */
#endif
- remainder = position % BLOCKSIZE;
+ remainder = oligo % BLOCKSIZE;
index = nwritten*16 + remainder % 16;
row = (remainder / 16) * (packsize / 2); /* Complexity of this calculation makes horizontal format slower */
#ifdef DEBUG
packsize = nwritten*2;
- printf("Entered Bitpack64_access with position %u, packsize %d, remainder %d, row %d, index %d\n",
- position,packsize,remainder,row,index);
+ printf("Entered Bitpack64_access with oligo %u, packsize %d, remainder %d, row %d, index %d\n",
+ oligo,packsize,remainder,row,index);
printf("bitpack:\n");
for (i = 0; i < nwritten*4; i += 4) {
printf("%08X %08X %08X %08X\n",bitpack[i],bitpack[i+1],bitpack[i+2],bitpack[i+3]);
@@ -2114,7 +2114,7 @@ Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
#else
UINT4
-Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
+Bitpack64_access (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp) {
UINT4 *info, start;
int nwritten, remainder;
UINT4 *bitpack;
@@ -2123,7 +2123,7 @@ Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
int packsize, i;
#endif
- info = &(ptrs[position/BLOCKSIZE * DIRECT_METAINFO_SIZE]);
+ info = &(ptrs[oligo/BLOCKSIZE * DIRECT_METAINFO_SIZE]);
#ifdef WORDS_BIGENDIAN
start = Bigendian_convert_uint(info[0]);
@@ -2135,14 +2135,14 @@ Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
nwritten = info[1] - start; /* In 128-bit registers */
#endif
- remainder = position % BLOCKSIZE;
+ remainder = oligo % BLOCKSIZE;
index = nwritten*16 + remainder/4;
column = remainder % 4;
#ifdef DEBUG
packsize = nwritten*2;
- printf("Entered Bitpack64_access with position %u, packsize %d, remainder %d, column %d, index %d\n",
- position,packsize,remainder,column,index);
+ printf("Entered Bitpack64_access with oligo %u, packsize %d, remainder %d, column %d, index %d\n",
+ oligo,packsize,remainder,column,index);
printf("bitpack:\n");
for (i = 0; i < nwritten*4; i += 4) {
printf("%08X %08X %08X %08X\n",bitpack[i],bitpack[i+1],bitpack[i+2],bitpack[i+3]);
@@ -2153,5 +2153,1345 @@ Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp) {
return (accessor_table[index])(&(bitpack[column]));
}
+UINT4
+Bitpack64_access_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack) {
+ int nregisters, remainder; /* nregisters is same as nwritten */
+ int index, column;
+
+ nregisters = packsize / 2;
+ remainder = oligo % BLOCKSIZE;
+ index = nregisters*16 + remainder/4;
+ column = remainder % 4;
+
+ return (accessor_table[index])(&(bitpack[column]));
+}
+
+static UINT4 threshold[17] =
+ {/*0*/0U, /*2*/3U, /*4*/15U, /*6*/63U,
+ /*8*/255U, /*10*/1023U, /*12*/4095U, /*14*/16383U,
+ /*16*/65535U, /*18*/262143U, /*20*/1048575U, /*22*/4194303U,
+ /*24*/16777215U, /*26*/67108863U, /*28*/268435455U, /*30*/1073741823U,
+ /*32*/4294967295U};
+
+
+bool
+Bitpack64_access_filledp (Oligospace_T oligo, int packsize, UINT4 *bitpack) {
+ int nregisters, remainder; /* nregisters is same as nwritten */
+ int index, column;
+ UINT4 value;
+
+ nregisters = packsize / 2;
+ remainder = oligo % BLOCKSIZE;
+ index = nregisters*16 + remainder/4;
+ column = remainder % 4;
+
+ value = (accessor_table[index])(&(bitpack[column]));
+ if (value == threshold[nregisters]) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+int
+Bitpack64_access_new_packsize (Oligospace_T oligo, int old_packsize, UINT4 *bitpack, int increment) {
+ int new_packsize;
+ int nregisters, remainder; /* nregisters is same as nwritten */
+ int index, column;
+ UINT4 value;
+ Blocksize_T firstbit;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
+
+
+ nregisters = old_packsize / 2;
+ remainder = oligo % BLOCKSIZE;
+ index = nregisters*16 + remainder/4;
+ column = remainder % 4;
+
+ value = (accessor_table[index])(&(bitpack[column]));
+ value += increment;
+
+ if (value == 0) {
+ new_packsize = 0;
+ } else {
+#ifdef HAVE_BUILTIN_CLZ
+ firstbit = __builtin_clz(value);
+ new_packsize = 32 - firstbit;
+#elif defined(HAVE_ASM_BSR)
+ asm("bsr %1,%0" : "=r"(msb) : "r"(value));
+ new_packsize = msb + 1;
+#else
+ firstbit = ((value >> 16) ? clz_table[value >> 16] : 16 + clz_table[value]);
+ new_packsize = 32 - firstbit;
+#endif
+ }
+
+ new_packsize = (new_packsize + 1) & ~1; /* Converts packsizes to the next multiple of 2 */
+ if (new_packsize > old_packsize) {
+ return new_packsize;
+ } else {
+ return old_packsize;
+ }
+}
+
+
+
#endif
+
+
+static void
+extract_00 (UINT4 *out, const UINT4 *in) {
+ /* 00 */
+ out[0] = 0;
+
+ /* 01 */
+ out[4] = 0;
+
+ /* 02 */
+ out[8] = 0;
+
+ /* 03 */
+ out[12] = 0;
+
+ /* 04 */
+ out[16] = 0;
+
+ /* 05 */
+ out[20] = 0;
+
+ /* 06 */
+ out[24] = 0;
+
+ /* 07 */
+ out[28] = 0;
+
+ /* 08 */
+ out[32] = 0;
+
+ /* 09 */
+ out[36] = 0;
+
+ /* 10 */
+ out[40] = 0;
+
+ /* 11 */
+ out[44] = 0;
+
+ /* 12 */
+ out[48] = 0;
+
+ /* 13 */
+ out[52] = 0;
+
+ /* 14 */
+ out[56] = 0;
+
+ /* 15 */
+ out[60] = 0;
+
+ return;
+}
+
+static void
+extract_02 (UINT4 *out, const UINT4 *in) {
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 2 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 2 ) % (1U << 2 ) ;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 4 ) % (1U << 2 ) ;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 6 ) % (1U << 2 ) ;
+
+ /* 04 */
+ out[16] = ( CONVERT(*in) >> 8 ) % (1U << 2 ) ;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 10 ) % (1U << 2 ) ;
+
+ /* 06 */
+ out[24] = ( CONVERT(*in) >> 12 ) % (1U << 2 ) ;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 14 ) % (1U << 2 ) ;
+
+ /* 08 */
+ out[32] = ( CONVERT(*in) >> 16 ) % (1U << 2 ) ;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 18 ) % (1U << 2 ) ;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 20 ) % (1U << 2 ) ;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 22 ) % (1U << 2 ) ;
+
+ /* 12 */
+ out[48] = ( CONVERT(*in) >> 24 ) % (1U << 2 ) ;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 26 ) % (1U << 2 ) ;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 28 ) % (1U << 2 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 30 ) % (1U << 2 ) ;
+
+ return;
+}
+
+static void
+extract_04 (UINT4 *out, const UINT4 *in) {
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 4 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 4 ) % (1U << 4 ) ;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 8 ) % (1U << 4 ) ;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 12 ) % (1U << 4 ) ;
+
+ /* 04 */
+ out[16] = ( CONVERT(*in) >> 16 ) % (1U << 4 ) ;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 20 ) % (1U << 4 ) ;
+
+ /* 06 */
+ out[24] = ( CONVERT(*in) >> 24 ) % (1U << 4 ) ;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 28 ) % (1U << 4 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 4 ) ;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 4 ) % (1U << 4 ) ;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 8 ) % (1U << 4 ) ;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 12 ) % (1U << 4 ) ;
+
+ /* 12 */
+ out[48] = ( CONVERT(*in) >> 16 ) % (1U << 4 ) ;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 20 ) % (1U << 4 ) ;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 24 ) % (1U << 4 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 28 ) % (1U << 4 ) ;
+
+ return;
+}
+
+
+static void
+extract_06 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 6 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 6 ) % (1U << 6 ) ;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 12 ) % (1U << 6 ) ;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 18 ) % (1U << 6 ) ;
+
+ /* 04 */
+ out[16] = ( CONVERT(*in) >> 24 ) % (1U << 6 ) ;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 6 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 6 - 4 );
+ out[20] = value;
+
+ /* 06 */
+ out[24] = ( CONVERT(*in) >> 4 ) % (1U << 6 ) ;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 10 ) % (1U << 6 ) ;
+
+ /* 08 */
+ out[32] = ( CONVERT(*in) >> 16 ) % (1U << 6 ) ;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 22 ) % (1U << 6 ) ;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 6 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 6 - 2 );
+ out[40] = value;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 2 ) % (1U << 6 ) ;
+
+ /* 12 */
+ out[48] = ( CONVERT(*in) >> 8 ) % (1U << 6 ) ;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 14 ) % (1U << 6 ) ;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 20 ) % (1U << 6 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 26 ) % (1U << 6 ) ;
+
+ return;
+}
+
+
+static void
+extract_08 (UINT4 *out, const UINT4 *in) {
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+
+ /* 04 */
+ in += WORD_INCR;
+ out[16] = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+
+ /* 06 */
+ out[24] = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+
+ /* 12 */
+ in += WORD_INCR;
+ out[48] = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+
+ return;
+}
+
+static void
+extract_10 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 10 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 10 ) % (1U << 10 ) ;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 20 ) % (1U << 10 ) ;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 10 - 8 );
+ out[12] = value;
+
+ /* 04 */
+ out[16] = ( CONVERT(*in) >> 8 ) % (1U << 10 ) ;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 18 ) % (1U << 10 ) ;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 10 - 6 );
+ out[24] = value;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 6 ) % (1U << 10 ) ;
+
+ /* 08 */
+ out[32] = ( CONVERT(*in) >> 16 ) % (1U << 10 ) ;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 10 - 4 );
+ out[36] = value;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 4 ) % (1U << 10 ) ;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 14 ) % (1U << 10 ) ;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 10 - 2 );
+ out[48] = value;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 2 ) % (1U << 10 ) ;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 12 ) % (1U << 10 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 22 ) % (1U << 10 ) ;
+
+ return;
+}
+
+static void
+extract_12 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 12 ) % (1U << 12 ) ;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 );
+ out[8] = value;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 4 ) % (1U << 12 ) ;
+
+ /* 04 */
+ out[16] = ( CONVERT(*in) >> 16 ) % (1U << 12 ) ;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 );
+ out[20] = value;
+
+ /* 06 */
+ out[24] = ( CONVERT(*in) >> 8 ) % (1U << 12 ) ;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 20 ) % (1U << 12 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 12 ) % (1U << 12 ) ;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 );
+ out[40] = value;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 4 ) % (1U << 12 ) ;
+
+ /* 12 */
+ out[48] = ( CONVERT(*in) >> 16 ) % (1U << 12 ) ;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 );
+ out[52] = value;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 8 ) % (1U << 12 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 20 ) % (1U << 12 ) ;
+
+ return;
+}
+
+
+static void
+extract_14 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 14 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 14 ) % (1U << 14 ) ;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 14 - 10 );
+ out[8] = value;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 10 ) % (1U << 14 ) ;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 14 - 6 );
+ out[16] = value;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 6 ) % (1U << 14 ) ;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 14 - 2 );
+ out[24] = value;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 2 ) % (1U << 14 ) ;
+
+ /* 08 */
+ out[32] = ( CONVERT(*in) >> 16 ) % (1U << 14 ) ;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 14 - 12 );
+ out[36] = value;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 12 ) % (1U << 14 ) ;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 14 - 8 );
+ out[44] = value;
+
+ /* 12 */
+ out[48] = ( CONVERT(*in) >> 8 ) % (1U << 14 ) ;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 14 - 4 );
+ out[52] = value;
+
+ /* 14 */
+ out[56] = ( CONVERT(*in) >> 4 ) % (1U << 14 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 18 ) % (1U << 14 ) ;
+
+ return;
+}
+
+static void
+extract_16 (UINT4 *out, const UINT4 *in) {
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 01 */
+ out[4] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 02 */
+ in += WORD_INCR;
+ out[8] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 04 */
+ in += WORD_INCR;
+ out[16] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 06 */
+ in += WORD_INCR;
+ out[24] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 10 */
+ in += WORD_INCR;
+ out[40] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 12 */
+ in += WORD_INCR;
+ out[48] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ /* 14 */
+ in += WORD_INCR;
+ out[56] = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+
+ return;
+}
+
+
+static void
+extract_18 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 18 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 18 - 4 );
+ out[4] = value;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 4 ) % (1U << 18 ) ;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 18 - 8 );
+ out[12] = value;
+
+ /* 04 */
+ out[16] = ( CONVERT(*in) >> 8 ) % (1U << 18 ) ;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 18 - 12 );
+ out[20] = value;
+
+ /* 06 */
+ out[24] = ( CONVERT(*in) >> 12 ) % (1U << 18 ) ;
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 18 - 16 );
+ out[28] = value;
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 18 - 2 );
+ out[32] = value;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 2 ) % (1U << 18 ) ;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 18 - 6 );
+ out[40] = value;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 6 ) % (1U << 18 ) ;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 18 - 10 );
+ out[48] = value;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 10 ) % (1U << 18 ) ;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 18 - 14 );
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 14 ) % (1U << 18 ) ;
+
+ return;
+}
+
+static void
+extract_20 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 );
+ out[4] = value;
+
+ /* 02 */
+ out[8] = ( CONVERT(*in) >> 8 ) % (1U << 20 ) ;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 );
+ out[12] = value;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 );
+ out[16] = value;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 4 ) % (1U << 20 ) ;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 );
+ out[24] = value;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 12 ) % (1U << 20 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 );
+ out[36] = value;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 8 ) % (1U << 20 ) ;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 );
+ out[44] = value;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 );
+ out[48] = value;
+
+ /* 13 */
+ out[52] = ( CONVERT(*in) >> 4 ) % (1U << 20 ) ;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 );
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 12 ) % (1U << 20 ) ;
+
+ return;
+}
+
+static void
+extract_22 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 22 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 22 - 12 );
+ out[4] = value;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 22 - 2 );
+ out[8] = value;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 2 ) % (1U << 22 ) ;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 22 - 14 );
+ out[16] = value;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 22 - 4 );
+ out[20] = value;
+
+ /* 06 */
+ out[24] = value = ( CONVERT(*in) >> 4 ) % (1U << 22 ) ;
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 22 - 16 );
+ out[28] = value;
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 22 - 6 );
+ out[32] = value;
+
+ /* 09 */
+ out[36] = ( CONVERT(*in) >> 6 ) % (1U << 22 ) ;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 18 ))<<( 22 - 18 );
+ out[40] = value;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 22 - 8 );
+ out[44] = value;
+
+ /* 12 */
+ out[48] = ( CONVERT(*in) >> 8 ) % (1U << 22 ) ;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 22 - 20 );
+ out[52] = value;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 22 - 10 );
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 10 ) % (1U << 22 ) ;
+
+ return;
+}
+
+static void
+extract_24 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ out[4] = value;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ out[8] = value;
+
+ /* 03 */
+ out[12] = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+
+ /* 04 */
+ in += WORD_INCR;
+ out[16] = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ out[20] = value;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ out[24] = value;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ out[36] = value;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ out[40] = value;
+
+ /* 11 */
+ out[44] = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+
+ /* 12 */
+ in += WORD_INCR;
+ out[48] = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ out[52] = value;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+
+ return;
+}
+
+static void
+extract_26 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 26 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 26 - 20 );
+ out[4] = value;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 26 - 14 );
+ out[8] = value;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 26 - 8 );
+ out[12] = value;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 26 - 2 );
+ out[16] = value;
+
+ /* 05 */
+ out[20] = ( CONVERT(*in) >> 2 ) % (1U << 26 ) ;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 22 ))<<( 26 - 22 );
+ out[24] = value;
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 26 - 16 );
+ out[28] = value;
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 26 - 10 );
+ out[32] = value;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 26 - 4 );
+ out[36] = value;
+
+ /* 10 */
+ out[40] = ( CONVERT(*in) >> 4 ) % (1U << 26 ) ;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 26 - 24 );
+ out[44] = value;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 18 ))<<( 26 - 18 );
+ out[48] = value;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 26 - 12 );
+ out[52] = value;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 26 - 6 );
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 6 ) % (1U << 26 ) ;
+
+ return;
+}
+
+static void
+extract_28 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 28 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 );
+ out[4] = value;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 );
+ out[8] = value;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 );
+ out[12] = value;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 );
+ out[16] = value;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 );
+ out[20] = value;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 );
+ out[24] = value;
+
+ /* 07 */
+ out[28] = ( CONVERT(*in) >> 4 ) % (1U << 28 ) ;
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = ( CONVERT(*in) >> 0 ) % (1U << 28 ) ;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 );
+ out[36] = value;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 );
+ out[40] = value;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 );
+ out[44] = value;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 );
+ out[48] = value;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 );
+ out[52] = value;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 );
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 4 ) % (1U << 28 ) ;
+
+ return;
+}
+
+
+static void
+extract_30 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ out[0] = ( CONVERT(*in) >> 0 ) % (1U << 30 ) ;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 28 ))<<( 30 - 28 );
+ out[4] = value;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 26 ))<<( 30 - 26 );
+ out[8] = value;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 30 - 24 );
+ out[12] = value;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 22 ))<<( 30 - 22 );
+ out[16] = value;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 30 - 20 );
+ out[20] = value;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 18 ))<<( 30 - 18 );
+ out[24] = value;
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 30 - 16 );
+ out[28] = value;
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 30 - 14 );
+ out[32] = value;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 30 - 12 );
+ out[36] = value;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 30 - 10 );
+ out[40] = value;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 30 - 8 );
+ out[44] = value;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 30 - 6 );
+ out[48] = value;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 30 - 4 );
+ out[52] = value;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 30 - 2 );
+ out += WORD_INCR;
+ out[56] = value;
+
+ /* 15 */
+ out[60] = ( CONVERT(*in) >> 2 ) % (1U << 30 ) ;
+
+ return;
+}
+
+
+static void
+extract_32 (UINT4 *out, const UINT4 *in) {
+
+ /* 00 */
+ out[0] = CONVERT(*in);
+
+ /* 01 */
+ in += WORD_INCR;
+ out[4] = CONVERT(*in);
+
+ /* 02 */
+ in += WORD_INCR;
+ out[8] = CONVERT(*in);
+
+ /* 03 */
+ in += WORD_INCR;
+ out[12] = CONVERT(*in);
+
+ /* 04 */
+ in += WORD_INCR;
+ out[16] = CONVERT(*in);
+
+ /* 05 */
+ in += WORD_INCR;
+ out[20] = CONVERT(*in);
+
+ /* 06 */
+ in += WORD_INCR;
+ out[24] = CONVERT(*in);
+
+ /* 07 */
+ in += WORD_INCR;
+ out[28] = CONVERT(*in);
+
+ /* 08 */
+ in += WORD_INCR;
+ out[32] = CONVERT(*in);
+
+ /* 09 */
+ in += WORD_INCR;
+ out[36] = CONVERT(*in);
+
+ /* 10 */
+ in += WORD_INCR;
+ out[40] = CONVERT(*in);
+
+ /* 11 */
+ in += WORD_INCR;
+ out[44] = CONVERT(*in);
+
+ /* 12 */
+ in += WORD_INCR;
+ out[48] = CONVERT(*in);
+
+ /* 13 */
+ in += WORD_INCR;
+ out[52] = CONVERT(*in);
+
+ /* 14 */
+ in += WORD_INCR;
+ out[56] = CONVERT(*in);
+
+ /* 15 */
+ in += WORD_INCR;
+ out[60] = CONVERT(*in);
+
+ return;
+}
+
+
+typedef void (*Extractor_T) (UINT4 *, const UINT4 *);
+
+static Extractor_T extractor_table[17] =
+ {extract_00, extract_02, extract_04, extract_06,
+ extract_08, extract_10, extract_12, extract_14,
+ extract_16, extract_18, extract_20, extract_22,
+ extract_24, extract_26, extract_28, extract_30,
+ extract_32};
+
+void
+Bitpack64_extract_bitpack (UINT4 *out, int packsize, UINT4 *bitpack) {
+ int nregisters;
+
+ nregisters = packsize / 2;
+ (extractor_table[nregisters])(&(out[0]),&(bitpack[/*column*/0]));
+ (extractor_table[nregisters])(&(out[1]),&(bitpack[/*column*/1]));
+ (extractor_table[nregisters])(&(out[2]),&(bitpack[/*column*/2]));
+ (extractor_table[nregisters])(&(out[3]),&(bitpack[/*column*/3]));
+
+ return;
+}
diff --git a/src/bitpack64-access.h b/src/bitpack64-access.h
index 11a7597..7ba05c7 100644
--- a/src/bitpack64-access.h
+++ b/src/bitpack64-access.h
@@ -1,9 +1,22 @@
#ifndef BITPACK64_ACCESS_INCLUDED
#define BITPACK64_ACCESS_INCLUDED
#include "types.h"
+#include "bool.h"
/* For reading direct-coded bitstreams */
extern UINT4
-Bitpack64_access (UINT4 position, UINT4 *ptrs, UINT4 *comp);
+Bitpack64_access (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp);
+
+extern UINT4
+Bitpack64_access_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack);
+
+extern bool
+Bitpack64_access_filledp (Oligospace_T oligo, int packsize, UINT4 *bitpack);
+
+extern int
+Bitpack64_access_new_packsize (Oligospace_T oligo, int old_packsize, UINT4 *bitpack, int increment);
+
+extern void
+Bitpack64_extract_bitpack (UINT4 *out, int packsize, UINT4 *bitpack);
#endif
diff --git a/src/bitpack64-incr.c b/src/bitpack64-incr.c
new file mode 100644
index 0000000..1146aee
--- /dev/null
+++ b/src/bitpack64-incr.c
@@ -0,0 +1,10115 @@
+static char rcsid[] = "$Id: bitpack64-incr.c 180341 2015-12-07 18:29:40Z twu $";
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "bitpack64-incr.h"
+#include "bitpack64-access.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "mem.h"
+
+#ifdef WORDS_BIGENDIAN
+#include "bigendian.h"
+#define CONVERT(x) Bigendian_convert_uint(x)
+#else
+#define CONVERT(x) x
+#endif
+
+
+#define CHECK 1
+
+
+#ifdef DEBUG
+#define debug(x) x
+#else
+#define debug(x)
+#endif
+
+
+#define BLOCKSIZE 64
+
+/* Vertical access is slightly more efficient than horizontal */
+/* Choice needs to match that in bitpack64-access */
+
+#ifdef HORIZONTAL
+#define WORD_INCR 1 /* 1 for horizontal; 4 for vertical */
+#else
+#define WORD_INCR 4
+#endif
+
+
+#define BIT0 0x1;
+#define BIT2 0x4;
+#define BIT4 0x10;
+#define BIT6 0x40;
+#define BIT8 0x100;
+#define BIT10 0x400;
+#define BIT12 0x1000;
+#define BIT14 0x4000;
+#define BIT16 0x10000;
+#define BIT18 0x40000;
+#define BIT20 0x100000;
+#define BIT22 0x400000;
+#define BIT24 0x1000000;
+#define BIT26 0x4000000;
+#define BIT28 0x10000000;
+#define BIT30 0x40000000;
+
+
+
+static UINT4
+incr_00 (UINT4 *in) {
+ abort();
+ return 0U;
+}
+
+
+
+static UINT4
+incr_02_00 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 0 ) % (1U << 2 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_02_01 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 2 ) % (1U << 2 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_02_02 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 4 ) % (1U << 2 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_02_03 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 6 ) % (1U << 2 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+static UINT4
+incr_02_04 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 8 ) % (1U << 2 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_02_05 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 10 ) % (1U << 2 ) ;
+ *in += BIT10;
+ return prev;
+}
+
+static UINT4
+incr_02_06 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 12 ) % (1U << 2 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_02_07 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 14 ) % (1U << 2 ) ;
+ *in += BIT14;
+ return prev;
+}
+
+static UINT4
+incr_02_08 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 16 ) % (1U << 2 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_02_09 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 18 ) % (1U << 2 ) ;
+ *in += BIT18;
+ return prev;
+}
+
+static UINT4
+incr_02_10 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 20 ) % (1U << 2 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+static UINT4
+incr_02_11 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 22 ) % (1U << 2 ) ;
+ *in += BIT22;
+ return prev;
+}
+
+static UINT4
+incr_02_12 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 24 ) % (1U << 2 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_02_13 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 26 ) % (1U << 2 ) ;
+ *in += BIT26;
+ return prev;
+}
+
+static UINT4
+incr_02_14 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 28 ) % (1U << 2 ) ;
+ *in += BIT28;
+ return prev;
+}
+
+static UINT4
+incr_02_15 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 30 ) % (1U << 2 ) ;
+ *in += BIT30;
+ return prev;
+}
+
+
+
+static UINT4
+incr_04_00 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 0 ) % (1U << 4 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_04_01 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 4 ) % (1U << 4 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_04_02 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 8 ) % (1U << 4 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_04_03 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 12 ) % (1U << 4 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_04_04 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 16 ) % (1U << 4 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_04_05 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 20 ) % (1U << 4 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+static UINT4
+incr_04_06 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 24 ) % (1U << 4 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_04_07 (UINT4 *in) {
+ UINT4 prev = ( CONVERT(*in) >> 28 ) % (1U << 4 ) ;
+ *in += BIT28;
+ return prev;
+}
+
+static UINT4
+incr_04_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 4 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_04_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 4 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_04_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 4 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_04_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 4 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_04_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 4 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_04_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 4 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+static UINT4
+incr_04_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 4 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_04_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 4 ) ;
+ *in += BIT28;
+ return prev;
+}
+
+
+static UINT4
+incr_06_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 6 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_06_01 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 6 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+static UINT4
+incr_06_02 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 6 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_06_03 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 6 ) ;
+ *in += BIT18;
+ return prev;
+}
+
+static UINT4
+incr_06_04 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 6 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_06_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 6 ) ;
+ carry = ( (prev + 1) >> (6 - 4) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 6 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_06_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 6 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_06_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 6 ) ;
+ *in += BIT10;
+ return prev;
+}
+
+static UINT4
+incr_06_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 6 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_06_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 6 ) ;
+ *in += BIT22;
+ return prev;
+}
+
+static UINT4
+incr_06_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 6 ) ;
+ carry = ( (prev + 1) >> (6 - 2) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 6 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_06_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 6 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_06_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 6 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_06_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 6 ) ;
+ *in += BIT14;
+ return prev;
+}
+
+static UINT4
+incr_06_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 6 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+static UINT4
+incr_06_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 6 ) ;
+ *in += BIT26;
+ return prev;
+}
+
+
+static UINT4
+incr_08_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_08_01 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_08_02 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_08_03 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_08_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_08_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_08_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_08_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_08_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_08_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_08_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_08_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+static UINT4
+incr_08_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_08_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_08_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_08_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *in += BIT24;
+ return prev;
+}
+
+
+
+static UINT4
+incr_10_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 10 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_10_01 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 10 ) ;
+ *in += BIT10;
+ return prev;
+}
+
+static UINT4
+incr_10_02 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 10 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+static UINT4
+incr_10_03 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 10 ) ;
+ carry = ( (prev + 1) >> (10 - 8) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 10 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_10_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 10 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_10_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 10 ) ;
+ *in += BIT18;
+ return prev;
+}
+
+static UINT4
+incr_10_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 10 ) ;
+ carry = ( (prev + 1) >> (10 - 6) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 6 ))<<( 10 - 6 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_10_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 10 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+static UINT4
+incr_10_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 10 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_10_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 10 ) ;
+ carry = ( (prev + 1) >> (10 - 4) );
+ *in += BIT26;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 10 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_10_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 10 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_10_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 10 ) ;
+ *in += BIT14;
+ return prev;
+}
+
+static UINT4
+incr_10_12 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 10 ) ;
+ carry = ( (prev + 1) >> (10 - 2) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 10 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_10_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 10 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_10_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 10 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_10_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 10 ) ;
+ *in += BIT22;
+ return prev;
+}
+
+
+
+static UINT4
+incr_12_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_12_01 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 12 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_12_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ carry = ( (prev + 1) >> (12 - 4) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_12_03 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 12 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_12_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 12 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_12_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ carry = ( (prev + 1) >> (12 - 8));
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_12_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 12 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_12_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 12 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+static UINT4
+incr_12_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_12_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 12 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_12_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ carry = ( (prev + 1) >> (12 - 4) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_12_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 12 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_12_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 12 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_12_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ carry = ( (prev + 1) >> (12 - 8));
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_12_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 12 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_12_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 12 ) ;
+ *in += BIT20;
+ return prev;
+}
+
+
+static UINT4
+incr_14_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 14 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_14_01 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 14 ) ;
+ *in += BIT14;
+ return prev;
+}
+
+static UINT4
+incr_14_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 14 ) ;
+ carry = ( (prev + 1) >> (14 - 10) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 10 ))<<( 14 - 10 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_14_03 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 14 ) ;
+ *in += BIT10;
+ return prev;
+}
+
+static UINT4
+incr_14_04 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 14 ) ;
+ carry = ( (prev + 1) >> (14 - 6) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 6 ))<<( 14 - 6 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_14_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 14 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+static UINT4
+incr_14_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 14 ) ;
+ carry = ( (prev + 1) >> (14 - 2) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 14 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_14_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 14 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_14_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 14 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_14_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 14 ) ;
+ carry = ( (prev + 1) >> (14 - 12) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 14 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_14_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 14 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_14_11 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 14 ) ;
+ carry = ( (prev + 1) >> (14 - 8) );
+ *in += BIT26;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 14 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_14_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 14 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_14_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 14 ) ;
+ carry = ( (prev + 1) >> (14 - 4) );
+ *in += BIT22;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 14 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_14_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 14 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_14_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 14 ) ;
+ *in += BIT18;
+ return prev;
+}
+
+
+static UINT4
+incr_16_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_01 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_02 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_03 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+static UINT4
+incr_16_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_16_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *in += BIT16;
+ return prev;
+}
+
+
+static UINT4
+incr_18_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 18 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_18_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 4) );
+ *in += BIT18;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 18 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_02 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 18 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_18_03 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 8) );
+ *in += BIT22;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 18 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 18 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_18_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 12) );
+ *in += BIT26;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 18 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 18 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_18_07 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 16) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 18 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_08 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 2) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 18 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 18 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_18_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 6) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 6 ))<<( 18 - 6 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 18 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+static UINT4
+incr_18_12 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 10) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 10 ))<<( 18 - 10 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 18 ) ;
+ *in += BIT10;
+ return prev;
+}
+
+static UINT4
+incr_18_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 18 ) ;
+ carry = ( (prev + 1) >> (18 - 14) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 14 ))<<( 18 - 14 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_18_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 18 ) ;
+ *in += BIT14;
+ return prev;
+}
+
+
+static UINT4
+incr_20_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_20_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 8) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_02 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 20 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_20_03 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 16) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_04 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 4) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 20 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_20_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 12) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 20 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+static UINT4
+incr_20_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_20_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 8) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 20 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_20_11 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 16) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_12 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 4) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 20 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_20_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ carry = ( (prev + 1) >> (20 - 12) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_20_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 20 ) ;
+ *in += BIT12;
+ return prev;
+}
+
+
+static UINT4
+incr_22_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 22 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_22_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 12) );
+ *in += BIT22;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 22 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 2) );
+ *in += BIT12;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 22 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_03 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 22 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_22_04 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 14) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 14 ))<<( 22 - 14 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 4) );
+ *in += BIT14;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 22 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 22 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_22_07 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 16) );
+ *in += BIT26;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 22 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_08 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 6) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 6 ))<<( 22 - 6 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 22 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+static UINT4
+incr_22_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 18) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 18 ))<<( 22 - 18 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_11 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 8) );
+ *in += BIT18;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 22 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 22 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_22_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 20) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 20 ))<<( 22 - 20 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 22 ) ;
+ carry = ( (prev + 1) >> (22 - 10) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 10 ))<<( 22 - 10 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_22_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 22 ) ;
+ *in += BIT10;
+ return prev;
+}
+
+
+
+static UINT4
+incr_24_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_24_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 16) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 8) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_03 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_24_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_24_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 16) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 8) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_24_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_24_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 16) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 8) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+static UINT4
+incr_24_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_24_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 16) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + 1) >> (24 - 8) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_24_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *in += BIT8;
+ return prev;
+}
+
+
+
+static UINT4
+incr_26_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 26 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_26_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 20) );
+ *in += BIT26;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 20 ))<<( 26 - 20 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 14) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 14 ))<<( 26 - 14 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_03 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 8) );
+ *in += BIT14;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 26 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_04 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 2) );
+ *in += BIT8;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 26 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 26 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+static UINT4
+incr_26_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 22) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 22 ))<<( 26 - 22 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_07 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 16) );
+ *in += BIT22;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 26 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_08 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 10) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 10 ))<<( 26 - 10 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 4) );
+ *in += BIT10;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 26 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 26 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_26_11 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 24) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 24 ))<<( 26 - 24 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_12 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 18) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 18 ))<<( 26 - 18 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 12) );
+ *in += BIT18;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 26 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 26 ) ;
+ carry = ( (prev + 1) >> (26 - 6) );
+ *in += BIT12;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 6 ))<<( 26 - 6 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_26_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 26 ) ;
+ *in += BIT6;
+ return prev;
+}
+
+
+static UINT4
+incr_28_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 28 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_28_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 24) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 20) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_03 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 16) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_04 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 12) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 8) );
+ *in += BIT12;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 4) );
+ *in += BIT8;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 28 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+static UINT4
+incr_28_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 28 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_28_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 24) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 20) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_11 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 16) );
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_12 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 12) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 8) );
+ *in += BIT12;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ carry = ( (prev + 1) >> (28 - 4) );
+ *in += BIT8;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_28_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 13 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 28 ) ;
+ *in += BIT4;
+ return prev;
+}
+
+
+static UINT4
+incr_30_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = ( CONVERT(*in) >> 0 ) % (1U << 30 ) ;
+ *in += BIT0;
+ return prev;
+}
+
+static UINT4
+incr_30_01 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 28) );
+ *in += BIT30;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 28 ))<<( 30 - 28 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_02 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 26) );
+ *in += BIT28;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 26 ))<<( 30 - 26 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_03 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 24) );
+ *in += BIT26;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 24 ))<<( 30 - 24 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_04 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 22) );
+ *in += BIT24;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 22 ))<<( 30 - 22 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_05 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 20) );
+ *in += BIT22;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 20 ))<<( 30 - 20 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_06 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 18));
+ *in += BIT20;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 18 ))<<( 30 - 18 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_07 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 16) );
+ *in += BIT18;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 16 ))<<( 30 - 16 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_08 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 14) );
+ *in += BIT16;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 14 ))<<( 30 - 14 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_09 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 12) );
+ *in += BIT14;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 12 ))<<( 30 - 12 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_10 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 10) );
+ *in += BIT12;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 10 ))<<( 30 - 10 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_11 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 8) );
+ *in += BIT10;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 8 ))<<( 30 - 8 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_12 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 6) );
+ *in += BIT8;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 6 ))<<( 30 - 6 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_13 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 4) );
+ *in += BIT6;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 4 ))<<( 30 - 4 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_14 (UINT4 *in) {
+ UINT4 prev, carry;
+
+ in += 13 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 30 ) ;
+ carry = ( (prev + 1) >> (30 - 2) );
+ *in += BIT4;
+
+ in += 1 * WORD_INCR;
+ prev |= (CONVERT(*in) % (1U<< 2 ))<<( 30 - 2 );
+ *in += carry;
+
+ return prev;
+}
+
+static UINT4
+incr_30_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 14 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 2 ) % (1U << 30 ) ;
+ *in += BIT2;
+ return prev;
+}
+
+
+static UINT4
+incr_32_00 (UINT4 *in) {
+ UINT4 prev;
+
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_01 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 1 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_02 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 2 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_03 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 3 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_04 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 4 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_05 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 5 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_06 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 6 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+
+static UINT4
+incr_32_07 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 7 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_08 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 8 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_09 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 9 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_10 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 10 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_11 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 11 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_12 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 12 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_13 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 13 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_14 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 14 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+static UINT4
+incr_32_15 (UINT4 *in) {
+ UINT4 prev;
+
+ in += 15 * WORD_INCR;
+ prev = CONVERT(*in);
+ *in += 1;
+ return prev;
+}
+
+
+
+
+typedef UINT4 (*Incrementor_T) (UINT4 *);
+
+static Incrementor_T incrementor_table[272] =
+ {incr_00, incr_00, incr_00, incr_00,
+ incr_00, incr_00, incr_00, incr_00,
+ incr_00, incr_00, incr_00, incr_00,
+ incr_00, incr_00, incr_00, incr_00,
+
+ incr_02_00, incr_02_01, incr_02_02, incr_02_03,
+ incr_02_04, incr_02_05, incr_02_06, incr_02_07,
+ incr_02_08, incr_02_09, incr_02_10, incr_02_11,
+ incr_02_12, incr_02_13, incr_02_14, incr_02_15,
+
+ incr_04_00, incr_04_01, incr_04_02, incr_04_03,
+ incr_04_04, incr_04_05, incr_04_06, incr_04_07,
+ incr_04_08, incr_04_09, incr_04_10, incr_04_11,
+ incr_04_12, incr_04_13, incr_04_14, incr_04_15,
+
+ incr_06_00, incr_06_01, incr_06_02, incr_06_03,
+ incr_06_04, incr_06_05, incr_06_06, incr_06_07,
+ incr_06_08, incr_06_09, incr_06_10, incr_06_11,
+ incr_06_12, incr_06_13, incr_06_14, incr_06_15,
+
+ incr_08_00, incr_08_01, incr_08_02, incr_08_03,
+ incr_08_04, incr_08_05, incr_08_06, incr_08_07,
+ incr_08_08, incr_08_09, incr_08_10, incr_08_11,
+ incr_08_12, incr_08_13, incr_08_14, incr_08_15,
+
+ incr_10_00, incr_10_01, incr_10_02, incr_10_03,
+ incr_10_04, incr_10_05, incr_10_06, incr_10_07,
+ incr_10_08, incr_10_09, incr_10_10, incr_10_11,
+ incr_10_12, incr_10_13, incr_10_14, incr_10_15,
+
+ incr_12_00, incr_12_01, incr_12_02, incr_12_03,
+ incr_12_04, incr_12_05, incr_12_06, incr_12_07,
+ incr_12_08, incr_12_09, incr_12_10, incr_12_11,
+ incr_12_12, incr_12_13, incr_12_14, incr_12_15,
+
+ incr_14_00, incr_14_01, incr_14_02, incr_14_03,
+ incr_14_04, incr_14_05, incr_14_06, incr_14_07,
+ incr_14_08, incr_14_09, incr_14_10, incr_14_11,
+ incr_14_12, incr_14_13, incr_14_14, incr_14_15,
+
+ incr_16_00, incr_16_01, incr_16_02, incr_16_03,
+ incr_16_04, incr_16_05, incr_16_06, incr_16_07,
+ incr_16_08, incr_16_09, incr_16_10, incr_16_11,
+ incr_16_12, incr_16_13, incr_16_14, incr_16_15,
+
+ incr_18_00, incr_18_01, incr_18_02, incr_18_03,
+ incr_18_04, incr_18_05, incr_18_06, incr_18_07,
+ incr_18_08, incr_18_09, incr_18_10, incr_18_11,
+ incr_18_12, incr_18_13, incr_18_14, incr_18_15,
+
+ incr_20_00, incr_20_01, incr_20_02, incr_20_03,
+ incr_20_04, incr_20_05, incr_20_06, incr_20_07,
+ incr_20_08, incr_20_09, incr_20_10, incr_20_11,
+ incr_20_12, incr_20_13, incr_20_14, incr_20_15,
+
+ incr_22_00, incr_22_01, incr_22_02, incr_22_03,
+ incr_22_04, incr_22_05, incr_22_06, incr_22_07,
+ incr_22_08, incr_22_09, incr_22_10, incr_22_11,
+ incr_22_12, incr_22_13, incr_22_14, incr_22_15,
+
+ incr_24_00, incr_24_01, incr_24_02, incr_24_03,
+ incr_24_04, incr_24_05, incr_24_06, incr_24_07,
+ incr_24_08, incr_24_09, incr_24_10, incr_24_11,
+ incr_24_12, incr_24_13, incr_24_14, incr_24_15,
+
+ incr_26_00, incr_26_01, incr_26_02, incr_26_03,
+ incr_26_04, incr_26_05, incr_26_06, incr_26_07,
+ incr_26_08, incr_26_09, incr_26_10, incr_26_11,
+ incr_26_12, incr_26_13, incr_26_14, incr_26_15,
+
+ incr_28_00, incr_28_01, incr_28_02, incr_28_03,
+ incr_28_04, incr_28_05, incr_28_06, incr_28_07,
+ incr_28_08, incr_28_09, incr_28_10, incr_28_11,
+ incr_28_12, incr_28_13, incr_28_14, incr_28_15,
+
+ incr_30_00, incr_30_01, incr_30_02, incr_30_03,
+ incr_30_04, incr_30_05, incr_30_06, incr_30_07,
+ incr_30_08, incr_30_09, incr_30_10, incr_30_11,
+ incr_30_12, incr_30_13, incr_30_14, incr_30_15,
+
+ incr_32_00, incr_32_01, incr_32_02, incr_32_03,
+ incr_32_04, incr_32_05, incr_32_06, incr_32_07,
+ incr_32_08, incr_32_09, incr_32_10, incr_32_11,
+ incr_32_12, incr_32_13, incr_32_14, incr_32_15,
+ };
+
+
+
+static void
+add_00 (UINT4 *in, UINT4 increment) {
+ abort();
+ return;
+}
+
+
+
+static void
+add_02_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_02_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_02_02 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_02_03 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 6);
+ return;
+}
+
+static void
+add_02_04 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_02_05 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 10);
+ return;
+}
+
+static void
+add_02_06 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_02_07 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 14);
+ return;
+}
+
+static void
+add_02_08 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_02_09 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 18);
+ return;
+}
+
+static void
+add_02_10 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 20);
+ return;
+}
+
+static void
+add_02_11 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 22);
+ return;
+}
+
+static void
+add_02_12 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_02_13 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 26);
+ return;
+}
+
+static void
+add_02_14 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 28);
+ return;
+}
+
+static void
+add_02_15 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 30);
+ return;
+}
+
+
+static void
+add_04_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_04_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_04_02 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_04_03 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_04_04 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_04_05 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 20);
+ return;
+}
+
+static void
+add_04_06 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_04_07 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 28);
+ return;
+}
+
+static void
+add_04_08 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_04_09 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_04_10 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_04_11 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_04_12 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_04_13 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 20);
+ return;
+}
+
+static void
+add_04_14 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_04_15 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 28);
+ return;
+}
+
+
+static void
+add_06_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_06_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 6);
+ return;
+}
+
+static void
+add_06_02 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_06_03 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 18);
+ return;
+}
+
+static void
+add_06_04 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_06_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 6 ) ;
+ carry = ( (prev + increment) >> (6 - 4) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 6 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_06_06 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_06_07 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 10);
+ return;
+}
+
+static void
+add_06_08 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_06_09 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 22);
+ return;
+}
+
+static void
+add_06_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 6 ) ;
+ carry = ( (prev + increment) >> (6 - 2) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 6 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_06_11 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_06_12 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_06_13 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 14);
+ return;
+}
+
+static void
+add_06_14 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 20);
+ return;
+}
+
+static void
+add_06_15 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 26);
+ return;
+}
+
+
+static void
+add_08_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_08_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_08_02 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_08_03 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_08_04 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_08_05 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_08_06 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_08_07 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_08_08 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_08_09 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_08_10 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_08_11 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 24);
+ return;
+}
+
+static void
+add_08_12 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_08_13 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_08_14 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_08_15 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 24);
+ return;
+}
+
+
+
+static void
+add_10_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_10_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 10);
+ return;
+}
+
+static void
+add_10_02 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 20);
+ return;
+}
+
+static void
+add_10_03 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 10 ) ;
+ carry = ( (prev + increment) >> (10 - 8) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 10 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_10_04 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_10_05 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 18);
+ return;
+}
+
+static void
+add_10_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 10 ) ;
+ carry = ( (prev + increment) >> (10 - 6) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 6 ))<<( 10 - 6 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_10_07 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 6);
+ return;
+}
+
+static void
+add_10_08 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_10_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 10 ) ;
+ carry = ( (prev + increment) >> (10 - 4) );
+ *in += (increment << 26);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 10 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_10_10 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_10_11 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 14);
+ return;
+}
+
+static void
+add_10_12 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 10 ) ;
+ carry = ( (prev + increment) >> (10 - 2) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 10 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_10_13 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_10_14 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_10_15 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 22);
+ return;
+}
+
+
+
+static void
+add_12_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_12_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_12_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ carry = ( (prev + increment) >> (12 - 4) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_12_03 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_12_04 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_12_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ carry = ( (prev + increment) >> (12 - 8));
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_12_06 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_12_07 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 20);
+ return;
+}
+
+static void
+add_12_08 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_12_09 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_12_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ carry = ( (prev + increment) >> (12 - 4) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_12_11 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_12_12 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_12_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ carry = ( (prev + increment) >> (12 - 8));
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_12_14 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_12_15 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 20);
+ return;
+}
+
+
+static void
+add_14_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_14_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 14);
+ return;
+}
+
+static void
+add_14_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 14 ) ;
+ carry = ( (prev + increment) >> (14 - 10) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 10 ))<<( 14 - 10 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_14_03 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 10);
+ return;
+}
+
+static void
+add_14_04 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 14 ) ;
+ carry = ( (prev + increment) >> (14 - 6) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 6 ))<<( 14 - 6 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_14_05 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 6);
+ return;
+}
+
+static void
+add_14_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 14 ) ;
+ carry = ( (prev + increment) >> (14 - 2) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 14 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_14_07 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_14_08 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_14_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 14 ) ;
+ carry = ( (prev + increment) >> (14 - 12) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 14 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_14_10 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_14_11 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 14 ) ;
+ carry = ( (prev + increment) >> (14 - 8) );
+ *in += (increment << 26);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 14 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_14_12 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_14_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 14 ) ;
+ carry = ( (prev + increment) >> (14 - 4) );
+ *in += (increment << 22);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 14 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_14_14 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_14_15 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 18);
+ return;
+}
+
+
+static void
+add_16_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_01 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_02 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_03 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_04 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_05 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_06 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_07 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_08 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_09 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_10 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_11 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_12 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_13 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+static void
+add_16_14 (UINT4 *in, UINT4 increment) {
+ in += 7 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_16_15 (UINT4 *in, UINT4 increment) {
+ in += 7 * WORD_INCR;
+ *in += (increment << 16);
+ return;
+}
+
+
+static void
+add_18_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_18_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 4) );
+ *in += (increment << 18);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 18 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_02 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_18_03 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 8) );
+ *in += (increment << 22);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 18 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_04 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_18_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 12) );
+ *in += (increment << 26);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 18 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_06 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_18_07 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 16) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 18 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_08 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 2) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 18 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_09 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_18_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 6) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 6 ))<<( 18 - 6 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_11 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 6);
+ return;
+}
+
+static void
+add_18_12 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 10) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 10 ))<<( 18 - 10 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_13 (UINT4 *in, UINT4 increment) {
+ in += 7 * WORD_INCR;
+ *in += (increment << 10);
+ return;
+}
+
+static void
+add_18_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 18 ) ;
+ carry = ( (prev + increment) >> (18 - 14) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 14 ))<<( 18 - 14 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_18_15 (UINT4 *in, UINT4 increment) {
+ in += 8 * WORD_INCR;
+ *in += (increment << 14);
+ return;
+}
+
+
+static void
+add_20_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_20_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 8) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_02 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_20_03 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 16) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_04 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 4) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_05 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_20_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 12) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_07 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+static void
+add_20_08 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_20_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 8) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_10 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_20_11 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 16) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_12 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 4) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_13 (UINT4 *in, UINT4 increment) {
+ in += 8 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_20_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ carry = ( (prev + increment) >> (20 - 12) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_20_15 (UINT4 *in, UINT4 increment) {
+ in += 9 * WORD_INCR;
+ *in += (increment << 12);
+ return;
+}
+
+
+static void
+add_22_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_22_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 12) );
+ *in += (increment << 22);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 22 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 2) );
+ *in += (increment << 12);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 22 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_03 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_22_04 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 14) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 14 ))<<( 22 - 14 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 4) );
+ *in += (increment << 14);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 22 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_06 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_22_07 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 16) );
+ *in += (increment << 26);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 22 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_08 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 6) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 6 ))<<( 22 - 6 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_09 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 6);
+ return;
+}
+
+static void
+add_22_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 18) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 18 ))<<( 22 - 18 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_11 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 8) );
+ *in += (increment << 18);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 22 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_12 (UINT4 *in, UINT4 increment) {
+ in += 8 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_22_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 20) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 20 ))<<( 22 - 20 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 22 ) ;
+ carry = ( (prev + increment) >> (22 - 10) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 10 ))<<( 22 - 10 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_22_15 (UINT4 *in, UINT4 increment) {
+ in += 10 * WORD_INCR;
+ *in += (increment << 10);
+ return;
+}
+
+
+
+static void
+add_24_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_24_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 16) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 8) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_03 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_24_04 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_24_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 16) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 8) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_07 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_24_08 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_24_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 16) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 8) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_11 (UINT4 *in, UINT4 increment) {
+ in += 8 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+static void
+add_24_12 (UINT4 *in, UINT4 increment) {
+ in += 9 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_24_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 16) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev + increment) >> (24 - 8) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_24_15 (UINT4 *in, UINT4 increment) {
+ in += 11 * WORD_INCR;
+ *in += (increment << 8);
+ return;
+}
+
+
+
+static void
+add_26_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_26_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 20) );
+ *in += (increment << 26);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 20 ))<<( 26 - 20 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 14) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 14 ))<<( 26 - 14 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_03 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 8) );
+ *in += (increment << 14);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 26 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_04 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 2) );
+ *in += (increment << 8);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 26 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_05 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+static void
+add_26_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 22) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 22 ))<<( 26 - 22 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_07 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 16) );
+ *in += (increment << 22);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 26 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_08 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 10) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 10 ))<<( 26 - 10 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 4) );
+ *in += (increment << 10);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 26 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_10 (UINT4 *in, UINT4 increment) {
+ in += 8 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_26_11 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 24) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 24 ))<<( 26 - 24 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_12 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 18) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 18 ))<<( 26 - 18 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 12) );
+ *in += (increment << 18);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 26 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 26 ) ;
+ carry = ( (prev + increment) >> (26 - 6) );
+ *in += (increment << 12);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 6 ))<<( 26 - 6 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_26_15 (UINT4 *in, UINT4 increment) {
+ in += 12 * WORD_INCR;
+ *in += (increment << 6);
+ return;
+}
+
+
+static void
+add_28_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_28_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 24) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 20) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_03 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 16) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_04 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 12) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 8) );
+ *in += (increment << 12);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 4) );
+ *in += (increment << 8);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_07 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+static void
+add_28_08 (UINT4 *in, UINT4 increment) {
+ in += 7 * WORD_INCR;
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_28_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 24) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 20) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_11 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 16) );
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_12 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 12) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 8) );
+ *in += (increment << 12);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ carry = ( (prev + increment) >> (28 - 4) );
+ *in += (increment << 8);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_28_15 (UINT4 *in, UINT4 increment) {
+ in += 13 * WORD_INCR;
+ *in += (increment << 4);
+ return;
+}
+
+
+static void
+add_30_00 (UINT4 *in, UINT4 increment) {
+ *in += (increment << 0);
+ return;
+}
+
+static void
+add_30_01 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 28) );
+ *in += (increment << 30);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 28 ))<<( 30 - 28 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_02 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 26) );
+ *in += (increment << 28);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 26 ))<<( 30 - 26 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_03 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 24) );
+ *in += (increment << 26);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 24 ))<<( 30 - 24 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_04 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 22) );
+ *in += (increment << 24);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 22 ))<<( 30 - 22 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_05 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 20) );
+ *in += (increment << 22);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 20 ))<<( 30 - 20 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_06 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 18));
+ *in += (increment << 20);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 18 ))<<( 30 - 18 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_07 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 16) );
+ *in += (increment << 18);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 16 ))<<( 30 - 16 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_08 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 14) );
+ *in += (increment << 16);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 14 ))<<( 30 - 14 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_09 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 12) );
+ *in += (increment << 14);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 12 ))<<( 30 - 12 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_10 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 10) );
+ *in += (increment << 12);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 10 ))<<( 30 - 10 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_11 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 8) );
+ *in += (increment << 10);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 8 ))<<( 30 - 8 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_12 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 6) );
+ *in += (increment << 8);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 6 ))<<( 30 - 6 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_13 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 4) );
+ *in += (increment << 6);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 4 ))<<( 30 - 4 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_14 (UINT4 *in, UINT4 increment) {
+ UINT4 prev, carry;
+
+ in += 13 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 30 ) ;
+ carry = ( (prev + increment) >> (30 - 2) );
+ *in += (increment << 4);
+
+ in += 1 * WORD_INCR;
+ /* prev |= (CONVERT(*in) % (1U<< 2 ))<<( 30 - 2 ); */
+ *in += carry;
+
+ return;
+}
+
+static void
+add_30_15 (UINT4 *in, UINT4 increment) {
+ in += 14 * WORD_INCR;
+ *in += (increment << 2);
+ return;
+}
+
+
+static void
+add_32_00 (UINT4 *in, UINT4 increment) {
+ *in += increment;
+ return;
+}
+
+static void
+add_32_01 (UINT4 *in, UINT4 increment) {
+ in += 1 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_02 (UINT4 *in, UINT4 increment) {
+ in += 2 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_03 (UINT4 *in, UINT4 increment) {
+ in += 3 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_04 (UINT4 *in, UINT4 increment) {
+ in += 4 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_05 (UINT4 *in, UINT4 increment) {
+ in += 5 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_06 (UINT4 *in, UINT4 increment) {
+ in += 6 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_07 (UINT4 *in, UINT4 increment) {
+ in += 7 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_08 (UINT4 *in, UINT4 increment) {
+ in += 8 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_09 (UINT4 *in, UINT4 increment) {
+ in += 9 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_10 (UINT4 *in, UINT4 increment) {
+ in += 10 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_11 (UINT4 *in, UINT4 increment) {
+ in += 11 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_12 (UINT4 *in, UINT4 increment) {
+ in += 12 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_13 (UINT4 *in, UINT4 increment) {
+ in += 13 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_14 (UINT4 *in, UINT4 increment) {
+ in += 14 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+static void
+add_32_15 (UINT4 *in, UINT4 increment) {
+ in += 15 * WORD_INCR;
+ *in += increment;
+ return;
+}
+
+
+typedef void (*Adder_T) (UINT4 *, UINT4);
+
+static Adder_T adder_table[272] =
+ {add_00, add_00, add_00, add_00,
+ add_00, add_00, add_00, add_00,
+ add_00, add_00, add_00, add_00,
+ add_00, add_00, add_00, add_00,
+
+ add_02_00, add_02_01, add_02_02, add_02_03,
+ add_02_04, add_02_05, add_02_06, add_02_07,
+ add_02_08, add_02_09, add_02_10, add_02_11,
+ add_02_12, add_02_13, add_02_14, add_02_15,
+
+ add_04_00, add_04_01, add_04_02, add_04_03,
+ add_04_04, add_04_05, add_04_06, add_04_07,
+ add_04_08, add_04_09, add_04_10, add_04_11,
+ add_04_12, add_04_13, add_04_14, add_04_15,
+
+ add_06_00, add_06_01, add_06_02, add_06_03,
+ add_06_04, add_06_05, add_06_06, add_06_07,
+ add_06_08, add_06_09, add_06_10, add_06_11,
+ add_06_12, add_06_13, add_06_14, add_06_15,
+
+ add_08_00, add_08_01, add_08_02, add_08_03,
+ add_08_04, add_08_05, add_08_06, add_08_07,
+ add_08_08, add_08_09, add_08_10, add_08_11,
+ add_08_12, add_08_13, add_08_14, add_08_15,
+
+ add_10_00, add_10_01, add_10_02, add_10_03,
+ add_10_04, add_10_05, add_10_06, add_10_07,
+ add_10_08, add_10_09, add_10_10, add_10_11,
+ add_10_12, add_10_13, add_10_14, add_10_15,
+
+ add_12_00, add_12_01, add_12_02, add_12_03,
+ add_12_04, add_12_05, add_12_06, add_12_07,
+ add_12_08, add_12_09, add_12_10, add_12_11,
+ add_12_12, add_12_13, add_12_14, add_12_15,
+
+ add_14_00, add_14_01, add_14_02, add_14_03,
+ add_14_04, add_14_05, add_14_06, add_14_07,
+ add_14_08, add_14_09, add_14_10, add_14_11,
+ add_14_12, add_14_13, add_14_14, add_14_15,
+
+ add_16_00, add_16_01, add_16_02, add_16_03,
+ add_16_04, add_16_05, add_16_06, add_16_07,
+ add_16_08, add_16_09, add_16_10, add_16_11,
+ add_16_12, add_16_13, add_16_14, add_16_15,
+
+ add_18_00, add_18_01, add_18_02, add_18_03,
+ add_18_04, add_18_05, add_18_06, add_18_07,
+ add_18_08, add_18_09, add_18_10, add_18_11,
+ add_18_12, add_18_13, add_18_14, add_18_15,
+
+ add_20_00, add_20_01, add_20_02, add_20_03,
+ add_20_04, add_20_05, add_20_06, add_20_07,
+ add_20_08, add_20_09, add_20_10, add_20_11,
+ add_20_12, add_20_13, add_20_14, add_20_15,
+
+ add_22_00, add_22_01, add_22_02, add_22_03,
+ add_22_04, add_22_05, add_22_06, add_22_07,
+ add_22_08, add_22_09, add_22_10, add_22_11,
+ add_22_12, add_22_13, add_22_14, add_22_15,
+
+ add_24_00, add_24_01, add_24_02, add_24_03,
+ add_24_04, add_24_05, add_24_06, add_24_07,
+ add_24_08, add_24_09, add_24_10, add_24_11,
+ add_24_12, add_24_13, add_24_14, add_24_15,
+
+ add_26_00, add_26_01, add_26_02, add_26_03,
+ add_26_04, add_26_05, add_26_06, add_26_07,
+ add_26_08, add_26_09, add_26_10, add_26_11,
+ add_26_12, add_26_13, add_26_14, add_26_15,
+
+ add_28_00, add_28_01, add_28_02, add_28_03,
+ add_28_04, add_28_05, add_28_06, add_28_07,
+ add_28_08, add_28_09, add_28_10, add_28_11,
+ add_28_12, add_28_13, add_28_14, add_28_15,
+
+ add_30_00, add_30_01, add_30_02, add_30_03,
+ add_30_04, add_30_05, add_30_06, add_30_07,
+ add_30_08, add_30_09, add_30_10, add_30_11,
+ add_30_12, add_30_13, add_30_14, add_30_15,
+
+ add_32_00, add_32_01, add_32_02, add_32_03,
+ add_32_04, add_32_05, add_32_06, add_32_07,
+ add_32_08, add_32_09, add_32_10, add_32_11,
+ add_32_12, add_32_13, add_32_14, add_32_15,
+ };
+
+
+
+#if 0
+/* No need currently for a subtraction routine */
+
+static void
+sub_00 (UINT4 *in, UINT4 decrement) {
+ abort();
+ return;
+}
+
+
+
+static void
+sub_02_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_02_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_02_02 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_02_03 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 6);
+ return;
+}
+
+static void
+sub_02_04 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_02_05 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 10);
+ return;
+}
+
+static void
+sub_02_06 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_02_07 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 14);
+ return;
+}
+
+static void
+sub_02_08 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_02_09 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 18);
+ return;
+}
+
+static void
+sub_02_10 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 20);
+ return;
+}
+
+static void
+sub_02_11 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 22);
+ return;
+}
+
+static void
+sub_02_12 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_02_13 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 26);
+ return;
+}
+
+static void
+sub_02_14 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 28);
+ return;
+}
+
+static void
+sub_02_15 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 30);
+ return;
+}
+
+
+static void
+sub_04_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_04_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_04_02 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_04_03 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_04_04 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_04_05 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 20);
+ return;
+}
+
+static void
+sub_04_06 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_04_07 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 28);
+ return;
+}
+
+static void
+sub_04_08 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_04_09 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_04_10 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_04_11 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_04_12 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_04_13 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 20);
+ return;
+}
+
+static void
+sub_04_14 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_04_15 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 28);
+ return;
+}
+
+
+static void
+sub_06_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_06_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 6);
+ return;
+}
+
+static void
+sub_06_02 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_06_03 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 18);
+ return;
+}
+
+static void
+sub_06_04 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_06_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 6 ) ;
+ carry = ( (prev - decrement) >> (6 - 4) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 6 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_06_06 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_06_07 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 10);
+ return;
+}
+
+static void
+sub_06_08 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_06_09 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 22);
+ return;
+}
+
+static void
+sub_06_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 6 ) ;
+ carry = ( (prev - decrement) >> (6 - 2) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 6 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_06_11 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_06_12 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_06_13 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 14);
+ return;
+}
+
+static void
+sub_06_14 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 20);
+ return;
+}
+
+static void
+sub_06_15 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 26);
+ return;
+}
+
+
+static void
+sub_08_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_08_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_08_02 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_08_03 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_08_04 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_08_05 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_08_06 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_08_07 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_08_08 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_08_09 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_08_10 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_08_11 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 24);
+ return;
+}
+
+static void
+sub_08_12 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_08_13 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_08_14 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_08_15 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 24);
+ return;
+}
+
+
+
+static void
+sub_10_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_10_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 10);
+ return;
+}
+
+static void
+sub_10_02 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 20);
+ return;
+}
+
+static void
+sub_10_03 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 10 ) ;
+ carry = ( (prev - decrement) >> (10 - 8) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 10 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_10_04 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_10_05 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 18);
+ return;
+}
+
+static void
+sub_10_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 10 ) ;
+ carry = ( (prev - decrement) >> (10 - 6) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 10 - 6 )) + carry;
+
+ return;
+}
+
+static void
+sub_10_07 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 6);
+ return;
+}
+
+static void
+sub_10_08 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_10_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 10 ) ;
+ carry = ( (prev - decrement) >> (10 - 4) ) & 0x1;
+ *in -= (decrement << 26);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 10 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_10_10 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_10_11 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 14);
+ return;
+}
+
+static void
+sub_10_12 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 10 ) ;
+ carry = ( (prev - decrement) >> (10 - 2) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 10 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_10_13 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_10_14 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_10_15 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 22);
+ return;
+}
+
+
+
+static void
+sub_12_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_12_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_12_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ carry = ( (prev - decrement) >> (12 - 4) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 12 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_12_03 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_12_04 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_12_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ carry = ( (prev - decrement) >> (12 - 8)) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 12 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_12_06 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_12_07 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 20);
+ return;
+}
+
+static void
+sub_12_08 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_12_09 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_12_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ carry = ( (prev - decrement) >> (12 - 4) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 12 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_12_11 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_12_12 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_12_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ carry = ( (prev - decrement) >> (12 - 8)) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 12 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_12_14 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_12_15 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 20);
+ return;
+}
+
+
+static void
+sub_14_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_14_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 14);
+ return;
+}
+
+static void
+sub_14_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 14 ) ;
+ carry = ( (prev - decrement) >> (14 - 10) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 14 - 10 )) + carry;
+
+ return;
+}
+
+static void
+sub_14_03 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 10);
+ return;
+}
+
+static void
+sub_14_04 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 14 ) ;
+ carry = ( (prev - decrement) >> (14 - 6) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 14 - 6 )) + carry;
+
+ return;
+}
+
+static void
+sub_14_05 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 6);
+ return;
+}
+
+static void
+sub_14_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 14 ) ;
+ carry = ( (prev - decrement) >> (14 - 2) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 14 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_14_07 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_14_08 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_14_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 14 ) ;
+ carry = ( (prev - decrement) >> (14 - 12) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 14 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_14_10 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_14_11 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 14 ) ;
+ carry = ( (prev - decrement) >> (14 - 8) ) & 0x1;
+ *in -= (decrement << 26);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 14 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_14_12 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_14_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 14 ) ;
+ carry = ( (prev - decrement) >> (14 - 4) ) & 0x1;
+ *in -= (decrement << 22);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 14 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_14_14 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_14_15 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 18);
+ return;
+}
+
+
+static void
+sub_16_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_01 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_02 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_03 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_04 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_05 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_06 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_07 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_08 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_09 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_10 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_11 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_12 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_13 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+static void
+sub_16_14 (UINT4 *in, UINT4 decrement) {
+ in += 7 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_16_15 (UINT4 *in, UINT4 decrement) {
+ in += 7 * WORD_INCR;
+ *in -= (decrement << 16);
+ return;
+}
+
+
+static void
+sub_18_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_18_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 4) ) & 0x1;
+ *in -= (decrement << 18);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_02 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_18_03 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 8) ) & 0x1;
+ *in -= (decrement << 22);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_04 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_18_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 12) ) & 0x1;
+ *in -= (decrement << 26);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_06 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_18_07 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 16) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_08 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 2) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_09 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_18_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 6) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 6 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_11 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 6);
+ return;
+}
+
+static void
+sub_18_12 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 10) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 10 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_13 (UINT4 *in, UINT4 decrement) {
+ in += 7 * WORD_INCR;
+ *in -= (decrement << 10);
+ return;
+}
+
+static void
+sub_18_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 18 ) ;
+ carry = ( (prev - decrement) >> (18 - 14) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 18 - 14 )) + carry;
+
+ return;
+}
+
+static void
+sub_18_15 (UINT4 *in, UINT4 decrement) {
+ in += 8 * WORD_INCR;
+ *in -= (decrement << 14);
+ return;
+}
+
+
+static void
+sub_20_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_20_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 8) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_02 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_20_03 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 16) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_04 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 4) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_05 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_20_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 12) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_07 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+static void
+sub_20_08 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_20_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 8) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_10 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_20_11 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 16) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_12 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 4) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_13 (UINT4 *in, UINT4 decrement) {
+ in += 8 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_20_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ carry = ( (prev - decrement) >> (20 - 12) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 20 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_20_15 (UINT4 *in, UINT4 decrement) {
+ in += 9 * WORD_INCR;
+ *in -= (decrement << 12);
+ return;
+}
+
+
+static void
+sub_22_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_22_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 12) ) & 0x1;
+ *in -= (decrement << 22);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 2) ) & 0x1;
+ *in -= (decrement << 12);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_03 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_22_04 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 14) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 14 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 4) ) & 0x1;
+ *in -= (decrement << 14);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_06 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_22_07 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 16) ) & 0x1;
+ *in -= (decrement << 26);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_08 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 6) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 6 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_09 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 6);
+ return;
+}
+
+static void
+sub_22_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 18) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 18 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_11 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 8) ) & 0x1;
+ *in -= (decrement << 18);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_12 (UINT4 *in, UINT4 decrement) {
+ in += 8 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_22_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 20) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 20 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 22 ) ;
+ carry = ( (prev - decrement) >> (22 - 10) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 22 - 10 )) + carry;
+
+ return;
+}
+
+static void
+sub_22_15 (UINT4 *in, UINT4 decrement) {
+ in += 10 * WORD_INCR;
+ *in -= (decrement << 10);
+ return;
+}
+
+
+
+static void
+sub_24_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_24_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 16) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 8) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_03 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_24_04 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_24_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 16) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 8) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_07 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_24_08 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_24_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 16) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 8) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_11 (UINT4 *in, UINT4 decrement) {
+ in += 8 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+static void
+sub_24_12 (UINT4 *in, UINT4 decrement) {
+ in += 9 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_24_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 16) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ carry = ( (prev - decrement) >> (24 - 8) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 24 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_24_15 (UINT4 *in, UINT4 decrement) {
+ in += 11 * WORD_INCR;
+ *in -= (decrement << 8);
+ return;
+}
+
+
+
+static void
+sub_26_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_26_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 20) ) & 0x1;
+ *in -= (decrement << 26);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 20 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 14) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 14 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_03 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 8) ) & 0x1;
+ *in -= (decrement << 14);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_04 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 2) ) & 0x1;
+ *in -= (decrement << 8);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_05 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+static void
+sub_26_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 22) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 22 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_07 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 16) ) & 0x1;
+ *in -= (decrement << 22);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_08 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 10) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 10 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 4) ) & 0x1;
+ *in -= (decrement << 10);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_10 (UINT4 *in, UINT4 decrement) {
+ in += 8 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_26_11 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 24) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 24 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_12 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 18) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 18 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 12) ) & 0x1;
+ *in -= (decrement << 18);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 26 ) ;
+ carry = ( (prev - decrement) >> (26 - 6) ) & 0x1;
+ *in -= (decrement << 12);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 26 - 6 )) + carry;
+
+ return;
+}
+
+static void
+sub_26_15 (UINT4 *in, UINT4 decrement) {
+ in += 12 * WORD_INCR;
+ *in -= (decrement << 6);
+ return;
+}
+
+
+static void
+sub_28_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_28_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 24) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 24 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 20) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 20 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_03 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 16) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_04 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 12) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 8) ) & 0x1;
+ *in -= (decrement << 12);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 4) ) & 0x1;
+ *in -= (decrement << 8);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_07 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+static void
+sub_28_08 (UINT4 *in, UINT4 decrement) {
+ in += 7 * WORD_INCR;
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_28_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 24) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 24 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 20) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 20 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_11 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 16) ) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_12 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 12) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 8) ) & 0x1;
+ *in -= (decrement << 12);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ carry = ( (prev - decrement) >> (28 - 4) ) & 0x1;
+ *in -= (decrement << 8);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 28 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_28_15 (UINT4 *in, UINT4 decrement) {
+ in += 13 * WORD_INCR;
+ *in -= (decrement << 4);
+ return;
+}
+
+
+static void
+sub_30_00 (UINT4 *in, UINT4 decrement) {
+ *in -= (decrement << 0);
+ return;
+}
+
+static void
+sub_30_01 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ prev = ( CONVERT(*in) >> 30 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 28) ) & 0x1;
+ *in -= (decrement << 30);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 28 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_02 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 1 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 28 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 26) ) & 0x1;
+ *in -= (decrement << 28);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 26 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_03 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 2 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 26 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 24) ) & 0x1;
+ *in -= (decrement << 26);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 24 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_04 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 3 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 24 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 22) ) & 0x1;
+ *in -= (decrement << 24);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 22 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_05 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 4 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 22 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 20) ) & 0x1;
+ *in -= (decrement << 22);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 20 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_06 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 5 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 20 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 18)) & 0x1;
+ *in -= (decrement << 20);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 18 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_07 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 6 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 18 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 16) ) & 0x1;
+ *in -= (decrement << 18);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 16 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_08 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 7 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 16 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 14) ) & 0x1;
+ *in -= (decrement << 16);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 14 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_09 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 8 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 14 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 12) ) & 0x1;
+ *in -= (decrement << 14);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 12 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_10 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 9 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 12 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 10) ) & 0x1;
+ *in -= (decrement << 12);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 10 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_11 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 10 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 10 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 8) ) & 0x1;
+ *in -= (decrement << 10);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 8 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_12 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 11 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 8 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 6) ) & 0x1;
+ *in -= (decrement << 8);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 6 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_13 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 12 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 6 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 4) ) & 0x1;
+ *in -= (decrement << 6);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 4 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_14 (UINT4 *in, UINT4 decrement) {
+ UINT4 prev, carry;
+
+ in += 13 * WORD_INCR;
+ prev = ( CONVERT(*in) >> 4 ) % (1U << 30 ) ;
+ carry = ( (prev - decrement) >> (30 - 2) ) & 0x1;
+ *in -= (decrement << 4);
+
+ in += 1 * WORD_INCR;
+ *in -= (decrement >> ( 30 - 2 )) + carry;
+
+ return;
+}
+
+static void
+sub_30_15 (UINT4 *in, UINT4 decrement) {
+ in += 14 * WORD_INCR;
+ *in -= (decrement << 2);
+ return;
+}
+
+
+static void
+sub_32_00 (UINT4 *in, UINT4 decrement) {
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_01 (UINT4 *in, UINT4 decrement) {
+ in += 1 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_02 (UINT4 *in, UINT4 decrement) {
+ in += 2 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_03 (UINT4 *in, UINT4 decrement) {
+ in += 3 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_04 (UINT4 *in, UINT4 decrement) {
+ in += 4 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_05 (UINT4 *in, UINT4 decrement) {
+ in += 5 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_06 (UINT4 *in, UINT4 decrement) {
+ in += 6 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_07 (UINT4 *in, UINT4 decrement) {
+ in += 7 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_08 (UINT4 *in, UINT4 decrement) {
+ in += 8 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_09 (UINT4 *in, UINT4 decrement) {
+ in += 9 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_10 (UINT4 *in, UINT4 decrement) {
+ in += 10 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_11 (UINT4 *in, UINT4 decrement) {
+ in += 11 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_12 (UINT4 *in, UINT4 decrement) {
+ in += 12 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_13 (UINT4 *in, UINT4 decrement) {
+ in += 13 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_14 (UINT4 *in, UINT4 decrement) {
+ in += 14 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+static void
+sub_32_15 (UINT4 *in, UINT4 decrement) {
+ in += 15 * WORD_INCR;
+ *in -= decrement;
+ return;
+}
+
+
+typedef void (*Subtractor_T) (UINT4 *, UINT4);
+
+static Subtractor_T subtractor_table[272] =
+ {sub_00, sub_00, sub_00, sub_00,
+ sub_00, sub_00, sub_00, sub_00,
+ sub_00, sub_00, sub_00, sub_00,
+ sub_00, sub_00, sub_00, sub_00,
+
+ sub_02_00, sub_02_01, sub_02_02, sub_02_03,
+ sub_02_04, sub_02_05, sub_02_06, sub_02_07,
+ sub_02_08, sub_02_09, sub_02_10, sub_02_11,
+ sub_02_12, sub_02_13, sub_02_14, sub_02_15,
+
+ sub_04_00, sub_04_01, sub_04_02, sub_04_03,
+ sub_04_04, sub_04_05, sub_04_06, sub_04_07,
+ sub_04_08, sub_04_09, sub_04_10, sub_04_11,
+ sub_04_12, sub_04_13, sub_04_14, sub_04_15,
+
+ sub_06_00, sub_06_01, sub_06_02, sub_06_03,
+ sub_06_04, sub_06_05, sub_06_06, sub_06_07,
+ sub_06_08, sub_06_09, sub_06_10, sub_06_11,
+ sub_06_12, sub_06_13, sub_06_14, sub_06_15,
+
+ sub_08_00, sub_08_01, sub_08_02, sub_08_03,
+ sub_08_04, sub_08_05, sub_08_06, sub_08_07,
+ sub_08_08, sub_08_09, sub_08_10, sub_08_11,
+ sub_08_12, sub_08_13, sub_08_14, sub_08_15,
+
+ sub_10_00, sub_10_01, sub_10_02, sub_10_03,
+ sub_10_04, sub_10_05, sub_10_06, sub_10_07,
+ sub_10_08, sub_10_09, sub_10_10, sub_10_11,
+ sub_10_12, sub_10_13, sub_10_14, sub_10_15,
+
+ sub_12_00, sub_12_01, sub_12_02, sub_12_03,
+ sub_12_04, sub_12_05, sub_12_06, sub_12_07,
+ sub_12_08, sub_12_09, sub_12_10, sub_12_11,
+ sub_12_12, sub_12_13, sub_12_14, sub_12_15,
+
+ sub_14_00, sub_14_01, sub_14_02, sub_14_03,
+ sub_14_04, sub_14_05, sub_14_06, sub_14_07,
+ sub_14_08, sub_14_09, sub_14_10, sub_14_11,
+ sub_14_12, sub_14_13, sub_14_14, sub_14_15,
+
+ sub_16_00, sub_16_01, sub_16_02, sub_16_03,
+ sub_16_04, sub_16_05, sub_16_06, sub_16_07,
+ sub_16_08, sub_16_09, sub_16_10, sub_16_11,
+ sub_16_12, sub_16_13, sub_16_14, sub_16_15,
+
+ sub_18_00, sub_18_01, sub_18_02, sub_18_03,
+ sub_18_04, sub_18_05, sub_18_06, sub_18_07,
+ sub_18_08, sub_18_09, sub_18_10, sub_18_11,
+ sub_18_12, sub_18_13, sub_18_14, sub_18_15,
+
+ sub_20_00, sub_20_01, sub_20_02, sub_20_03,
+ sub_20_04, sub_20_05, sub_20_06, sub_20_07,
+ sub_20_08, sub_20_09, sub_20_10, sub_20_11,
+ sub_20_12, sub_20_13, sub_20_14, sub_20_15,
+
+ sub_22_00, sub_22_01, sub_22_02, sub_22_03,
+ sub_22_04, sub_22_05, sub_22_06, sub_22_07,
+ sub_22_08, sub_22_09, sub_22_10, sub_22_11,
+ sub_22_12, sub_22_13, sub_22_14, sub_22_15,
+
+ sub_24_00, sub_24_01, sub_24_02, sub_24_03,
+ sub_24_04, sub_24_05, sub_24_06, sub_24_07,
+ sub_24_08, sub_24_09, sub_24_10, sub_24_11,
+ sub_24_12, sub_24_13, sub_24_14, sub_24_15,
+
+ sub_26_00, sub_26_01, sub_26_02, sub_26_03,
+ sub_26_04, sub_26_05, sub_26_06, sub_26_07,
+ sub_26_08, sub_26_09, sub_26_10, sub_26_11,
+ sub_26_12, sub_26_13, sub_26_14, sub_26_15,
+
+ sub_28_00, sub_28_01, sub_28_02, sub_28_03,
+ sub_28_04, sub_28_05, sub_28_06, sub_28_07,
+ sub_28_08, sub_28_09, sub_28_10, sub_28_11,
+ sub_28_12, sub_28_13, sub_28_14, sub_28_15,
+
+ sub_30_00, sub_30_01, sub_30_02, sub_30_03,
+ sub_30_04, sub_30_05, sub_30_06, sub_30_07,
+ sub_30_08, sub_30_09, sub_30_10, sub_30_11,
+ sub_30_12, sub_30_13, sub_30_14, sub_30_15,
+
+ sub_32_00, sub_32_01, sub_32_02, sub_32_03,
+ sub_32_04, sub_32_05, sub_32_06, sub_32_07,
+ sub_32_08, sub_32_09, sub_32_10, sub_32_11,
+ sub_32_12, sub_32_13, sub_32_14, sub_32_15,
+ };
+#endif
+
+
+
+
+
+#define DIRECT_METAINFO_SIZE 1
+
+/* Vertical */
+UINT4
+Bitpack64_incr (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp) {
+ UINT4 *info, start;
+ int nwritten, remainder;
+ UINT4 *bitpack;
+ int index, column;
+#ifdef CHECK
+ UINT4 prev, value;
+ int packsize, i;
+#endif
+
+ info = &(ptrs[oligo/BLOCKSIZE * DIRECT_METAINFO_SIZE]);
+
+#ifdef WORDS_BIGENDIAN
+ start = Bigendian_convert_uint(info[0]);
+ bitpack = (UINT4 *) &(comp[start*4]);
+ nwritten = Bigendian_convert_uint(info[1]) - start; /* In 128-bit registers */
+#else
+ start = info[0];
+ bitpack = (UINT4 *) &(comp[start*4]);
+ nwritten = info[1] - start; /* In 128-bit registers */
+#endif
+
+ remainder = oligo % BLOCKSIZE;
+ index = nwritten*16 + remainder/4;
+ column = remainder % 4;
+
+#ifdef CHECK
+ prev = Bitpack64_access(oligo,ptrs,comp);
+ value = (incrementor_table[index])(&(bitpack[column]));
+ if (value != prev || Bitpack64_access(oligo,ptrs,comp) != prev + 1) {
+ packsize = nwritten*2;
+ printf("Error at Bitpack64_incr with oligo %llu, packsize %d, remainder %d, column %d, index %d\n",
+ oligo,packsize,remainder,column,index);
+ printf("bitpack:\n");
+ for (i = 0; i < nwritten*4; i += 4) {
+ printf("%08X %08X %08X %08X\n",bitpack[i],bitpack[i+1],bitpack[i+2],bitpack[i+3]);
+ }
+ printf("\n");
+ abort();
+ }
+ return value;
+#else
+ return (incrementor_table[index])(&(bitpack[column]));
+#endif
+
+}
+
+
+UINT4
+Bitpack64_incr_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack) {
+ int nregisters, remainder;
+ int index, column;
+#ifdef CHECK
+ UINT4 prev, value;
+#endif
+
+ nregisters = packsize / 2;
+ remainder = oligo % BLOCKSIZE;
+ index = nregisters*16 + remainder/4;
+ column = remainder % 4;
+
+#ifdef CHECK
+ prev = Bitpack64_access_bitpack(oligo,packsize,bitpack);
+ value = (incrementor_table[index])(&(bitpack[column]));
+ if (value != prev || Bitpack64_access_bitpack(oligo,packsize,bitpack) != prev + 1) {
+ printf("Error at Bitpack64_incr_bitpack with oligo %llu, packsize %d, remainder %d, column %d, index %d\n",
+ oligo,packsize,remainder,column,index);
+ abort();
+ }
+ return value;
+#else
+ return (incrementor_table[index])(&(bitpack[column]));
+#endif
+}
+
+
+void
+Bitpack64_add (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp, UINT4 increment) {
+ UINT4 *info, start;
+ int nwritten, remainder;
+ UINT4 *bitpack;
+ int index, column;
+#ifdef CHECK
+ UINT4 prev;
+ int packsize, i;
+#endif
+
+ info = &(ptrs[oligo/BLOCKSIZE * DIRECT_METAINFO_SIZE]);
+
+#ifdef WORDS_BIGENDIAN
+ start = Bigendian_convert_uint(info[0]);
+ bitpack = (UINT4 *) &(comp[start*4]);
+ nwritten = Bigendian_convert_uint(info[1]) - start; /* In 128-bit registers */
+#else
+ start = info[0];
+ bitpack = (UINT4 *) &(comp[start*4]);
+ nwritten = info[1] - start; /* In 128-bit registers */
+#endif
+
+ remainder = oligo % BLOCKSIZE;
+ index = nwritten*16 + remainder/4;
+ column = remainder % 4;
+
+#ifdef CHECK
+ prev = Bitpack64_access(oligo,ptrs,comp);
+ (adder_table[index])(&(bitpack[column]),increment);
+ if (Bitpack64_access(oligo,ptrs,comp) != prev + increment) {
+ packsize = nwritten*2;
+ printf("Error at Bitpack64_add with oligo %llu, packsize %d, remainder %d, column %d, index %d\n",
+ oligo,packsize,remainder,column,index);
+ printf("bitpack:\n");
+ for (i = 0; i < nwritten*4; i += 4) {
+ printf("%08X %08X %08X %08X\n",bitpack[i],bitpack[i+1],bitpack[i+2],bitpack[i+3]);
+ }
+ printf("\n");
+ abort();
+ }
+#else
+ (adder_table[index])(&(bitpack[column]),increment);
+#endif
+
+ return;
+}
+
+
+
+/* Assumes that increment > 0 */
+void
+Bitpack64_add_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack, UINT4 increment) {
+ int nregisters, remainder;
+ int index, column;
+#ifdef CHECK
+ UINT4 prev;
+#endif
+
+ nregisters = packsize / 2;
+ remainder = oligo % BLOCKSIZE;
+ index = nregisters*16 + remainder/4;
+ column = remainder % 4;
+
+#ifdef CHECK
+ prev = Bitpack64_access_bitpack(oligo,packsize,bitpack);
+ (adder_table[index])(&(bitpack[column]),increment);
+ if (Bitpack64_access_bitpack(oligo,packsize,bitpack) != prev + increment) {
+ printf("Error at Bitpack64_add_bitpack with oligo %llu, packsize %d, remainder %d, column %d, index %d\n",
+ oligo,packsize,remainder,column,index);
+ abort();
+ }
+#else
+ (adder_table[index])(&(bitpack[column]),increment);
+#endif
+
+ return;
+}
+
+
+
+
+#if 0
+/* No need currently for a subtraction routine */
+
+void
+Bitpack64_sub_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack, UINT4 decrement) {
+ int nregisters, remainder;
+ int index, column;
+#ifdef CHECK
+ UINT4 prev;
+#endif
+
+ nregisters = packsize / 2;
+ remainder = oligo % BLOCKSIZE;
+ index = nregisters*16 + remainder/4;
+ column = remainder % 4;
+
+#ifdef CHECK
+ prev = Bitpack64_access_bitpack(oligo,packsize,bitpack);
+ (subtractor_table[index])(&(bitpack[column]),decrement);
+ if (Bitpack64_access_bitpack(oligo,packsize,bitpack) != prev - decrement) {
+ printf("Error at Bitpack64_sub_bitpack with oligo %llu, packsize %d, remainder %d, column %d, index %d\n",
+ oligo,packsize,remainder,column,index);
+ abort();
+ }
+#else
+ (subtractor_table[index])(&(bitpack[column]),decrement);
+#endif
+
+ return;
+}
+#endif
+
+
+static void
+transfer_00_02 (UINT4 *out, const UINT4 *in) {
+ return;
+}
+
+static void
+transfer_02_04 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 2 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 2 ) ;
+ *out |= (value << 4);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 2 ) ;
+ *out |= (value << 8);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 2 ) ;
+ *out |= (value << 12);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 2 ) ;
+ *out |= (value << 16);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 2 ) ;
+ *out |= (value << 20);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 2 ) ;
+ *out |= (value << 24);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 2 ) ;
+ *out |= (value << 28);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 2 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 2 ) ;
+ *out |= (value << 4);
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 2 ) ;
+ *out |= (value << 8);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 2 ) ;
+ *out |= (value << 12);
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 2 ) ;
+ *out |= (value << 16);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 2 ) ;
+ *out |= (value << 20);
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 2 ) ;
+ *out |= (value << 24);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 2 ) ;
+ *out |= (value << 28);
+
+ return;
+}
+
+static void
+transfer_04_06 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 4 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 4 ) ;
+ *out |= (value << 6);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 4 ) ;
+ *out |= (value << 12);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 4 ) ;
+ *out |= (value << 18);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 4 ) ;
+ *out |= (value << 24);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 4 ) ;
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (6 - 4));
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 4 ) ;
+ *out |= (value << 4);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 4 ) ;
+ *out |= (value << 10);
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 4 ) ;
+ *out |= (value << 16);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 4 ) ;
+ *out |= (value << 22);
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 4 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (6 - 2));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 4 ) ;
+ *out |= (value << 2);
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 4 ) ;
+ *out |= (value << 8);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 4 ) ;
+ *out |= (value << 14);
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 4 ) ;
+ *out |= (value << 20);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 4 ) ;
+ *out |= (value << 26);
+
+ return;
+}
+
+
+static void
+transfer_06_08 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 6 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 6 ) ;
+ *out |= (value << 8);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 6 ) ;
+ *out |= (value << 16);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 6 ) ;
+ *out |= (value << 24);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 6 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 6 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 6 - 4 );
+ *out |= (value << 8);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 6 ) ;
+ *out |= (value << 16);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 6 ) ;
+ *out |= (value << 24);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 6 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 6 ) ;
+ *out |= (value << 8);
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 6 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 6 - 2 );
+ *out |= (value << 16);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 6 ) ;
+ *out |= (value << 24);
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 6 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 6 ) ;
+ *out |= (value << 8);
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 6 ) ;
+ *out |= (value << 16);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 6 ) ;
+ *out |= (value << 24);
+
+ return;
+}
+
+
+static void
+transfer_08_10 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *out |= (value << 10);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *out |= (value << 20);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (10 - 8));
+
+ /* 04 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *out |= (value << 8);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *out |= (value << 18);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (10 - 6));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *out |= (value << 6);
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *out |= (value << 16);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *out |= (value << 26);
+ out += WORD_INCR;
+ *out |= (value >> (10 - 4));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *out |= (value << 4);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *out |= (value << 14);
+
+ /* 12 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 8 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (10 - 2));
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 8 ) ;
+ *out |= (value << 2);
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 8 ) ;
+ *out |= (value << 12);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 8 ) ;
+ *out |= (value << 22);
+
+ return;
+}
+
+static void
+transfer_10_12 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 10 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 10 ) ;
+ *out |= (value << 12);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 10 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (12 - 4));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 10 - 8 );
+ *out |= (value << 4);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 10 ) ;
+ *out |= (value << 16);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 10 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (12 - 8));
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 10 - 6 );
+ *out |= (value << 8);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 10 ) ;
+ *out |= (value << 20);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 10 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 10 - 4 );
+ *out |= (value << 12);
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 10 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (12 - 4));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 10 ) ;
+ *out |= (value << 4);
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 10 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 10 - 2 );
+ *out |= (value << 16);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 10 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (12 - 8));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 10 ) ;
+ *out |= (value << 8);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 10 ) ;
+ *out |= (value << 20);
+
+ return;
+}
+
+static void
+transfer_12_14 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 12 ) ;
+ *out |= (value << 14);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 );
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (14 - 10));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 12 ) ;
+ *out |= (value << 10);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 12 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (14 - 6));
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 );
+ *out |= (value << 6);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 12 ) ;
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (14 - 2));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 12 ) ;
+ *out |= (value << 2);
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 12 ) ;
+ *out |= (value << 16);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 12 ) ;
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (14 - 12));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 12 - 4 );
+ *out |= (value << 12);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 12 ) ;
+ *out |= (value << 26);
+ out += WORD_INCR;
+ *out |= (value >> (14 - 8));
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 12 ) ;
+ *out |= (value << 8);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 12 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 12 - 8 );
+ *out |= (value << 22);
+ out += WORD_INCR;
+ *out |= (value >> (14 - 4));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 12 ) ;
+ *out |= (value << 4);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 12 ) ;
+ *out |= (value << 18);
+
+ return;
+}
+
+
+static void
+transfer_14_16 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 14 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 14 ) ;
+ *out |= (value << 16);
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 14 - 10 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 14 ) ;
+ *out |= (value << 16);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 14 - 6 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 14 ) ;
+ *out |= (value << 16);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 14 - 2 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 14 ) ;
+ *out |= (value << 16);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 14 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 14 - 12 );
+ *out |= (value << 16);
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 14 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 14 - 8 );
+ *out |= (value << 16);
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 14 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 14 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 14 - 4 );
+ *out |= (value << 16);
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 14 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 14 ) ;
+ *out |= (value << 16);
+
+ return;
+}
+
+static void
+transfer_16_18 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 18);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 4));
+
+ /* 02 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 4);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 22);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 8));
+
+ /* 04 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 8);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 26);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 12));
+
+ /* 06 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 12);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 16));
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 2));
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 2);
+
+ /* 10 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 6));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 6);
+
+ /* 12 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 10));
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 10);
+
+ /* 14 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 16 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (18 - 14));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 16 ) ;
+ *out |= (value << 14);
+
+ return;
+}
+
+
+static void
+transfer_18_20 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 18 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 18 - 4 );
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 8));
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 18 ) ;
+ *out |= (value << 8);
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 18 - 8 );
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 16));
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 18 ) ;
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 4));
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 18 - 12 );
+ *out |= (value << 4);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 18 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 12));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 18 - 16 );
+ *out |= (value << 12);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 18 - 2 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 18 ) ;
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 8));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 18 - 6 );
+ *out |= (value << 8);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 18 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 16));
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 18 - 10 );
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 4));
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 18 ) ;
+ *out |= (value << 4);
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 18 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 18 - 14 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (20 - 12));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 18 ) ;
+ *out |= (value << 12);
+
+ return;
+}
+
+static void
+transfer_20_22 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 );
+ *out |= (value << 22);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 12));
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 20 ) ;
+ *out |= (value << 12);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 2));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 );
+ *out |= (value << 2);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 14));
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 20 ) ;
+ *out |= (value << 14);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 4));
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 );
+ *out |= (value << 4);
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 20 ) ;
+ *out |= (value << 26);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 16));
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 20 ) ;
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 6));
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 20 - 8 );
+ *out |= (value << 6);
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 20 ) ;
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 18));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 20 - 16 );
+ *out |= (value << 18);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 8));
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 20 - 4 );
+ *out |= (value << 8);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 20 ) ;
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 20));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 20 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 20 - 12 );
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (22 - 10));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 20 ) ;
+ *out |= (value << 10);
+
+ return;
+}
+
+static void
+transfer_22_24 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 22 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 22 - 12 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 16));
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 22 - 2 );
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 8));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 22 ) ;
+ *out |= (value << 8);
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 22 - 14 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 22 - 4 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 16));
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 22 ) ;
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 8));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 22 - 16 );
+ *out |= (value << 8);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 22 - 6 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 22 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 16));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 18 ))<<( 22 - 18 );
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 8));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 22 - 8 );
+ *out |= (value << 16);
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 22 ) ;
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 22 - 20 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 16));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 22 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 22 - 10 );
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (24 - 8));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 22 ) ;
+ *out |= (value << 8);
+
+ return;
+}
+
+static void
+transfer_24_26 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *out |= (value << 26);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 20));
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 14));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *out |= (value << 14);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 8));
+
+ /* 04 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *out |= (value << 8);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 2));
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *out |= (value << 2);
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 22));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *out |= (value << 22);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 16));
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 10));
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *out |= (value << 10);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 4));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *out |= (value << 4);
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 24));
+
+ /* 12 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 24 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 18));
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 24 - 16 );
+ *out |= (value << 18);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 12));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 24 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 24 - 8 );
+ *out |= (value << 12);
+ out += WORD_INCR;
+ *out |= (value >> (26 - 6));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 24 ) ;
+ *out |= (value << 6);
+
+ return;
+}
+
+static void
+transfer_26_28 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 26 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 26 - 20 );
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 24));
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 26 - 14 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 20));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 26 - 8 );
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 16));
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 26 - 2 );
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 8));
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 26 ) ;
+ *out |= (value << 12);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 8));
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 22 ))<<( 26 - 22 );
+ *out |= (value << 8);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 4));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 26 - 16 );
+ *out |= (value << 4);
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 26 - 10 );
+ out += WORD_INCR;
+ *out |= (value << 0);
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 26 - 4 );
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 24));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 26 ) ;
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 20));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 26 - 24 );
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 16));
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 18 ))<<( 26 - 18 );
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 12));
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 26 - 12 );
+ *out |= (value << 12);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 8));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 26 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 26 - 6 );
+ *out |= (value << 8);
+ out += WORD_INCR;
+ *out |= (value >> (28 - 4));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 26 ) ;
+ *out |= (value << 4);
+
+ return;
+}
+
+static void
+transfer_28_30 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 28 ) ;
+ *out |= (value << 0);
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 );
+ *out |= (value << 30);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 28));
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 );
+ *out |= (value << 28);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 26));
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 );
+ *out |= (value << 26);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 24));
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 );
+ *out |= (value << 24);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 22));
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 );
+ *out |= (value << 22);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 20));
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 );
+ *out |= (value << 20);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 18));
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 28 ) ;
+ *out |= (value << 18);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 16));
+
+ /* 08 */
+ in += WORD_INCR;
+ value = ( CONVERT(*in) >> 0 ) % (1U << 28 ) ;
+ *out |= (value << 16);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 14));
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 28 - 24 );
+ *out |= (value << 14);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 12));
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 28 - 20 );
+ *out |= (value << 12);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 10));
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 28 - 16 );
+ *out |= (value << 10);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 8));
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 28 - 12 );
+ *out |= (value << 8);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 6));
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 28 - 8 );
+ *out |= (value << 6);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 4));
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 28 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 28 - 4 );
+ *out |= (value << 4);
+ out += WORD_INCR;
+ *out |= (value >> (30 - 2));
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 28 ) ;
+ *out |= (value << 2);
+
+ return;
+}
+
+
+static void
+transfer_30_32 (UINT4 *out, const UINT4 *in) {
+ UINT4 value;
+
+ /* 00 */
+ value = ( CONVERT(*in) >> 0 ) % (1U << 30 ) ;
+ *out |= value;
+
+ /* 01 */
+ value = ( CONVERT(*in) >> 30 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 28 ))<<( 30 - 28 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 02 */
+ value = ( CONVERT(*in) >> 28 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 26 ))<<( 30 - 26 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 03 */
+ value = ( CONVERT(*in) >> 26 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 24 ))<<( 30 - 24 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 04 */
+ value = ( CONVERT(*in) >> 24 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 22 ))<<( 30 - 22 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 05 */
+ value = ( CONVERT(*in) >> 22 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 20 ))<<( 30 - 20 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 06 */
+ value = ( CONVERT(*in) >> 20 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 18 ))<<( 30 - 18 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 07 */
+ value = ( CONVERT(*in) >> 18 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 16 ))<<( 30 - 16 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 08 */
+ value = ( CONVERT(*in) >> 16 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 14 ))<<( 30 - 14 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 09 */
+ value = ( CONVERT(*in) >> 14 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 12 ))<<( 30 - 12 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 10 */
+ value = ( CONVERT(*in) >> 12 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 10 ))<<( 30 - 10 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 11 */
+ value = ( CONVERT(*in) >> 10 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 8 ))<<( 30 - 8 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 12 */
+ value = ( CONVERT(*in) >> 8 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 6 ))<<( 30 - 6 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 13 */
+ value = ( CONVERT(*in) >> 6 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 4 ))<<( 30 - 4 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 14 */
+ value = ( CONVERT(*in) >> 4 ) % (1U << 30 ) ;
+ in += WORD_INCR;
+ value |= (CONVERT(*in) % (1U<< 2 ))<<( 30 - 2 );
+ out += WORD_INCR;
+ *out |= value;
+
+ /* 15 */
+ value = ( CONVERT(*in) >> 2 ) % (1U << 30 ) ;
+ out += WORD_INCR;
+ *out |= value;
+
+ return;
+}
+
+
+
+typedef void (*Transfer_T) (UINT4 *, const UINT4 *);
+
+static Transfer_T transfer_table[16] =
+ {transfer_00_02, transfer_02_04, transfer_04_06, transfer_06_08,
+ transfer_08_10, transfer_10_12, transfer_12_14, transfer_14_16,
+ transfer_16_18, transfer_18_20, transfer_20_22, transfer_22_24,
+ transfer_24_26, transfer_26_28, transfer_28_30, transfer_30_32};
+
+UINT4 *
+Bitpack64_realloc_one (int packsize, UINT4 *bitpack) {
+ UINT4 *new;
+ int nregisters;
+#ifdef CHECK
+ int i;
+#endif
+
+ new = (UINT4 *) CALLOC((packsize + 2) / 2 * 4,sizeof(UINT4));
+
+ nregisters = packsize/2;
+ (transfer_table[nregisters])(&(new[/*column*/0]),&(bitpack[/*column*/0]));
+ (transfer_table[nregisters])(&(new[/*column*/1]),&(bitpack[/*column*/1]));
+ (transfer_table[nregisters])(&(new[/*column*/2]),&(bitpack[/*column*/2]));
+ (transfer_table[nregisters])(&(new[/*column*/3]),&(bitpack[/*column*/3]));
+
+#ifdef CHECK
+ for (i = 0; i < 64; i++) {
+ if (Bitpack64_access_bitpack(i,packsize+2,new) != Bitpack64_access_bitpack(i,packsize,bitpack)) {
+ fprintf(stderr,"Difference in packsize %d -> %d, index %d: %u != %u\n",
+ packsize,packsize+2,i,
+ Bitpack64_access_bitpack(i,packsize,bitpack),
+ Bitpack64_access_bitpack(i,packsize+2,new));
+ abort();
+ }
+ }
+#endif
+
+ FREE(bitpack);
+ return new;
+}
+
+
+UINT4 *
+Bitpack64_realloc_multiple (int old_packsize, int new_packsize, UINT4 *bitpack) {
+ UINT4 *new;
+ int nregisters, packsize;
+#ifdef CHECK
+ int i;
+#endif
+
+ for (packsize = old_packsize; packsize < new_packsize; packsize += 2) {
+ new = (UINT4 *) CALLOC((packsize + 2) / 2 * 4,sizeof(UINT4));
+
+ nregisters = packsize/2;
+ (transfer_table[nregisters])(&(new[/*column*/0]),&(bitpack[/*column*/0]));
+ (transfer_table[nregisters])(&(new[/*column*/1]),&(bitpack[/*column*/1]));
+ (transfer_table[nregisters])(&(new[/*column*/2]),&(bitpack[/*column*/2]));
+ (transfer_table[nregisters])(&(new[/*column*/3]),&(bitpack[/*column*/3]));
+
+#ifdef CHECK
+ for (i = 0; i < 64; i++) {
+ if (Bitpack64_access_bitpack(i,packsize+2,new) != Bitpack64_access_bitpack(i,packsize,bitpack)) {
+ fprintf(stderr,"Difference in packsize %d -> %d, index %d: %u != %u\n",
+ packsize,packsize+2,i,
+ Bitpack64_access_bitpack(i,packsize,bitpack),
+ Bitpack64_access_bitpack(i,packsize+2,new));
+ abort();
+ }
+ }
+#endif
+
+ FREE(bitpack);
+ bitpack = new;
+ }
+
+ return bitpack;
+}
+
diff --git a/src/bitpack64-incr.h b/src/bitpack64-incr.h
new file mode 100644
index 0000000..90f4506
--- /dev/null
+++ b/src/bitpack64-incr.h
@@ -0,0 +1,29 @@
+#ifndef BITPACK64_INCR_INCLUDED
+#define BITPACK64_INCR_INCLUDED
+#include "types.h"
+
+/* For reading direct-coded bitstreams. Horizontal format. */
+extern UINT4
+Bitpack64_incr (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp);
+
+extern UINT4
+Bitpack64_incr_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack);
+
+extern void
+Bitpack64_add (Oligospace_T oligo, UINT4 *ptrs, UINT4 *comp, UINT4 increment);
+
+extern void
+Bitpack64_add_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack, UINT4 increment);
+
+#if 0
+extern void
+Bitpack64_sub_bitpack (Oligospace_T oligo, int packsize, UINT4 *bitpack, UINT4 decrement);
+#endif
+
+extern UINT4 *
+Bitpack64_realloc_one (int packsize, UINT4 *bitpack);
+
+extern UINT4 *
+Bitpack64_realloc_multiple (int old_packsize, int new_packsize, UINT4 *bitpack);
+
+#endif
diff --git a/src/bitpack64-read.c b/src/bitpack64-read.c
index d611400..d6b1025 100644
--- a/src/bitpack64-read.c
+++ b/src/bitpack64-read.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: bitpack64-read.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: bitpack64-read.c 184374 2016-02-16 23:39:06Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -13769,8 +13769,8 @@ static Unpacker_T unpacker_table[17][17] =
/* bitpackpages: A list of b-mers (12-mers by default), ending with -1U */
UINT4
-Bitpack64_offsetptr (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
- Storedoligomer_T bmer;
+Bitpack64_offsetptr (UINT4 *end0, Oligospace_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
+ Oligospace_T bmer;
UINT4 *info, nwritten, packsize_div2;
int delta, remainder0, remainder1, quarter_block_0, quarter_block_1, column, row;
#ifdef HAVE_SSE2
@@ -14076,9 +14076,9 @@ Bitpack64_offsetptr (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UI
/* bitpackpages: A list of b-mers (12-mers by default), ending with -1U */
UINT8
-Bitpack64_offsetptr_huge (UINT8 *end0, Storedoligomer_T oligo,
+Bitpack64_offsetptr_huge (UINT8 *end0, Oligospace_T oligo,
UINT4 *bitpackpages, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
- Storedoligomer_T bmer;
+ Oligospace_T bmer;
UINT4 *info, nwritten;
UINT8 offset0, offset1;
UINT4 packsize_div2;
@@ -14405,9 +14405,9 @@ Bitpack64_offsetptr_huge (UINT8 *end0, Storedoligomer_T oligo,
#if 0
/* bitpackpages: A list of b-mers (12-mers by default), ending with -1U */
UINT4
-Bitpack64_offsetptr_paired (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
+Bitpack64_offsetptr_paired (UINT4 *end0, Oligospace_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
UINT4 ptr0;
- Storedoligomer_T bmer;
+ Oligospace_T bmer;
UINT4 *info, nwritten, packsize_div2;
int delta, remainder, quarter_block, column, row;
#ifdef HAVE_SSE2
@@ -14660,10 +14660,10 @@ Bitpack64_offsetptr_paired (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackp
/* Needed for poly-T to avoid computing on metablock after the last
one to find end0 */
UINT4
-Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
- Storedoligomer_T bmer;
+Bitpack64_read_one (Oligospace_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
+ Oligospace_T bmer;
UINT4 *info, nwritten, packsize_div2;
- int delta, remainder, quarter_block, column, row;
+ int delta, remainder, column, row;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
UINT4 ptr;
UINT4 diffs[BLOCKSIZE+1], *bitpack;
@@ -14677,6 +14677,7 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
#ifdef BRANCH_FREE_QTR_BLOCK
UINT4 psums[4];
#endif
+ int quarter_block;
__m128i *bitpack;
UINT4 *_diffs;
#endif
@@ -14708,14 +14709,17 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
#endif
remainder = oligo % BLOCKSIZE;
- quarter_block = remainder / 16;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
- /* Unpack all 64 diffs for non-SIMD */
- (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
+ if (remainder == 0) {
+#ifdef WORDS_BIGENDIAN
+ ptr = Bigendian_convert_uint(/*offset0*/info[1]);
+#else
+ ptr = /*offset0*/info[1];
+#endif
- if (remainder <= 16) {
+ } else if (remainder <= 16) {
#ifdef WORDS_BIGENDIAN
ptr = Bigendian_convert_uint(/*offset0*/info[1]);
#else
@@ -14727,6 +14731,8 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
row = get_row(delta);
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 1, i = 0; i <= row; k += BLOCKSIZE/4, i++) {
debug(printf("Adding diffs[%d] = %u\n",k,diffs[k]));
ptr += diffs[k];
@@ -14744,6 +14750,8 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
row = get_row(delta);
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 1, i = 0; i < 4; k += BLOCKSIZE/4, i++) {
debug(printf("Adding diffs[%d] = %u\n",k,diffs[k]));
ptr += diffs[k];
@@ -14766,6 +14774,8 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
row = get_row(delta);
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 9, i = 0; i < 4; k += BLOCKSIZE/4, i++) {
debug(printf("Subtracting diffs[%d] = %u\n",k,diffs[k]));
ptr -= diffs[k];
@@ -14788,6 +14798,8 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
row = get_row(delta);
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 9, i = 0; i <= row; k += BLOCKSIZE/4, i++) {
debug(printf("Subtracting diffs[%d] = %u\n",k,diffs[k]));
ptr -= diffs[k];
@@ -14813,6 +14825,7 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
#else
+ quarter_block = remainder / 16;
if (quarter_block <= 1) {
delta = remainder - 1;
column = get_column(delta);
@@ -14848,13 +14861,12 @@ Bitpack64_read_one (Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackco
/* Needed for poly-T to avoid computing on metablock after the last
one to find end0 */
UINT8
-Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
+Bitpack64_read_one_huge (Oligospace_T oligo, UINT4 *bitpackpages,
UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
UINT4 *pageptr;
- Storedoligomer_T bmer;
+ Oligospace_T bmer;
UINT4 *info, nwritten, packsize_div2;
- UINT8 offset0, offset1;
- int delta, remainder, quarter_block, column, row;
+ int remainder, column, row;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
UINT8 ptr;
UINT4 diffs[BLOCKSIZE+1], *bitpack;
@@ -14868,16 +14880,20 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
#ifdef BRANCH_FREE_QTR_BLOCK
UINT8 psums[4];
#endif
+ UINT8 offset0, offset1;
+ int delta, quarter_block;
__m128i *bitpack;
UINT4 *_diffs;
#endif
+#if defined(DEBUG) || defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
int i;
+#endif
bmer = oligo/BLOCKSIZE;
info = &(bitpackptrs[bmer * DIFFERENTIAL_METAINFO_SIZE]);
- debug(printf("Entered Bitpack64_read_one_huge with oligo %u => bmer %u\n",oligo,bmer));
+ debug(printf("Entered Bitpack64_read_one_huge with oligo %llu => bmer %u\n",oligo,bmer));
#ifdef WORDS_BIGENDIAN
nwritten = Bigendian_convert_uint(info[0]); /* In 128-bit registers */
@@ -14906,18 +14922,28 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
#endif
remainder = oligo % BLOCKSIZE;
- quarter_block = remainder / 16;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
- /* Unpack all 64 diffs for non-SIMD */
- (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
-
- if ((remainder = oligo % BLOCKSIZE) == 0) {
+ if (remainder == 0) {
#ifdef WORDS_BIGENDIAN
ptr = Bigendian_convert_uint(/*offset0*/info[1]);
+ if (bitpackpages != NULL) {
+ pageptr = bitpackpages;
+ while (bmer >= Bigendian_convert_uint(*pageptr)) {
+ ptr += POSITIONS_PAGE;
+ pageptr++;
+ }
+ }
#else
- ptr = /*offset0*/info[1];
+ ptr = /*offset0*/ (UINT8) info[1];
+ if (bitpackpages != NULL) {
+ pageptr = bitpackpages;
+ while (bmer >= *pageptr) {
+ ptr += POSITIONS_PAGE;
+ pageptr++;
+ }
+ }
#endif
} else if (remainder <= 16) {
@@ -14925,16 +14951,16 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
ptr = Bigendian_convert_uint(/*offset0*/info[1]);
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= Bigendian_convert_uint(*pageptr)) {
+ while (bmer >= Bigendian_convert_uint(*pageptr)) {
ptr += POSITIONS_PAGE;
pageptr++;
}
}
#else
- ptr = /*offset0*/info[1];
+ ptr = /*offset0*/ (UINT8) info[1];
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= *pageptr) {
+ while (bmer >= *pageptr) {
ptr += POSITIONS_PAGE;
pageptr++;
}
@@ -14945,6 +14971,8 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
row = (remainder - 1) / 4;
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 1, i = 0; i <= row; k += BLOCKSIZE/4, i++) {
debug(printf("Adding diffs[%d] = %u\n",k,diffs[k]));
ptr += diffs[k];
@@ -14955,16 +14983,16 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
ptr = Bigendian_convert_uint(/*offset0*/info[1]);
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= Bigendian_convert_uint(*pageptr)) {
+ while (bmer >= Bigendian_convert_uint(*pageptr)) {
ptr += POSITIONS_PAGE;
pageptr++;
}
}
#else
- ptr = /*offset0*/info[1];
+ ptr = /*offset0*/ (UINT8) info[1];
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= *pageptr) {
+ while (bmer >= *pageptr) {
ptr += POSITIONS_PAGE;
pageptr++;
}
@@ -14975,6 +15003,8 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
row = (remainder - 1) / 4;
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 1, i = 0; i < 4; k += BLOCKSIZE/4, i++) {
debug(printf("Adding diffs[%d] = %u\n",k,diffs[k]));
ptr += diffs[k];
@@ -14990,16 +15020,16 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
ptr = Bigendian_convert_uint(/*offset1*/info[DIFFERENTIAL_METAINFO_SIZE+1]);
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= Bigendian_convert_uint(*pageptr)) {
+ while (bmer + 1 >= Bigendian_convert_uint(*pageptr)) {
ptr += POSITIONS_PAGE;
pageptr++;
}
}
#else
- ptr = /*offset1*/info[DIFFERENTIAL_METAINFO_SIZE+1];
+ ptr = /*offset1*/ (UINT8) info[DIFFERENTIAL_METAINFO_SIZE+1];
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= *pageptr) {
+ while (bmer + 1 >= *pageptr) {
ptr += POSITIONS_PAGE;
pageptr++;
}
@@ -15010,6 +15040,8 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
row = (63 - remainder) / 4;
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 9, i = 0; i < 4; k += BLOCKSIZE/4, i++) {
debug(printf("Subtracting diffs[%d] = %u\n",k,diffs[k]));
ptr -= diffs[k];
@@ -15025,16 +15057,16 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
ptr = Bigendian_convert_uint(/*offset1*/info[DIFFERENTIAL_METAINFO_SIZE+1]);
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= Bigendian_convert_uint(*pageptr)) {
+ while (bmer + 1 >= Bigendian_convert_uint(*pageptr)) {
ptr += POSITIONS_PAGE;
pageptr++;
}
}
#else
- ptr = /*offset1*/info[DIFFERENTIAL_METAINFO_SIZE+1];
+ ptr = /*offset1*/(UINT8) info[DIFFERENTIAL_METAINFO_SIZE+1];
if (bitpackpages != NULL) {
pageptr = bitpackpages;
- while (bmer+1 >= *pageptr) {
+ while (bmer + 1 >= *pageptr) {
ptr += POSITIONS_PAGE;
pageptr++;
}
@@ -15045,6 +15077,8 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
row = (63 - remainder) / 4;
debug(printf("column %d, row %d\n",column,row));
+ /* Unpack all 64 diffs for non-SIMD */
+ (unpacker_all_table[packsize_div2*2])(&(diffs[1]),bitpack);
for (k = column*2 + 9, i = 0; i <= row; k += BLOCKSIZE/4, i++) {
debug(printf("Subtracting diffs[%d] = %u\n",k,diffs[k]));
ptr -= diffs[k];
@@ -15055,6 +15089,7 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
#else /* littleendian and SSE2 */
_diffs = (UINT4 *) diffs; /* Assumes a dummy register in diffs[0] */
+ quarter_block = remainder / 16;
#ifdef BRANCH_FREE_QTR_BLOCK
if (bitpackpages == NULL) {
@@ -15165,10 +15200,9 @@ Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
}
-#ifndef PMAP
/* Unpack all offsets. Can treat offset0 as a special case */
void
-Bitpack64_block_offsets (UINT4 *offsets, Storedoligomer_T oligo,
+Bitpack64_block_offsets (UINT4 *offsets, Oligospace_T oligo,
UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
UINT4 *info, nwritten;
UINT4 offset0, offset1, temp;
@@ -15318,18 +15352,16 @@ Bitpack64_block_offsets (UINT4 *offsets, Storedoligomer_T oligo,
return;
}
-#endif
-#ifndef PMAP
#if defined(HAVE_64_BIT) && (defined(UTILITYP) || defined(LARGE_GENOMES))
/* Unpack all offsets. Can treat offset0 as a special case */
void
-Bitpack64_block_offsets_huge (UINT8 *offsets, Storedoligomer_T oligo,
+Bitpack64_block_offsets_huge (UINT8 *offsets, Oligospace_T oligo,
UINT4 *bitpackpages, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
UINT4 *pageptr;
UINT4 *info, nwritten;
- Storedoligomer_T bmer;
+ Oligospace_T bmer;
UINT8 offset0, offset1, temp;
int packsize, k;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
@@ -15508,4 +15540,3 @@ Bitpack64_block_offsets_huge (UINT8 *offsets, Storedoligomer_T oligo,
return;
}
#endif
-#endif
diff --git a/src/bitpack64-read.h b/src/bitpack64-read.h
index f42f9eb..2a40624 100644
--- a/src/bitpack64-read.h
+++ b/src/bitpack64-read.h
@@ -9,26 +9,22 @@
/* For reading differential-coded bitstreams */
extern UINT4
-Bitpack64_read_one (Storedoligomer_T oligo,
+Bitpack64_read_one (Oligospace_T oligo,
UINT4 *bitpackptrs, UINT4 *bitpackcomp);
extern UINT8
-Bitpack64_read_one_huge (Storedoligomer_T oligo, UINT4 *bitpackpages,
+Bitpack64_read_one_huge (Oligospace_T oligo, UINT4 *bitpackpages,
UINT4 *bitpackptrs, UINT4 *bitpackcomp);
-#ifndef PMAP
extern void
-Bitpack64_block_offsets (UINT4 *offsets, Storedoligomer_T oligo,
+Bitpack64_block_offsets (UINT4 *offsets, Oligospace_T oligo,
UINT4 *bitpackptrs, UINT4 *bitpackcomp);
-#endif
-#ifndef PMAP
#if defined(HAVE_64_BIT) && (defined(UTILITYP) || defined(LARGE_GENOMES))
extern void
-Bitpack64_block_offsets_huge (UINT8 *offsets, Storedoligomer_T oligo,
+Bitpack64_block_offsets_huge (UINT8 *offsets, Oligospace_T oligo,
UINT4 *bitpackpages, UINT4 *bitpackptrs, UINT4 *bitpackcomp);
#endif
-#endif
#endif
diff --git a/src/bitpack64-readtwo.c b/src/bitpack64-readtwo.c
index 5e143e9..b4ad85b 100644
--- a/src/bitpack64-readtwo.c
+++ b/src/bitpack64-readtwo.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: bitpack64-readtwo.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: bitpack64-readtwo.c 184456 2016-02-18 00:05:04Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -126,6 +126,7 @@ unpack_00 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_00 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i total = _mm_set1_epi32(0U);
@@ -141,6 +142,7 @@ unpack_00 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
/* Handles the case where remainder == 64 => column 3, row -1 */
static void
@@ -353,6 +355,7 @@ unpack_02 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_02_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -392,6 +395,7 @@ unpack_02_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_02_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -592,6 +596,7 @@ unpack_02_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_02_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -633,6 +638,7 @@ unpack_02_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_02_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -1037,6 +1043,7 @@ unpack_04 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_04_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -1076,6 +1083,7 @@ unpack_04_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_04_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -1273,6 +1281,7 @@ unpack_04_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
}
+#if 0
static void
unpack_04_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -1314,6 +1323,7 @@ unpack_04_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_04_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -1777,6 +1787,7 @@ unpack_06 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_06_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -1819,6 +1830,7 @@ unpack_06_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_06_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -2025,6 +2037,7 @@ unpack_06_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_06_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -2069,6 +2082,7 @@ unpack_06_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_06_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -2492,6 +2506,7 @@ unpack_08 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_08_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -2533,6 +2548,7 @@ unpack_08_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_08_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -2741,6 +2757,7 @@ unpack_08_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
}
+#if 0
static void
unpack_08_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -2786,6 +2803,7 @@ unpack_08_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_08_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -3283,6 +3301,7 @@ unpack_10 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_10_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -3328,6 +3347,7 @@ unpack_10_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_10_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -3551,6 +3571,7 @@ unpack_10_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_10_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -3600,6 +3621,7 @@ unpack_10_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_10_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -4115,6 +4137,7 @@ unpack_12 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_12_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -4160,6 +4183,7 @@ unpack_12_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_12_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -4384,6 +4408,7 @@ unpack_12_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_12_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -4433,6 +4458,7 @@ unpack_12_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_12_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -4958,6 +4984,7 @@ unpack_14 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_14_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -5006,6 +5033,7 @@ unpack_14_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_14_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -5247,6 +5275,7 @@ unpack_14_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_14_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -5299,6 +5328,7 @@ unpack_14_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_14_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -5759,6 +5789,7 @@ unpack_16 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_16_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -5804,6 +5835,7 @@ unpack_16_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_16_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -6035,6 +6067,7 @@ unpack_16_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_16_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -6084,6 +6117,7 @@ unpack_16_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_16_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -6628,6 +6662,7 @@ unpack_18 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_18_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -6679,6 +6714,7 @@ unpack_18_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_18_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -6917,6 +6953,7 @@ unpack_18_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_18_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -6972,6 +7009,7 @@ unpack_18_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_18_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -7546,6 +7584,7 @@ unpack_20 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_20_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -7597,6 +7636,7 @@ unpack_20_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_20_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -7846,6 +7886,7 @@ unpack_20_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_20_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -7900,6 +7941,7 @@ unpack_20_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_20_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -8474,6 +8516,7 @@ unpack_22 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_22_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -8528,6 +8571,7 @@ unpack_22_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_22_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -8781,6 +8825,7 @@ unpack_22_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_22_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -8839,6 +8884,7 @@ unpack_22_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_22_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -9427,6 +9473,7 @@ unpack_24 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_24_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -9480,6 +9527,7 @@ unpack_24_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_24_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -9733,6 +9781,7 @@ unpack_24_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_24_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -9790,6 +9839,7 @@ unpack_24_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_24_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -10384,6 +10434,7 @@ unpack_26 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_26_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -10441,6 +10492,7 @@ unpack_26_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_26_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -10705,6 +10757,7 @@ unpack_26_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_26_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -10766,6 +10819,7 @@ unpack_26_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_26_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -11379,6 +11433,7 @@ unpack_28 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_28_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -11436,6 +11491,7 @@ unpack_28_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_28_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -11703,6 +11759,7 @@ unpack_28_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_28_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -11764,6 +11821,7 @@ unpack_28_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_28_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -12385,6 +12443,7 @@ unpack_30 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_30_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg = _mm_load_si128(in);
@@ -12445,6 +12504,7 @@ unpack_30_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_30_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -12718,6 +12778,7 @@ unpack_30_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_30_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i InReg;
@@ -12782,6 +12843,7 @@ unpack_30_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_30_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -13392,6 +13454,7 @@ unpack_32 (UINT4* __restrict__ out, const UINT4* __restrict__ in) {
}
#else
+#if 0
static void
unpack_32_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i OutReg;
@@ -13429,6 +13492,7 @@ unpack_32_fwd (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_32_fwd_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -13594,6 +13658,7 @@ unpack_32_fwd_8_2 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#if 0
static void
unpack_32_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
__m128i OutReg;
@@ -13633,6 +13698,7 @@ unpack_32_rev (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
return;
}
+#endif
static void
unpack_32_rev_1_3 (__m128i* __restrict__ out, const __m128i* __restrict__ in) {
@@ -14010,6 +14076,7 @@ static Unpacker_T unpacker_all_table[33] =
unpack_00, unpack_30, unpack_00, unpack_32};
#else
+#if 0
static Unpacker_T unpacker_all_table[34] =
{unpack_00, unpack_00,
unpack_02_fwd, unpack_02_rev, unpack_04_fwd, unpack_04_rev,
@@ -14020,6 +14087,7 @@ static Unpacker_T unpacker_all_table[34] =
unpack_22_fwd, unpack_22_rev, unpack_24_fwd, unpack_24_rev,
unpack_26_fwd, unpack_26_rev, unpack_28_fwd, unpack_28_rev,
unpack_30_fwd, unpack_30_rev, unpack_32_fwd, unpack_32_rev};
+#endif
/* Entry 16 in each packsize handles remainder == 64 => quarter_block == 4, column 3, row -1 */
static Unpacker_T unpacker_table[17][17] =
@@ -14138,10 +14206,10 @@ static Unpacker_T unpacker_table[17][17] =
#ifndef LARGE_GENOMES
/* bitpackpages: A list of b-mers (12-mers by default), ending with -1U */
UINT4
-Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
- Storedoligomer_T bmer;
+Bitpack64_read_two (UINT4 *end0, Oligospace_T oligo, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
+ Oligospace_T bmer;
UINT4 *info, nwritten, packsize_div2;
- int remainder0, remainder1, column;
+ int remainder0, column;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
UINT4 offset0, offset1;
UINT4 ptr;
@@ -14149,6 +14217,7 @@ Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UIN
UINT4 diffs[BLOCKSIZE+1], *bitpack;
#else
__m128i diffs[4]; /* Need to provide space for 8 rows (or 2 128-bit registers) for ptr and for end0 */
+ int remainder1;
int delta, row0, row1;
#ifdef BRANCH_FREE_QTR_BLOCK
UINT4 psums[5]; /* Need 5 to handle case where remainder == 64 */
@@ -14164,7 +14233,7 @@ Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UIN
bmer = oligo/BLOCKSIZE;
info = &(bitpackptrs[bmer * METAINFO_SIZE]);
- debug(printf("Entered Bitpack64_read_two with oligo %u => bmer %u\n",oligo,bmer));
+ debug(printf("Entered Bitpack64_read_two with oligo %llu => bmer %u\n",oligo,bmer));
#ifdef WORDS_BIGENDIAN
nwritten = Bigendian_convert_uint(info[0]); /* In 128-bit registers */
@@ -14184,7 +14253,6 @@ Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UIN
#endif
remainder0 = oligo % BLOCKSIZE;
- remainder1 = remainder0 + 1;
debug(printf("nwritten %u, packsize %d\n",nwritten,packsize_div2 * 2));
debug(Bitpack64_block_offsets(offsets,oligo,bitpackptrs,bitpackcomp));
@@ -14358,6 +14426,7 @@ Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UIN
return ptr;
#else /* littleendian and SSE2 */
+ remainder1 = remainder0 + 1;
_diffs = (UINT4 *) diffs; /* Assumes a dummy register in diffs[0] */
#ifdef BRANCH_FREE_QTR_BLOCK
@@ -14450,18 +14519,19 @@ Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo, UINT4 *bitpackptrs, UIN
#ifdef LARGE_GENOMES
/* bitpackpages: A list of b-mers (12-mers by default), ending with -1U */
UINT8
-Bitpack64_read_two_huge (UINT8 *end0, Storedoligomer_T oligo,
+Bitpack64_read_two_huge (UINT8 *end0, Oligospace_T oligo,
UINT4 *bitpackpages, UINT4 *bitpackptrs, UINT4 *bitpackcomp) {
- Storedoligomer_T bmer;
+ Oligospace_T bmer;
UINT4 *info, nwritten;
UINT8 offset0, offset1;
UINT4 packsize_div2;
- int remainder0, remainder1, column;
+ int remainder0, column;
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
UINT4 ptr;
int remainder, row, k, i;
UINT4 diffs[BLOCKSIZE+1], *bitpack;
#else
+ int remainder1;
int delta, row0, row1;
#ifdef BRANCH_FREE_ROW_SUM
__m128i diffs[3];
@@ -14544,7 +14614,6 @@ Bitpack64_read_two_huge (UINT8 *end0, Storedoligomer_T oligo,
#endif
remainder0 = oligo % BLOCKSIZE;
- remainder1 = remainder0 + 1;
/* debug(Bitpack64_block_offsets_huge(offsets,oligo,bitpackpages,bitpackptrs,bitpackcomp)); */
@@ -14706,6 +14775,7 @@ Bitpack64_read_two_huge (UINT8 *end0, Storedoligomer_T oligo,
#else /* littleendian and SSE2 */
+ remainder1 = remainder0 + 1;
_diffs = (UINT4 *) diffs; /* Assumes a dummy register in diffs[0] */
#ifdef BRANCH_FREE_QTR_BLOCK
diff --git a/src/bitpack64-readtwo.h b/src/bitpack64-readtwo.h
index 86fe21d..9993c8b 100644
--- a/src/bitpack64-readtwo.h
+++ b/src/bitpack64-readtwo.h
@@ -5,11 +5,11 @@
/* For reading differential-coded bitstreams */
extern UINT4
-Bitpack64_read_two (UINT4 *end0, Storedoligomer_T oligo,
+Bitpack64_read_two (UINT4 *end0, Oligospace_T oligo,
UINT4 *bitpackptrs, UINT4 *bitpackcomp);
UINT8
-Bitpack64_read_two_huge (UINT8 *end0, Storedoligomer_T oligo,
+Bitpack64_read_two_huge (UINT8 *end0, Oligospace_T oligo,
UINT4 *bitpackpages, UINT4 *bitpackptrs, UINT4 *bitpackcomp);
#endif
diff --git a/src/bitpack64-write.c b/src/bitpack64-write.c
index 85ca9f8..9f2e7d9 100644
--- a/src/bitpack64-write.c
+++ b/src/bitpack64-write.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: bitpack64-write.c 179363 2015-11-20 22:13:52Z twu $";
+static char rcsid[] = "$Id: bitpack64-write.c 183888 2016-02-05 20:33:29Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -18,6 +18,7 @@ static char rcsid[] = "$Id: bitpack64-write.c 179363 2015-11-20 22:13:52Z twu $"
#include "assert.h"
#include "fopen.h"
#include "popcount.h"
+#include "bitpack64-access.h" /* For Bitpack64_extract_bitpack */
#ifdef HAVE_SSE2
#include <emmintrin.h>
@@ -4273,9 +4274,9 @@ columnar_order (UINT4 *columnar, const UINT4 *vertical) {
#ifdef HAVE_SSE2
-static int
-write_columnar (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buffer_size, int strm_buffer_i,
- const UINT4 *_in, int packsize) {
+int
+Bitpack64_write_columnar (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buffer_size, int strm_buffer_i,
+ const UINT4 *_in, int packsize) {
UINT4 columnar[BLOCKSIZE];
#if 0
@@ -4318,9 +4319,9 @@ write_columnar (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buffer_size
/* Non-SIMD code cannot write vertical format easily, so using
horizontal code and conversions */
-static int
-write_columnar (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buffer_size, int strm_buffer_i,
- const UINT4 *horizontal, int packsize) {
+int
+Bitpack64_write_columnar (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buffer_size, int strm_buffer_i,
+ const UINT4 *horizontal, int packsize) {
int nwritten;
UINT4 buffer[BLOCKSIZE], vertical[BLOCKSIZE];
UINT4 columnar[BLOCKSIZE];
@@ -4422,12 +4423,16 @@ Bitpack64_write_horiz (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buff
/* Handles first 32 values from the initial value, and the last 32
values from the final value. More efficient since we need to
process only half as many inputs. */
-static int
-compute_q4_diffs_bidir (UINT4 *diffs, UINT4 *values) {
+int
+Bitpack64_compute_q4_diffs_bidir (UINT4 *diffs, UINT4 *values) {
UINT4 packsize;
int i;
UINT4 maxdiff = 0;
- int firstbit, msb;
+ int firstbit;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
#if 0
for (i = 0; i < 64; i++) {
@@ -4475,12 +4480,17 @@ compute_q4_diffs_bidir (UINT4 *diffs, UINT4 *values) {
}
+#if 0
static int
compute_q1_diffs (UINT4 *diffs, UINT4 *values) {
UINT4 packsize;
int i;
UINT4 maxdiff = 0;
- int firstbit, msb;
+ int firstbit;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
#if 0
for (i = 0; i < 64; i++) {
@@ -4515,6 +4525,7 @@ compute_q1_diffs (UINT4 *diffs, UINT4 *values) {
#endif
}
}
+#endif
@@ -4524,7 +4535,11 @@ compute_q4_diffs_bidir_huge (UINT4 *diffs, UINT8 *values) {
UINT4 packsize;
int i;
UINT4 maxdiff = 0;
- int firstbit, msb;
+ int firstbit;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
maxdiff |= (diffs[32] = (UINT4) (values[64] - values[63]));
@@ -4592,7 +4607,7 @@ Bitpack64_write_differential (char *ptrsfile, char *compfile, UINT4 *ascending,
write_setup();
- printf("Entered Bitpack64_write_differential with n %llu\n",n);
+ /* printf("Entered Bitpack64_write_differential with n %llu\n",n); */
/* 2 metavalues: nwritten (pointer) and cumulative sum for block.
Packsize can be computed from difference between successive
@@ -4619,8 +4634,8 @@ Bitpack64_write_differential (char *ptrsfile, char *compfile, UINT4 *ascending,
ptrs[ptri++] = ascending[positioni];
/* Pack block of 64 diffs */
- packsize = compute_q4_diffs_bidir(diffs,&(ascending[positioni]));
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,&(ascending[positioni]));
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
#ifdef ALLOW_ODD_PACKSIZES
nwritten += 2 * ((packsize + 1) & ~1);
@@ -4648,8 +4663,8 @@ Bitpack64_write_differential (char *ptrsfile, char *compfile, UINT4 *ascending,
}
/* Pack block of < 64 diffs */
- packsize = compute_q4_diffs_bidir(diffs,last_block);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,last_block);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
#ifdef ALLOW_ODD_PACKSIZES
nwritten += 2 * ((packsize + 1) & ~1);
@@ -4686,6 +4701,140 @@ Bitpack64_write_differential (char *ptrsfile, char *compfile, UINT4 *ascending,
}
+static UINT4
+compute_ascending (UINT4 *ascending, UINT4 *counts) {
+ int i;
+
+ ascending[0] = 0;
+ for (i = 1; i <= 64; i++) {
+ ascending[i] = ascending[i-1] + counts[i-1];
+ }
+
+ return ascending[64];
+}
+
+/* We want to store values 0..n, with final value at ascending[n]
+ possibly stored as the final metainfo value */
+/* Stored in columnar order */
+void
+Bitpack64_write_differential_bitpacks (char *ptrsfile, char *compfile, char *packsizes, UINT4 **bitpacks,
+ Oligospace_T n) {
+ FILE *ptrs_fp, *comp_fp;
+ UINT4 *ptrs, nregisters;
+ UINT4 totalcount;
+ UINT4 ptri;
+ int i;
+ Oligospace_T positioni, bmer;
+
+ /* Buffer is used to avoid frequent writes to the file */
+ UINT4 *buffer;
+ int buffer_size = BUFFER_SIZE;
+ int buffer_i;
+
+ UINT4 diffs[BLOCKSIZE], ascending[BLOCKSIZE+1], counts[BLOCKSIZE], last_block[BLOCKSIZE];
+ int packsize;
+
+
+ write_setup();
+
+ /* printf("Entered Bitpack64_write_differential with n %llu\n",n); */
+
+ /* 2 metavalues: nwritten (pointer) and cumulative sum for block.
+ Packsize can be computed from difference between successive
+ pointers, if only even packsizes are allowed */
+ ptrs = (UINT4 *) CALLOC(((n + BLOCKSIZE)/BLOCKSIZE + 1) * DIFFERENTIAL_METAINFO_SIZE,sizeof(UINT4));
+ ptri = 0;
+
+ if ((comp_fp = FOPEN_WRITE_BINARY(compfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",compfile);
+ exit(9);
+ }
+ buffer = (UINT4 *) CALLOC(buffer_size,sizeof(UINT4));
+ buffer_i = 0;
+
+ nregisters = 0U;
+
+ /* Last value of ascending is at ascending[n] */
+ /* Use <= n instead of < n, because we want ascending[n] to be taken care of by unpack_00, not a check for remainder == 0 */
+ totalcount = 0;
+ for (positioni = 0, bmer = 0; positioni + BLOCKSIZE <= n; positioni += BLOCKSIZE, bmer++) {
+ /* Pointer */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for start of block */
+ ptrs[ptri++] = totalcount;
+
+ /* Pack block of 64 diffs */
+ Bitpack64_extract_bitpack(counts,packsizes[bmer],bitpacks[bmer]);
+ totalcount += compute_ascending(ascending,counts);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending); /* Note: This packsize may differ from packsizes[bmer] */
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+
+ nregisters += packsize / 2;
+ }
+
+ /* Old: Check for positioni < n, because if positioni == n, ascending[n] will be taken care of as metainfo */
+ /* Use <= n instead of < n, because we want ascending[n] to be taken care of by unpack_00, not a check for remainder == 0 */
+ /* For nucleotides, expect a single final block where positioni == n */
+ if (positioni <= n) {
+ /* Finish last block of 64 */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for start of block */
+ ptrs[ptri++] = totalcount;
+
+ if (positioni == n) {
+ /* Don't have a bitpack at [bmerspace] */
+ Bitpack64_extract_bitpack(counts,/*packsize*/0,/*bitpack*/NULL);
+ } else {
+ Bitpack64_extract_bitpack(counts,packsizes[bmer],bitpacks[bmer]);
+ }
+
+ /* For differential, want <=. For direct, want < */
+ for (i = 0; i <= (int) (n - positioni); i++) {
+ last_block[i] = counts[i];
+ }
+ for ( ; i < BLOCKSIZE; i++) {
+ /* Copy last value for rest of block */
+ last_block[i] = 0;
+ }
+
+ /* Pack block of < 64 diffs */
+ totalcount += compute_ascending(ascending,last_block);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+
+ nregisters += packsize / 2;
+ }
+
+ /* Write the final pointer, which will point after the end of the file */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for end of block */
+ ptrs[ptri++] = totalcount;
+
+ if ((ptrs_fp = FOPEN_WRITE_BINARY(ptrsfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",ptrsfile);
+ exit(9);
+ } else {
+ FWRITE_UINTS(ptrs,ptri,ptrs_fp);
+ FREE(ptrs);
+ fclose(ptrs_fp);
+ }
+
+ /* Empty buffer */
+ if (buffer_i > 0) {
+ FWRITE_UINTS(buffer,buffer_i,comp_fp);
+ buffer_i = 0;
+ }
+ FREE(buffer);
+ fclose(comp_fp);
+
+ return;
+}
+
+
+#if 0
/* We want to store values 0..n, with final value at ascending[n]
possibly stored as the final metainfo value */
/* D4 stored in columnar order, plus D1 stored as direct */
@@ -4734,8 +4883,8 @@ Bitpack64_write_differential_paired (char *ptrsfile, char *compfile, UINT4 *asce
ptrs[ptri++] = ascending[positioni];
/* D4: Pack block of 64 diffs */
- packsize = compute_q4_diffs_bidir(diffs,&(ascending[positioni]));
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,&(ascending[positioni]));
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
#ifdef ALLOW_ODD_PACKSIZES
nwritten += 2 * ((packsize + 1) & ~1);
@@ -4777,8 +4926,8 @@ Bitpack64_write_differential_paired (char *ptrsfile, char *compfile, UINT4 *asce
}
/* D4: Pack block of < 64 diffs */
- packsize = compute_q4_diffs_bidir(diffs,last_block);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,last_block);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
#ifdef ALLOW_ODD_PACKSIZES
nwritten += 2 * ((packsize + 1) & ~1);
@@ -4819,10 +4968,12 @@ Bitpack64_write_differential_paired (char *ptrsfile, char *compfile, UINT4 *asce
return;
}
+#endif
+#if 0
/* Worst case:
64 128 192 256
256 256 256 256 */
@@ -4892,9 +5043,9 @@ Bitpack64_write_fixed10 (char *ptrsfile, char *compfile, UINT4 *ascending, Oligo
#endif
/* Pack block of 64 diffs */
- packsize = compute_q4_diffs_bidir(diffs,&(ascending[positioni]));
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,&(ascending[positioni]));
assert(packsize <= FIXED10_PACKSIZE);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
nwritten += 2 * FIXED10_PACKSIZE;
}
@@ -4926,9 +5077,9 @@ Bitpack64_write_fixed10 (char *ptrsfile, char *compfile, UINT4 *ascending, Oligo
}
/* Pack block of < 64 diffs */
- packsize = compute_q4_diffs_bidir(diffs,last_block);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,last_block);
assert(packsize <= FIXED10_PACKSIZE);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
nwritten += 2 * FIXED10_PACKSIZE;
}
@@ -4967,6 +5118,7 @@ Bitpack64_write_fixed10 (char *ptrsfile, char *compfile, UINT4 *ascending, Oligo
return;
}
+#endif
void
@@ -5019,7 +5171,7 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
/* Value for start of block */
while (ascending[positioni] >= nextpage) {
- fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu",
+ fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu",
positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage);
pages[pagei++] = positioni/BLOCKSIZE;
currpage = nextpage;
@@ -5030,7 +5182,7 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
/* Pack block of 64 diffs */
packsize = compute_q4_diffs_bidir_huge(diffs,&(ascending[positioni]));
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
#ifdef ALLOW_ODD_PACKSIZES
nwritten += 2 * ((packsize + 1) & ~1);
@@ -5047,7 +5199,7 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
/* Value for start of block */
while (ascending[positioni] >= nextpage) {
- fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu",
+ fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu",
positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage);
pages[pagei++] = positioni/BLOCKSIZE;
currpage = nextpage;
@@ -5066,7 +5218,7 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
/* Pack block of < 64 diffs */
packsize = compute_q4_diffs_bidir_huge(diffs,last_block);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
#ifdef ALLOW_ODD_PACKSIZES
nwritten += 2 * ((packsize + 1) & ~1);
@@ -5081,7 +5233,7 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
/* Value for end of block */
if (ascending[n] >= nextpage) {
- fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu",
+ fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu",
n,n/BLOCKSIZE,ascending[n],nextpage);
pages[pagei++] = n/BLOCKSIZE;
currpage = nextpage;
@@ -5130,6 +5282,171 @@ Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfi
void
+Bitpack64_write_differential_huge_bitpacks (char *pagesfile, char *ptrsfile, char *compfile,
+ char *packsizes, UINT4 **bitpacks, Oligospace_T n) {
+ UINT8 currpage, nextpage;
+ FILE *pages_fp, *ptrs_fp, *comp_fp;
+ UINT4 pages[25]; /* Allows us to handle up to 100 billion positions */
+ UINT4 *ptrs, nregisters;
+ UINT8 totalcount;
+ int ptri;
+ Oligospace_T positioni, bmer;
+
+ /* Buffer is used to avoid frequent writes to the file */
+ UINT4 *buffer;
+ int buffer_size = BUFFER_SIZE;
+ int buffer_i;
+
+ UINT4 diffs[BLOCKSIZE], counts[BLOCKSIZE], ascending[BLOCKSIZE+1], last_block[BLOCKSIZE];
+
+ int pagei = 0, i;
+ int packsize;
+
+
+ write_setup();
+
+ /* 2 metavalues: nwritten (pointer) and cumulative sum for block.
+ Packsize can be computed from difference between successive
+ pointers, if only even packsizes are allowed */
+ ptrs = (UINT4 *) CALLOC(((n + BLOCKSIZE)/BLOCKSIZE + 1) * DIFFERENTIAL_METAINFO_SIZE,sizeof(UINT4));
+ ptri = 0;
+
+ if ((comp_fp = FOPEN_WRITE_BINARY(compfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",compfile);
+ exit(9);
+ }
+ buffer = (UINT4 *) CALLOC(buffer_size,sizeof(UINT4));
+ buffer_i = 0;
+
+ currpage = 0;
+ nextpage = POSITIONS_PAGE;
+ nregisters = 0U;
+
+ /* Last value of ascending is at ascending[n] */
+ /* Use <= n instead of < n, because we want ascending[n] to be taken care of by unpack_00, not a check for remainder == 0 */
+ totalcount = 0;
+ for (positioni = 0, bmer = 0; positioni + BLOCKSIZE <= n; positioni += BLOCKSIZE, bmer++) {
+ /* Pointer */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for start of block */
+ while (totalcount >= nextpage) {
+ fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu",
+ positioni,positioni/BLOCKSIZE,totalcount,nextpage);
+ pages[pagei++] = positioni/BLOCKSIZE;
+ currpage = nextpage;
+ nextpage += POSITIONS_PAGE;
+ }
+ ptrs[ptri++] = totalcount - currpage;
+
+
+ /* Pack block of 64 diffs */
+ Bitpack64_extract_bitpack(counts,packsizes[bmer],bitpacks[bmer]);
+ totalcount += (UINT8) compute_ascending(ascending,counts);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending); /* Note: This packsize may differ from packsizes[bmer] */
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+
+ nregisters += packsize / 2;
+ }
+
+ /* Old: Check for positioni < n, because if positioni == n, ascending[n] will be taken care of as metainfo */
+ /* Use <= n instead of < n, because we want ascending[n] to be taken care of by unpack_00, not a check for remainder == 0 */
+ /* For nucleotides, expect a single final block where positioni == n */
+ if (positioni <= n) {
+ /* Finish last block of 64 */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for start of block */
+ while (totalcount >= nextpage) {
+ fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu",
+ positioni,positioni/BLOCKSIZE,totalcount,nextpage);
+ pages[pagei++] = positioni/BLOCKSIZE;
+ currpage = nextpage;
+ nextpage += POSITIONS_PAGE;
+ }
+ ptrs[ptri++] = totalcount - currpage;
+
+ if (positioni == n) {
+ /* Don't have a bitpack at [bmerspace] */
+ Bitpack64_extract_bitpack(counts,/*packsize*/0,/*bitpack*/NULL);
+ } else {
+ Bitpack64_extract_bitpack(counts,packsizes[bmer],bitpacks[bmer]);
+ }
+
+ /* For differential, want <=. For direct, want < */
+ for (i = 0; i <= (int) (n - positioni); i++) {
+ last_block[i] = counts[i];
+ }
+ for ( ; i <= BLOCKSIZE; i++) {
+ /* Copy last value for rest of block */
+ last_block[i] = 0;
+ }
+
+ /* Pack block of < 64 diffs */
+ totalcount += (UINT8) compute_ascending(ascending,last_block);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending); /* Note: This packsize may differ from packsizes[bmer] */
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+
+ nregisters += packsize / 2;
+ }
+
+
+ /* Write the final pointer, which will point after the end of the file */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for end of block */
+ if (totalcount >= nextpage) {
+ fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu",
+ n,n/BLOCKSIZE,totalcount,nextpage);
+ pages[pagei++] = n/BLOCKSIZE;
+ currpage = nextpage;
+ /* nextpage += POSITIONS_PAGE; */
+ }
+ ptrs[ptri++] = totalcount - currpage;
+
+
+ /* Write pages */
+ if (pagei > 0) {
+ pages[pagei++] = -1U; /* Final value */
+ if ((pages_fp = FOPEN_WRITE_BINARY(pagesfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",pagesfile);
+ exit(9);
+ } else {
+ fprintf(stderr,"\nHave %d pages:",pagei);
+ for (i = 0; i < pagei; i++) {
+ fprintf(stderr," %u",pages[i]);
+ }
+ fprintf(stderr,"\n");
+ FWRITE_UINTS(pages,pagei,pages_fp);
+ /* FREE(pages); */
+ fclose(pages_fp);
+ }
+ }
+
+ if ((ptrs_fp = FOPEN_WRITE_BINARY(ptrsfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",ptrsfile);
+ exit(9);
+ } else {
+ FWRITE_UINTS(ptrs,ptri,ptrs_fp);
+ FREE(ptrs);
+ fclose(ptrs_fp);
+ }
+
+ /* Empty buffer */
+ if (buffer_i > 0) {
+ FWRITE_UINTS(buffer,buffer_i,comp_fp);
+ buffer_i = 0;
+ }
+ FREE(buffer);
+ fclose(comp_fp);
+
+ return;
+}
+
+
+
+#if 0
+void
Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
UINT8 *ascending, Oligospace_T n) {
#ifndef USE_ONE_FILE_FOR_FIXED
@@ -5189,8 +5506,8 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
/* Value for start of block */
while (ascending[positioni] >= nextpage) {
- fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu",
- positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage);
+ fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu",
+ (unsigned long long) positioni,(unsigned long long) (positioni/BLOCKSIZE),ascending[positioni],nextpage);
pages[pagei++] = positioni/BLOCKSIZE;
currpage = nextpage;
nextpage += POSITIONS_PAGE;
@@ -5206,7 +5523,7 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
/* Pack block of 64 diffs */
packsize = compute_q4_diffs_bidir_huge(diffs,&(ascending[positioni]));
assert(packsize <= FIXED10_PACKSIZE);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
nwritten += 2 * packsize;
}
@@ -5221,8 +5538,8 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
/* Value for start of block */
while (ascending[positioni] >= nextpage) {
- fprintf(stderr,"\nAt position %u (block %u), ascending %llu >= nextpage %llu",
- positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage);
+ fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu",
+ (unsigned long long) positioni,(unsigned long long) (positioni/BLOCKSIZE),ascending[positioni],nextpage);
pages[pagei++] = positioni/BLOCKSIZE;
currpage = nextpage;
nextpage += POSITIONS_PAGE;
@@ -5247,7 +5564,7 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
/* Pack block of < 64 diffs */
packsize = compute_q4_diffs_bidir_huge(diffs,last_block);
assert(packsize <= FIXED10_PACKSIZE);
- buffer_i = write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,FIXED10_PACKSIZE);
nwritten += 2 * packsize;
}
@@ -5260,8 +5577,8 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
/* Value for end of block */
if (ascending[n] >= nextpage) {
- fprintf(stderr,"\nAt final oligo %u (block %u), ascending %llu >= nextpage %llu",
- n,n/BLOCKSIZE,ascending[n],nextpage);
+ fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu",
+ (unsigned long long) n,(unsigned long long) (n/BLOCKSIZE),ascending[n],nextpage);
pages[pagei++] = n/BLOCKSIZE;
currpage = nextpage;
/* nextpage += POSITIONS_PAGE; */
@@ -5311,7 +5628,7 @@ Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
return;
}
-
+#endif
@@ -5320,7 +5637,11 @@ compute_packsize (UINT4 *values) {
UINT4 packsize;
UINT4 maxvalue = 0;
int i;
- int firstbit, msb;
+ int firstbit;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
for (i = 0; i < 64; i++) {
maxvalue |= values[i];
diff --git a/src/bitpack64-write.h b/src/bitpack64-write.h
index 693c821..210d774 100644
--- a/src/bitpack64-write.h
+++ b/src/bitpack64-write.h
@@ -1,22 +1,27 @@
-/* $Id: bitpack64-write.h 179363 2015-11-20 22:13:52Z twu $ */
+/* $Id: bitpack64-write.h 180341 2015-12-07 18:29:40Z twu $ */
#ifndef BITPACK64_WRITE_INCLUDED
#define BITPACK64_WRITE_INCLUDED
#include <stdio.h>
#include "types.h"
+extern int
+Bitpack64_write_columnar (FILE *strm_fp, Positionsptr_T *strm_buffer, int strm_buffer_size, int strm_buffer_i,
+ const UINT4 *horizontal, int packsize);
+extern int
+Bitpack64_compute_q4_diffs_bidir (UINT4 *diffs, UINT4 *values);
+
/* Stores the $(n+1)$ values [0..n] */
extern void
Bitpack64_write_differential (char *ptrsfile, char *compfile, UINT4 *ascending, Oligospace_T n);
extern void
-Bitpack64_write_differential_paired (char *ptrsfile, char *compfile, UINT4 *ascending, Oligospace_T n);
-extern void
-Bitpack64_write_fixed10 (char *ptrsfile, char *compfile, UINT4 *ascending, Oligospace_T n);
+Bitpack64_write_differential_bitpacks (char *ptrsfile, char *compfile, char *packsizes, UINT4 **bitpacks,
+ Oligospace_T n);
extern void
Bitpack64_write_differential_huge (char *pagesfile, char *ptrsfile, char *compfile,
UINT8 *ascending, Oligospace_T n);
extern void
-Bitpack64_write_fixed10_huge (char *pagesfile, char *ptrsfile, char *compfile,
- UINT8 *ascending, Oligospace_T n);
+Bitpack64_write_differential_huge_bitpacks (char *pagesfile, char *ptrsfile, char *compfile,
+ char *packsizes, UINT4 **bitpacks, Oligospace_T n);
/* Stores the $n$ values [0..(n-1)] */
extern void
diff --git a/src/block.c b/src/block.c
index 189d01a..01ec723 100644
--- a/src/block.c
+++ b/src/block.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: block.c 99748 2013-06-27 21:01:48Z twu $";
+static char rcsid[] = "$Id: block.c 180699 2015-12-10 19:10:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -39,22 +39,22 @@ struct T {
Width_T oligosize;
#ifdef PMAP
- Storedoligomer_T aaindex;
+ Oligospace_T aaindex;
#else
int leftreadshift;
- Storedoligomer_T forward;
- Storedoligomer_T revcomp;
- Storedoligomer_T oligomask;
+ Oligospace_T forward;
+ Oligospace_T revcomp;
+ Oligospace_T oligomask;
#endif
/* For saving state */
int last_querypos_save;
Oligostate_T last_state_save;
#ifdef PMAP
- Storedoligomer_T aaindex_save;
+ Oligospace_T aaindex_save;
#else
- Storedoligomer_T forward_save;
- Storedoligomer_T revcomp_save;
+ Oligospace_T forward_save;
+ Oligospace_T revcomp_save;
#endif
};
@@ -70,12 +70,12 @@ Block_querypos (T this) {
}
#ifdef PMAP
-Storedoligomer_T
+Oligospace_T
Block_aaindex (T this) {
return this->aaindex;
}
#else
-Storedoligomer_T
+Oligospace_T
Block_forward (T this) {
if (this->cdnaend == FIVE) {
return this->forward & this->oligomask;
@@ -84,7 +84,7 @@ Block_forward (T this) {
}
}
-Storedoligomer_T
+Oligospace_T
Block_revcomp (T this) {
if (this->cdnaend == FIVE) {
return (this->revcomp >> this->leftreadshift) & this->oligomask;
@@ -180,7 +180,11 @@ Block_new (cDNAEnd_T cdnaend, Width_T oligosize,
new->cdnaend = cdnaend;
new->oligosize = oligosize;
#ifndef PMAP
- new->oligomask = ~(~0UL << 2*oligosize);
+#ifdef HAVE_64_BIT
+ new->oligomask = ~(~0ULL << 2*oligosize);
+#else
+ new->oligomask = ~(~0U << 2*oligosize);
+#endif
new->leftreadshift = leftreadshift;
#endif
diff --git a/src/block.h b/src/block.h
index a6dc69e..0a6ef67 100644
--- a/src/block.h
+++ b/src/block.h
@@ -1,4 +1,4 @@
-/* $Id: block.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: block.h 180699 2015-12-10 19:10:10Z twu $ */
#ifndef BLOCK_INCLUDED
#define BLOCK_INCLUDED
@@ -17,12 +17,12 @@ extern int
Block_querypos (T this);
#ifdef PMAP
-extern Storedoligomer_T
+extern Oligospace_T
Block_aaindex (T this);
#else
-extern Storedoligomer_T
+extern Oligospace_T
Block_forward (T this);
-extern Storedoligomer_T
+extern Oligospace_T
Block_revcomp (T this);
#endif
diff --git a/src/bytecoding.c b/src/bytecoding.c
index a311650..d88d102 100644
--- a/src/bytecoding.c
+++ b/src/bytecoding.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: bytecoding.c 170515 2015-07-23 23:03:24Z twu $";
+static char rcsid[] = "$Id: bytecoding.c 179281 2015-11-20 00:10:35Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -85,6 +85,62 @@ Bytecoding_write (char *bytesfile, char *excfile, char *guidefile, UINT4 *values
}
+void
+Bytecoding_write_bytes (char *bytesfile, char *excfile, char *guidefile, unsigned char *bytes,
+ UINT4 *exceptions, UINT4 nexceptions, UINT4 genomelength, int guide_interval) {
+ FILE *fp_bytes, *fp_guide, *fp_exceptions;
+ UINT4 exceptionsi = 0;
+
+ UINT4 n = genomelength, i;
+ UINT4 guide_value = 0;
+
+
+ if (bytesfile != NULL) {
+ fp_bytes = FOPEN_WRITE_BINARY(bytesfile);
+ fwrite(bytes,sizeof(unsigned char),n+1,fp_bytes);
+ fclose(fp_bytes);
+ }
+
+ fp_exceptions = FOPEN_WRITE_BINARY(excfile);
+ fwrite(exceptions,sizeof(UINT4),2*nexceptions,fp_exceptions);
+ fclose(fp_exceptions);
+
+ fp_guide = FOPEN_WRITE_BINARY(guidefile);
+
+ for (i = 0; i <= n; i++) {
+ if (bytes[i] == 255) {
+ while (i >= guide_value) {
+ FWRITE_UINT(exceptionsi,fp_guide);
+ guide_value += guide_interval;
+ }
+
+ /* FWRITE_UINT(i,fp_exceptions); */
+ /* FWRITE_UINT(values[i],fp_exceptions); */
+ exceptionsi++;
+ }
+ }
+
+#if 0
+ /* Overkill */
+ while (i >= guide_value) {
+ FWRITE_UINT(nexceptions,fp_guide);
+ guide_value += guide_interval;
+ }
+#else
+ /* Just need this */
+ FWRITE_UINT(nexceptions,fp_guide);
+#endif
+
+ fclose(fp_guide);
+
+ fprintf(stderr,"Byte-coding: %u values < 255, %u exceptions >= 255 (%.1f%%)\n",
+ (n+1)-nexceptions,nexceptions,100*(double) nexceptions/(double) (n+1));
+
+ return;
+}
+
+
+
unsigned char *
Bytecoding_write_exceptions_only (char *excfile, char *guidefile, UINT4 *values,
UINT4 genomelength, int guide_interval) {
@@ -139,6 +195,59 @@ Bytecoding_write_exceptions_only (char *excfile, char *guidefile, UINT4 *values,
}
+#if 0
+void
+Bytecoding_write_exceptions_from_table (char *excfile, char *guidefile, unsigned char *bytes, Uinttableuint_T exceptions_table,
+ UINT4 genomelength, int guide_interval) {
+ FILE *fp_guide, *fp_exceptions;
+ UINT4 nexceptions = 0;
+
+ UINT4 n = genomelength, i;
+ UINT4 guide_value = 0;
+ UINT4 value;
+
+
+ fp_exceptions = FOPEN_WRITE_BINARY(excfile);
+ fp_guide = FOPEN_WRITE_BINARY(guidefile);
+
+ for (i = 0; i <= n; i++) {
+ if (bytes[i] == 255) {
+ while (i >= guide_value) {
+ FWRITE_UINT(nexceptions,fp_guide);
+ guide_value += guide_interval;
+ }
+
+ value = Uinttableuint_get(exceptions_table,i);
+ printf("At i = %u, value is %u\n",i,value);
+ FWRITE_UINT(i,fp_exceptions);
+ FWRITE_UINT(value,fp_exceptions);
+ nexceptions++;
+ }
+ }
+
+#if 0
+ /* Overkill */
+ while (i >= guide_value) {
+ FWRITE_UINT(nexceptions,fp_guide);
+ guide_value += guide_interval;
+ }
+#else
+ /* Just need this */
+ FWRITE_UINT(nexceptions,fp_guide);
+#endif
+
+
+ fclose(fp_exceptions);
+ fclose(fp_guide);
+
+ fprintf(stderr,"Byte-coding: %u values < 255, %u exceptions >= 255 (%.1f%%)\n",
+ (n+1)-nexceptions,nexceptions,100*(double) nexceptions/(double) (n+1));
+
+ return;
+}
+#endif
+
+
#define LCPCHILDDC_BLOCKSIZE 5
#define BUFFER_NBLOCKS 10000000
@@ -286,6 +395,74 @@ Bytecoding_write_lcpchilddc (char *bytesfile, char *excfile, char *guidefile, UI
}
+void
+Bytecoding_interleave_lcpchilddc (char *bytesfile, unsigned char *child_bytes, unsigned char *discrim_chars, unsigned char *lcpbytes,
+ UINT4 genomelength) {
+ FILE *fp_bytes;
+ unsigned char *bytes_buffer, *bytes_ptr;
+
+ UINT4 n = genomelength, i;
+ /* size_t nblocks; */
+ int b;
+
+ /* nblocks = ((n + 1) + 1)/2; */
+
+ bytes_buffer = (unsigned char *) MALLOC(BUFFER_NBLOCKS * LCPCHILDDC_BLOCKSIZE * sizeof(unsigned char));
+ fp_bytes = FOPEN_WRITE_BINARY(bytesfile);
+
+ i = 0;
+ bytes_ptr = &(bytes_buffer[0]);
+ b = 0;
+ fprintf(stderr,"Writing file %s",bytesfile);
+ while (i + 1 <= n) {
+ *bytes_ptr++ = lcpbytes[i]; /* Byte 0 */
+ *bytes_ptr++ = lcpbytes[i+1]; /* Byte 1 */
+
+ *bytes_ptr++ = *discrim_chars++; /* Byte 2 */
+
+ *bytes_ptr++ = child_bytes[i]; /* Byte 3 */
+ *bytes_ptr++ = child_bytes[i+1]; /* Byte 4 */
+
+ i += 2;
+
+ if (++b >= BUFFER_NBLOCKS) {
+ fwrite(bytes_buffer,sizeof(unsigned char),BUFFER_NBLOCKS*LCPCHILDDC_BLOCKSIZE,fp_bytes);
+ bytes_ptr = &(bytes_buffer[0]);
+ b = 0;
+ fprintf(stderr,".");
+ }
+ }
+
+ if (i <= n) {
+ *bytes_ptr++ = lcpbytes[i]; /* Byte 0 */
+ *bytes_ptr++ = 0x00; /* Byte 1 */
+
+ *bytes_ptr++ = *discrim_chars++; /* Byte 2 */
+
+ *bytes_ptr++ = child_bytes[i]; /* Byte 3 */
+ *bytes_ptr++ = 0x00; /* Byte 4 */
+
+ if (++b >= BUFFER_NBLOCKS) {
+ fwrite(bytes_buffer,sizeof(unsigned char),BUFFER_NBLOCKS*LCPCHILDDC_BLOCKSIZE,fp_bytes);
+ bytes_ptr = &(bytes_buffer[0]);
+ b = 0;
+ fprintf(stderr,".");
+ }
+ }
+
+ if (b > 0) {
+ fwrite(bytes_buffer,sizeof(unsigned char),b*LCPCHILDDC_BLOCKSIZE,fp_bytes);
+ }
+ fprintf(stderr,"done\n");
+
+ fclose(fp_bytes);
+
+ FREE(bytes_buffer);
+
+ return;
+}
+
+
#define get_bit(i,bitvector) ((bitvector)[(i)/64] & (1UL << ((i)%64)))
diff --git a/src/bytecoding.h b/src/bytecoding.h
index daf21ec..e7afe9d 100644
--- a/src/bytecoding.h
+++ b/src/bytecoding.h
@@ -1,4 +1,4 @@
-/* $Id: bytecoding.h 170515 2015-07-23 23:03:24Z twu $ */
+/* $Id: bytecoding.h 179281 2015-11-20 00:10:35Z twu $ */
#ifndef BYTECODING_INCLUDED
#define BYTECODING_INCLUDED
@@ -8,6 +8,10 @@
extern void
Bytecoding_write (char *bytesfile, char *excfile, char *guidefile, UINT4 *values,
UINT4 genomelength, int guide_interval);
+extern void
+Bytecoding_write_bytes (char *bytesfile, char *excfile, char *guidefile, unsigned char *bytes,
+ UINT4 *exceptions, UINT4 nexceptions, UINT4 genomelength, int guide_interval);
+
extern unsigned char *
Bytecoding_write_exceptions_only (char *excfile, char *guidefile, UINT4 *values,
UINT4 genomelength, int guide_interval);
@@ -16,6 +20,10 @@ extern void
Bytecoding_write_lcpchilddc (char *bytesfile, char *excfile, char *guidefile, UINT4 *child,
unsigned char *discrim_chars, unsigned char *lcpbytes,
UINT4 genomelength, int guide_interval);
+extern void
+Bytecoding_interleave_lcpchilddc (char *bytesfile, unsigned char *child_bytes, unsigned char *discrim_chars, unsigned char *lcpbytes,
+ UINT4 genomelength);
+
#if 0
extern void
Bytecoding_write_lcpchilddcn (char *bytesfile, char *excfile, char *guidefile, UINT4 *child,
diff --git a/src/chimera.c b/src/chimera.c
index 5a9a110..475776e 100644
--- a/src/chimera.c
+++ b/src/chimera.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: chimera.c 173190 2015-09-01 18:59:44Z twu $";
+static char rcsid[] = "$Id: chimera.c 184432 2016-02-17 20:00:02Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -255,7 +255,7 @@ Chimera_alignment_break (int *newstart, int *newend, Stage3_T stage3, int queryn
} else {
matchscores = (int *) CALLOC(queryntlength,sizeof(int));
}
- Pair_matchscores(matchscores,Stage3_pairarray(stage3),Stage3_npairs(stage3),queryntlength);
+ Pair_matchscores(matchscores,Stage3_pairarray(stage3),Stage3_npairs(stage3));
x = 0;
for (pos = start; pos < end; pos++) {
diff --git a/src/chimera.h b/src/chimera.h
index 6aa94f3..f2e2e8e 100644
--- a/src/chimera.h
+++ b/src/chimera.h
@@ -1,4 +1,4 @@
-/* $Id: chimera.h 173168 2015-09-01 18:20:01Z twu $ */
+/* $Id: chimera.h 173162 2015-09-01 18:13:07Z twu $ */
#ifndef CHIMERA_INCLUDED
#define CHIMERA_INCLUDED
diff --git a/src/chrom.c b/src/chrom.c
index b143ca1..3a70a4d 100644
--- a/src/chrom.c
+++ b/src/chrom.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: chrom.c 138522 2014-06-09 17:08:44Z twu $";
+static char rcsid[] = "$Id: chrom.c 182428 2016-01-15 22:08:51Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -45,6 +45,8 @@ struct T {
char *alpha; /* The alphabetic part, possibly after the number; valid only if numericp == true */
Chromtype_T chromtype;
bool circularp;
+ Chrpos_T alt_scaffold_start;
+ Chrpos_T alt_scaffold_end;
};
void
@@ -68,6 +70,19 @@ Chrom_circularp (T this) {
return this->circularp;
}
+bool
+Chrom_altlocp (Chrpos_T *alt_scaffold_start, Chrpos_T *alt_scaffold_end, T this) {
+ *alt_scaffold_start = this->alt_scaffold_start;
+ *alt_scaffold_end = this->alt_scaffold_end;
+
+ if (*alt_scaffold_end != *alt_scaffold_start) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+
/* Largest number for an unsigned int is 4294967295, which is 10
digits. However, the organism with the most chromosomes is the
@@ -76,7 +91,8 @@ Chrom_circularp (T this) {
a string. */
T
-Chrom_from_string (char *string, char *mitochondrial_string, Univcoord_T order, bool circularp) {
+Chrom_from_string (char *string, char *mitochondrial_string, Univcoord_T order,
+ bool circularp, Chrpos_T alt_scaffold_start, Chrpos_T alt_scaffold_end) {
T new = (T) MALLOC(sizeof(*new));
int ndigits = 0;
char *p;
@@ -86,8 +102,10 @@ Chrom_from_string (char *string, char *mitochondrial_string, Univcoord_T order,
new->order = order;
new->circularp = circularp;
+ new->alt_scaffold_start = alt_scaffold_start;
+ new->alt_scaffold_end = alt_scaffold_end;
- new->string = (char *) CALLOC(strlen(string)+1,sizeof(char));
+ new->string = (char *) MALLOC((strlen(string)+1) * sizeof(char));
strcpy(new->string,string);
if (mitochondrial_string != NULL && !strcmp(string,mitochondrial_string)) {
diff --git a/src/chrom.h b/src/chrom.h
index 2d75b08..8b6beeb 100644
--- a/src/chrom.h
+++ b/src/chrom.h
@@ -1,4 +1,4 @@
-/* $Id: chrom.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: chrom.h 182428 2016-01-15 22:08:51Z twu $ */
#ifndef CHROM_INCLUDED
#define CHROM_INCLUDED
@@ -15,8 +15,11 @@ extern char *
Chrom_string (T this);
extern bool
Chrom_circularp (T this);
+extern bool
+Chrom_altlocp (Chrpos_T *alt_scaffold_start, Chrpos_T *alt_scaffold_stop, T this);
extern T
-Chrom_from_string (char *string, char *mitochondrial_string, Univcoord_T order, bool circularp);
+Chrom_from_string (char *string, char *mitochondrial_string, Univcoord_T order,
+ bool circularp, Chrpos_T alt_scaffold_start, Chrpos_T alt_scaffold_end);
extern int
Chrom_cmp_alpha (T a, T b);
diff --git a/src/cmet.c b/src/cmet.c
index 082a407..dfd41b3 100644
--- a/src/cmet.c
+++ b/src/cmet.c
@@ -1,16 +1,15 @@
-static char rcsid[] = "$Id: cmet.c 99737 2013-06-27 19:33:03Z twu $";
+static char rcsid[] = "$Id: cmet.c 181327 2015-12-19 13:07:25Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "cmet.h"
-#include "types.h"
/* 0 1 2 3 4 5 6 7 8 9 A B C D E F */
/* 0 3 2 3 C F E F 8 B A B C F E F */
-static const Storedoligomer_T convert_ct[] =
+static const UINT4 convert_ct[] =
{0x0000,0x0003,0x0002,0x0003,0x000C,0x000F,0x000E,0x000F,
0x0008,0x000B,0x000A,0x000B,0x000C,0x000F,0x000E,0x000F,
0x0030,0x0033,0x0032,0x0033,0x003C,0x003F,0x003E,0x003F,
@@ -8205,7 +8204,7 @@ static const Storedoligomer_T convert_ct[] =
0xFFF8,0xFFFB,0xFFFA,0xFFFB,0xFFFC,0xFFFF,0xFFFE,0xFFFF,
};
-static const Storedoligomer_T convert_ga[] =
+static const UINT4 convert_ga[] =
{0x0000,0x0001,0x0000,0x0003,0x0004,0x0005,0x0004,0x0007,
0x0000,0x0001,0x0000,0x0003,0x000C,0x000D,0x000C,0x000F,
0x0010,0x0011,0x0010,0x0013,0x0014,0x0015,0x0014,0x0017,
@@ -16401,21 +16400,41 @@ static const Storedoligomer_T convert_ga[] =
};
-Storedoligomer_T
-Cmet_reduce_ct (Storedoligomer_T oligo) {
- Storedoligomer_T reduced;
+Oligospace_T
+Cmet_reduce_ct (Oligospace_T oligo) {
+ Oligospace_T reduced;
+#ifdef HAVE_64_BIT
+ /* Handles 48 bits, or k-mer up to 24 */
+ reduced = (Oligospace_T) convert_ct[oligo >> 32];
+ reduced <<= 32; /* Put in separate line to make it clear we want 64 bits */
+ reduced |= (Oligospace_T) (convert_ct[oligo >> 16 & 0xFFFF] << 16);
+ reduced |= (Oligospace_T) convert_ct[oligo & 0xFFFF];
+#else
+ /* Handles 32 bits, or k-mer up to 16 */
reduced = convert_ct[oligo >> 16] << 16;
- reduced |= convert_ct[oligo & 0x0000FFFF];
+ reduced |= convert_ct[oligo & 0xFFFF];
+#endif
+
return reduced;
}
-Storedoligomer_T
-Cmet_reduce_ga (Storedoligomer_T oligo) {
- Storedoligomer_T reduced;
+Oligospace_T
+Cmet_reduce_ga (Oligospace_T oligo) {
+ Oligospace_T reduced;
+#ifdef HAVE_64_BIT
+ /* Handles 48 bits, or k-mer up to 24 */
+ reduced = (Oligospace_T) convert_ga[oligo >> 32];
+ reduced <<= 32; /* Put in separate line to make it clear we want 64 bits */
+ reduced |= (Oligospace_T) (convert_ga[oligo >> 16 & 0xFFFF] << 16);
+ reduced |= (Oligospace_T) convert_ga[oligo & 0xFFFF];
+#else
+ /* Handles 32 bits, or k-mer up to 16 */
reduced = convert_ga[oligo >> 16] << 16;
- reduced |= convert_ga[oligo & 0x0000FFFF];
+ reduced |= convert_ga[oligo & 0xFFFF];
+#endif
+
return reduced;
}
diff --git a/src/cmet.h b/src/cmet.h
index 6e57b6c..ce4c8ae 100644
--- a/src/cmet.h
+++ b/src/cmet.h
@@ -1,13 +1,13 @@
-/* $Id: cmet.h 157222 2015-01-22 18:40:00Z twu $ */
+/* $Id: cmet.h 180699 2015-12-10 19:10:10Z twu $ */
#ifndef CMET_INCLUDED
#define CMET_INCLUDED
-#include "indexdb.h" /* For Storedoligomer_T */
+#include "types.h"
-extern Storedoligomer_T
-Cmet_reduce_ct (Storedoligomer_T oligo);
-extern Storedoligomer_T
-Cmet_reduce_ga (Storedoligomer_T oligo);
+extern Oligospace_T
+Cmet_reduce_ct (Oligospace_T oligo);
+extern Oligospace_T
+Cmet_reduce_ga (Oligospace_T oligo);
#endif
diff --git a/src/cmetindex.c b/src/cmetindex.c
index d44890d..325a46b 100644
--- a/src/cmetindex.c
+++ b/src/cmetindex.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: cmetindex.c 167263 2015-06-10 23:59:15Z twu $";
+static char rcsid[] = "$Id: cmetindex.c 184156 2016-02-12 18:30:44Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -48,7 +48,7 @@ static char rcsid[] = "$Id: cmetindex.c 167263 2015-06-10 23:59:15Z twu $";
#include "mem.h"
#include "fopen.h"
#include "access.h"
-#include "types.h" /* For Positionsptr_T, Oligospace_T, and Storedoligomer_T */
+#include "types.h" /* For Positionsptr_T and Oligospace_T */
#include "mode.h"
#include "cmet.h"
@@ -63,6 +63,10 @@ static char rcsid[] = "$Id: cmetindex.c 167263 2015-06-10 23:59:15Z twu $";
#include "bytecoding.h"
#include "sarray-write.h"
#include "bitpack64-write.h"
+#include "bitpack64-read.h"
+#include "bitpack64-readtwo.h"
+#include "bitpack64-access.h"
+#include "bitpack64-incr.h"
#include "datadir.h"
#include "getopt.h"
@@ -70,13 +74,19 @@ static char rcsid[] = "$Id: cmetindex.c 167263 2015-06-10 23:59:15Z twu $";
#define POSITIONS8_HIGH_SHIFT 32
#define POSITIONS8_LOW_MASK 0xFFFFFFFF
+#define DIFFERENTIAL_METAINFO_SIZE 2
+#define BLOCKSIZE 64
+#define BUFFER_SIZE 1000000
+
+#define MONITOR_INTERVAL 10000000
+
+
#ifdef DEBUG
#define debug(x) x
#else
#define debug(x)
#endif
-#define MONITOR_INTERVAL 10000000
static char *user_sourcedir = NULL;
@@ -138,25 +148,14 @@ power (int base, int exponent) {
}
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
-/* 87654321 */
-#define LEFT_A 0x00000000
-#define LEFT_C 0x40000000
-#define LEFT_G 0x80000000
-#define LEFT_T 0xC0000000
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
-static Storedoligomer_T
-reduce_oligo_old (Storedoligomer_T oligo, int oligosize) {
- Storedoligomer_T reduced = 0U, lowbits;
+#if 0
+static Oligospace_T
+reduce_oligo_old (Oligospace_T oligo, int oligosize) {
+ Oligospace_T reduced = 0U, lowbits;
int i;
for (i = 0; i < oligosize; i++) {
@@ -177,13 +176,15 @@ reduce_oligo_old (Storedoligomer_T oligo, int oligosize) {
return reduced;
}
+#endif
+#if 0
static char *
-shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
+shortoligo_nt (Oligospace_T oligo, int oligosize) {
char *nt;
int i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -201,10 +202,13 @@ shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
return nt;
}
+#endif
+#if 0
+/* Old method */
static Positionsptr_T *
-compute_offsets_ct (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedoligomer_T mask) {
+compute_offsets_ct_using_array (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Oligospace_T mask) {
Positionsptr_T *offsets;
Oligospace_T oligoi, reduced;
#ifdef DEBUG
@@ -248,10 +252,13 @@ compute_offsets_ct (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedo
return offsets;
}
+#endif
+#if 0
+/* Old method */
static Positionsptr_T *
-compute_offsets_ga (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedoligomer_T mask) {
+compute_offsets_ga_using_array (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Oligospace_T mask) {
Positionsptr_T *offsets;
Oligospace_T oligoi, reduced;
#ifdef DEBUG
@@ -274,7 +281,7 @@ compute_offsets_ga (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedo
/*size*/offsets[reduced+1] += (oldoffsets[oligoi+1] - oldoffsets[oligoi]);
#endif
debug(
- printf(" to %d\n",offsets[reduced+1]);
+ printf(" to %u\n",offsets[reduced+1]);
FREE(nt2);
FREE(nt1);
);
@@ -290,6 +297,105 @@ compute_offsets_ga (Positionsptr_T *oldoffsets, Oligospace_T oligospace, Storedo
return offsets;
}
+#endif
+
+
+static void
+compute_offsets_ct_using_bitpack (char *new_pointers_filename, char *new_offsets_filename,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm,
+ Oligospace_T oligospace, Oligospace_T mask) {
+ Oligospace_T bmerspace;
+ char *packsizes;
+ UINT4 **bitpacks;
+ UINT4 increment;
+ int new_packsize;
+ UINT4 offsets[BLOCKSIZE+1];
+ Oligospace_T oligoi, reduced, bmer;
+ int ii;
+#ifdef DEBUG
+ char *nt1, *nt2;
+#endif
+
+ /* Fill with sizes */
+ bmerspace = oligospace/BLOCKSIZE;
+ packsizes = (char *) CALLOC(bmerspace,sizeof(char));
+ bitpacks = (UINT4 **) CALLOC(bmerspace,sizeof(UINT4 *));
+
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(offsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((increment = offsets[ii+1] - offsets[ii]) > 0) {
+ reduced = Cmet_reduce_ct(oligoi + ii) & mask;
+ bmer = reduced/BLOCKSIZE;
+ if ((new_packsize = Bitpack64_access_new_packsize(reduced,/*old_packsize*/(int) packsizes[bmer],
+ bitpacks[bmer],increment)) != (int) packsizes[bmer]) {
+ bitpacks[bmer] = Bitpack64_realloc_multiple((int) packsizes[bmer],new_packsize,bitpacks[bmer]);
+ packsizes[bmer] = (char) new_packsize;
+ }
+ Bitpack64_add_bitpack(reduced,(int) packsizes[bmer],bitpacks[bmer],increment);
+ }
+ }
+ }
+
+ Bitpack64_write_differential_bitpacks(new_pointers_filename,new_offsets_filename,packsizes,bitpacks,oligospace);
+
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
+ }
+ FREE(bitpacks);
+ FREE(packsizes);
+
+ return;
+}
+
+
+static void
+compute_offsets_ga_using_bitpack (char *new_pointers_filename, char *new_offsets_filename,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm,
+ Oligospace_T oligospace, Oligospace_T mask) {
+ Oligospace_T bmerspace;
+ char *packsizes;
+ UINT4 **bitpacks;
+ UINT4 increment;
+ int new_packsize;
+ UINT4 offsets[BLOCKSIZE+1];
+ Oligospace_T oligoi, reduced, bmer;
+ int ii;
+#ifdef DEBUG
+ char *nt1, *nt2;
+#endif
+
+ /* Fill with sizes */
+ bmerspace = oligospace/BLOCKSIZE;
+ packsizes = (char *) CALLOC(bmerspace,sizeof(char));
+ bitpacks = (UINT4 **) CALLOC(bmerspace,sizeof(UINT4 *));
+
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(offsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((increment = offsets[ii+1] - offsets[ii]) > 0) {
+ reduced = Cmet_reduce_ga(oligoi + ii) & mask;
+ bmer = reduced/BLOCKSIZE;
+ if ((new_packsize = Bitpack64_access_new_packsize(reduced,/*old_packsize*/(int) packsizes[bmer],
+ bitpacks[bmer],increment)) != (int) packsizes[bmer]) {
+ bitpacks[bmer] = Bitpack64_realloc_multiple((int) packsizes[bmer],new_packsize,bitpacks[bmer]);
+ packsizes[bmer] = (char) new_packsize;
+ }
+ Bitpack64_add_bitpack(reduced,(int) packsizes[bmer],bitpacks[bmer],increment);
+ }
+ }
+ }
+
+ Bitpack64_write_differential_bitpacks(new_pointers_filename,new_offsets_filename,packsizes,bitpacks,oligospace);
+
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
+ }
+ FREE(bitpacks);
+ FREE(packsizes);
+
+ return;
+}
static void
@@ -310,31 +416,229 @@ sort_8mers (unsigned char *positions8_high, UINT4 *positions8_low, Positionsptr_
}
+static void
+sort_positions (char *ptrsfile, char *compfile, FILE *positions_high_fp, FILE *positions_low_fp,
+ unsigned char *positions8_high, UINT4 *positions8_low, UINT4 *positions4,
+ UINT4 *newoffsetsmeta, UINT4 *newoffsetsstrm, Oligospace_T oligospace, bool coord_values_8p) {
+ Oligospace_T oligoi;
+ Positionsptr_T block_start, block_end, j, npositions;
+
+ FILE *ptrs_fp, *comp_fp;
+ UINT4 *ptrs, nregisters;
+ UINT4 ptri;
+ int ii;
+
+ /* Buffer is used to avoid frequent writes to the file */
+ UINT4 *buffer;
+ int buffer_size = BUFFER_SIZE;
+ int buffer_i;
+
+ UINT4 newoffsets[BLOCKSIZE+1];
+ UINT4 diffs[BLOCKSIZE], ascending[BLOCKSIZE+1];
+ UINT4 totalcount;
+ int packsize;
+
+
+ /* Sort positions in each block. For snps_root, use code from Bitpack64_write_differential */
+ if (snps_root) {
+ ptrs = (UINT4 *) CALLOC(((oligospace + BLOCKSIZE)/BLOCKSIZE + 1) * DIFFERENTIAL_METAINFO_SIZE,sizeof(UINT4));
+ ptri = 0;
+
+ if ((comp_fp = FOPEN_WRITE_BINARY(compfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",compfile);
+ exit(9);
+ }
+ buffer = (UINT4 *) CALLOC(buffer_size,sizeof(UINT4));
+ buffer_i = 0;
+ nregisters = 0;
+ }
+
+ totalcount = 0;
+ for (oligoi = 0; oligoi + BLOCKSIZE <= oligospace; oligoi += BLOCKSIZE) {
+ if (snps_root) {
+ ptrs[ptri++] = nregisters;
+ ptrs[ptri++] = totalcount;
+ }
+ ascending[0] = totalcount;
+ Bitpack64_block_offsets(newoffsets,oligoi,newoffsetsmeta,newoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ block_start = newoffsets[ii];
+ block_end = newoffsets[ii+1];
+ if ((npositions = block_end - block_start) > 0) {
+ if (coord_values_8p == true) {
+ sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
+ if (snps_root == NULL) {
+ /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
+ FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
+ FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
+ } else {
+ /* FWRITE_UINT8(positions8[block_start],positions_fp); */
+ FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
+ FWRITE_UINT(positions8_low[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
+ npositions--;
+ } else {
+ /* FWRITE_UINT8(positions8[j],positions_fp); */
+ FWRITE_CHAR(positions8_high[j],positions_high_fp);
+ FWRITE_UINT(positions8_low[j],positions_low_fp);
+ }
+ }
+ }
+
+ } else {
+ qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
+ if (snps_root == NULL) {
+ FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+ } else {
+ FWRITE_UINT(positions4[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions4[j] == positions4[j-1]) {
+ npositions--;
+ } else {
+ FWRITE_UINT(positions4[j],positions_low_fp);
+ }
+ }
+ }
+ }
+ totalcount += npositions;
+ }
+ ascending[ii+1] = totalcount;
+ }
+ if (snps_root) {
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ nregisters += packsize / 2;
+ }
+ }
+
+ if (oligoi <= oligospace) {
+ /* Finish last block (containing 1 entry, but expand to 64) */
+ if (snps_root) {
+ ptrs[ptri++] = nregisters;
+ ptrs[ptri++] = totalcount;
+ }
+ ascending[0] = totalcount;
+ for (ii = 0; ii <= (int) (oligospace - oligoi); ii++) {
+ block_start = Bitpack64_read_two(&block_end,oligoi+ii,newoffsetsmeta,newoffsetsstrm);
+ if ((npositions = block_end - block_start) > 0) {
+ if (coord_values_8p == true) {
+ sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
+ if (snps_root == NULL) {
+ /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
+ FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
+ FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
+ } else {
+ /* FWRITE_UINT8(positions8[block_start],positions_fp); */
+ FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
+ FWRITE_UINT(positions8_low[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
+ npositions--;
+ } else {
+ /* FWRITE_UINT8(positions8[j],positions_fp); */
+ FWRITE_CHAR(positions8_high[j],positions_high_fp);
+ FWRITE_UINT(positions8_low[j],positions_low_fp);
+ }
+ }
+ }
+
+ } else {
+ qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
+ if (snps_root == NULL) {
+ FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+ } else {
+ FWRITE_UINT(positions4[block_start],positions_low_fp);
+ for (j = block_start+1; j < block_end; j++) {
+ if (positions4[j] == positions4[j-1]) {
+ npositions--;
+ } else {
+ FWRITE_UINT(positions4[j],positions_low_fp);
+ }
+ }
+ }
+ }
+ totalcount += npositions;
+ }
+ ascending[ii+1] = totalcount;
+ }
+ if (snps_root) {
+ for ( ; ii < BLOCKSIZE; ii++) {
+ ascending[ii+1] = totalcount;
+ }
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+ nregisters += packsize / 2;
+ }
+ }
+
+ if (snps_root) {
+ /* Write the final pointer, which will point after the end of the file */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+
+ /* Value for end of block */
+ ptrs[ptri++] = totalcount;
+
+ if ((ptrs_fp = FOPEN_WRITE_BINARY(ptrsfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",ptrsfile);
+ exit(9);
+ } else {
+ FWRITE_UINTS(ptrs,ptri,ptrs_fp);
+ FREE(ptrs);
+ fclose(ptrs_fp);
+ }
+
+ /* Empty buffer */
+ if (buffer_i > 0) {
+ FWRITE_UINTS(buffer,buffer_i,comp_fp);
+ buffer_i = 0;
+ }
+ FREE(buffer);
+ fclose(comp_fp);
+ }
+
+ return;
+}
+
+
/* A T G T */
static unsigned char ct_conversion[4] = {0, 3, 2, 3};
static char CT_CHARTABLE[4] = {'A','T','G','T'};
static void
-compute_ct (char *pointers_filename, char *offsets_filename,
- FILE *positions_high_fp, FILE *positions_low_fp, Positionsptr_T *oldoffsets,
- UINT8 *oldpositions8, UINT4 *oldpositions4,
- Oligospace_T oligospace, Storedoligomer_T mask,
- bool coord_values_8p) {
+compute_ct (char *new_pointers_filename, char *new_offsets_filename,
+ FILE *positions_high_fp, FILE *positions_low_fp,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm, UINT8 *oldpositions8, UINT4 *oldpositions4,
+ Oligospace_T oligospace, Oligospace_T mask, bool coord_values_8p) {
+ char *ptrsfile, *compfile;
unsigned char *positions8_high;
UINT4 *positions8_low;
UINT4 *positions4;
- Positionsptr_T *snpoffsets, j;
- Oligospace_T oligoi, oligok, reduced;
- Positionsptr_T *pointers, *offsets, preunique_totalcounts, block_start, block_end, npositions, offsets_ptr;
+ Oligospace_T oligoi, reduced;
+ UINT4 oldoffsets[BLOCKSIZE+1];
+ UINT4 *newoffsetsmeta, *newoffsetsstrm, *countermeta, *counterstrm;
+ Positionsptr_T preunique_totalcounts, block_start, block_end, j, offset;
+ size_t offsetsmeta_len, offsetsstrm_len;
+ int ii;
+#ifdef HAVE_MMAP
+ int offsetsmeta_fd, offsetsstrm_fd;
+#else
+ double seconds;
+#endif
#ifdef DEBUG
char *nt1, *nt2;
#endif
- offsets = compute_offsets_ct(oldoffsets,oligospace,mask);
+ /* offsets = compute_offsets_ct_using_array(oldoffsets,oligospace,mask); */
+ compute_offsets_ct_using_bitpack(new_pointers_filename,new_offsets_filename,oldoffsetsmeta,oldoffsetsstrm,
+ oligospace,mask);
- preunique_totalcounts = offsets[oligospace];
+ preunique_totalcounts = Bitpack64_read_one(oligospace,oldoffsetsmeta,oldoffsetsstrm);
if (preunique_totalcounts == 0) {
fprintf(stderr,"Something is wrong with the offsets. Total counts is zero.\n");
exit(9);
@@ -365,162 +669,118 @@ compute_ct (char *pointers_filename, char *offsets_filename,
}
}
- /* Point to offsets and revise (previously copied) */
- pointers = offsets;
+ /* Point to offsets and revise */
fprintf(stderr,"Rearranging CT positions...");
-
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
- reduced = Cmet_reduce_ct(oligoi) & mask;
-#ifdef WORDS_BIGENDIAN
- if (coord_values_8p == true) {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
- }
- }
+#ifdef HAVE_MMAP
+ newoffsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,new_pointers_filename,/*randomp*/false);
+ newoffsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,new_offsets_filename,/*randomp*/false);
#else
- if (coord_values_8p == true) {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = oldpositions8[j] & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = oldpositions4[j];
- }
- }
+ newoffsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,new_pointers_filename,sizeof(UINT4));
+ newoffsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,new_offsets_filename,sizeof(UINT4));
#endif
- }
- FREE(offsets);
- fprintf(stderr,"done\n");
-
-
- fprintf(stderr,"Sorting CT positions...");
- offsets = compute_offsets_ct(oldoffsets,oligospace,mask);
+ countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,newoffsetsstrm,index1part);
- /* Sort positions in each block */
- if (snps_root) {
- oligok = 0;
- snpoffsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
- offsets_ptr = 0U;
- snpoffsets[oligok++] = offsets_ptr;
- }
- if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(oldoffsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
fprintf(stderr,".");
}
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- /* qsort(&(positions8[block_start]),npositions,sizeof(UINT8),UINT8_compare); */
- sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
- if (snps_root == NULL) {
- /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
- FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
- FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
-
- } else {
- /* FWRITE_UINT8(positions8[block_start],positions_fp); */
- FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
- FWRITE_UINT(positions8_low[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
- npositions--;
- } else {
- /* FWRITE_UINT8(positions8[j],positions_fp); */
- FWRITE_CHAR(positions8_high[j],positions_high_fp);
- FWRITE_UINT(positions8_low[j],positions_low_fp);
- }
- }
- offsets_ptr += npositions;
+ block_start = oldoffsets[ii];
+ block_end = oldoffsets[ii+1];
+#ifdef WORDS_BIGENDIAN
+ reduced = Cmet_reduce_ct(oligoi + ii) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = Bigendian_convert_uint(block_start); j < Bigendian_convert_uint(block_end); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
+ }
+ } else {
+ for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
}
}
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
- }
- }
- } else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
- if (snps_root == NULL) {
- FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+#else
+ if (block_end > block_start) {
+ reduced = Cmet_reduce_ct(oligoi + ii) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[offset] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[offset] = oldpositions8[j] & POSITIONS8_LOW_MASK;
+ offset++;
+ }
} else {
- FWRITE_UINT(positions4[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions4[j] == positions4[j-1]) {
- npositions--;
- } else {
- FWRITE_UINT(positions4[j],positions_low_fp);
- }
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[offset] = oldpositions4[j];
+ offset++;
}
- offsets_ptr += npositions;
}
- }
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
+ Bitpack64_add(reduced,countermeta,counterstrm,block_end - block_start);
}
}
+#endif
}
+
+ FREE(counterstrm);
+ FREE(countermeta);
fprintf(stderr,"done\n");
+
+ fprintf(stderr,"Sorting CT positions...");
if (snps_root == NULL) {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,offsets,oligospace);
- } else {
- abort();
- }
+ ptrsfile = compfile = (char *) NULL;
} else {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,snpoffsets,oligospace);
- } else {
- abort();
- }
- FREE(snpoffsets);
+ ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(ptrsfile,"%s.temp",new_pointers_filename);
+ compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(compfile,"%s.temp",new_offsets_filename);
}
- FREE(offsets);
+ sort_positions(ptrsfile,compfile,positions_high_fp,positions_low_fp,
+ positions8_high,positions8_low,positions4,
+ newoffsetsmeta,newoffsetsstrm,oligospace,coord_values_8p);
+
+ /* Clean up */
+#ifdef HAVE_MMAP
+ munmap((void *) newoffsetsmeta,offsetsmeta_len);
+ munmap((void *) newoffsetsstrm,offsetsstrm_len);
+ close(offsetsmeta_fd);
+ close(offsetsstrm_fd);
+#else
+ FREE(newoffsetsmeta);
+ FREE(newoffsetsstrm);
+#endif
+
if (coord_values_8p == true) {
FREE(positions8_high);
FREE(positions8_low);
@@ -528,6 +788,15 @@ compute_ct (char *pointers_filename, char *offsets_filename,
FREE(positions4);
}
+ if (snps_root) {
+ rename(ptrsfile,new_pointers_filename);
+ rename(compfile,new_offsets_filename);
+ FREE(ptrsfile);
+ FREE(compfile);
+ }
+
+ fprintf(stderr,"done\n");
+
return;
}
@@ -536,24 +805,35 @@ static unsigned char ga_conversion[4] = {0, 1, 0, 3};
static char GA_CHARTABLE[4] = {'A','C','A','T'};
static void
-compute_ga (char *pointers_filename, char *offsets_filename,
- FILE *positions_high_fp, FILE *positions_low_fp, Positionsptr_T *oldoffsets,
- UINT8 *oldpositions8, UINT4 *oldpositions4,
- Oligospace_T oligospace, Storedoligomer_T mask,
- bool coord_values_8p) {
+compute_ga (char *new_pointers_filename, char *new_offsets_filename,
+ FILE *positions_high_fp, FILE *positions_low_fp,
+ UINT4 *oldoffsetsmeta, UINT4 *oldoffsetsstrm, UINT8 *oldpositions8, UINT4 *oldpositions4,
+ Oligospace_T oligospace, Oligospace_T mask, bool coord_values_8p) {
+ char *ptrsfile, *compfile;
unsigned char *positions8_high;
UINT4 *positions8_low;
UINT4 *positions4;
- Positionsptr_T *snpoffsets, j;
- Oligospace_T oligoi, oligok, reduced;
- Positionsptr_T *pointers, *offsets, preunique_totalcounts, block_start, block_end, npositions, offsets_ptr;
+ Oligospace_T oligoi, reduced;
+ UINT4 oldoffsets[BLOCKSIZE+1];
+ UINT4 *newoffsetsmeta, *newoffsetsstrm, *countermeta, *counterstrm;
+ Positionsptr_T preunique_totalcounts, block_start, block_end, j, offset;
+ size_t offsetsmeta_len, offsetsstrm_len;
+ int ii;
+#ifdef HAVE_MMAP
+ int offsetsmeta_fd, offsetsstrm_fd;
+#else
+ double seconds;
+#endif
#ifdef DEBUG
char *nt1, *nt2;
#endif
- offsets = compute_offsets_ga(oldoffsets,oligospace,mask);
- preunique_totalcounts = offsets[oligospace];
+ /* offsets = compute_offsets_ga_using_array(oldoffsets,oligospace,mask); */
+ compute_offsets_ga_using_bitpack(new_pointers_filename,new_offsets_filename,oldoffsetsmeta,oldoffsetsstrm,
+ oligospace,mask);
+
+ preunique_totalcounts = Bitpack64_read_one(oligospace,oldoffsetsmeta,oldoffsetsstrm);
if (preunique_totalcounts == 0) {
fprintf(stderr,"Something is wrong with the offsets. Total counts is zero.\n");
exit(9);
@@ -584,163 +864,118 @@ compute_ga (char *pointers_filename, char *offsets_filename,
}
}
- /* Point to offsets and revise (previously copied) */
- pointers = offsets;
+ /* Point to offsets and revise */
fprintf(stderr,"Rearranging GA positions...");
-
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
-
- reduced = Cmet_reduce_ga(oligoi) & mask;
-#ifdef WORDS_BIGENDIAN
- if (coord_values_8p == true) {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
- }
- }
+#ifdef HAVE_MMAP
+ newoffsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,new_pointers_filename,/*randomp*/false);
+ newoffsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,new_offsets_filename,/*randomp*/false);
#else
- if (coord_values_8p == true) {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions8[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions8_high[pointers[reduced]/*++*/] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
- positions8_low[pointers[reduced]++] = oldpositions8[j] & POSITIONS8_LOW_MASK;
- }
- } else {
- for (j = oldoffsets[oligoi]; j < oldoffsets[oligoi+1]; j++) {
- debug(nt1 = shortoligo_nt(oligoi,index1part);
- nt2 = shortoligo_nt(reduced,index1part);
- printf("Oligo %s => %s: copying position %u to location %u\n",
- nt1,nt2,oldpositions4[j],pointers[oligoi]);
- FREE(nt2);
- FREE(nt1);
- );
- positions4[pointers[reduced]++] = oldpositions4[j];
- }
- }
+ newoffsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,new_pointers_filename,sizeof(UINT4));
+ newoffsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,new_offsets_filename,sizeof(UINT4));
#endif
- }
- FREE(offsets);
- fprintf(stderr,"done\n");
+ countermeta = Indexdb_bitpack_counter(&counterstrm,newoffsetsmeta,newoffsetsstrm,index1part);
-
- fprintf(stderr,"Sorting GA positions...");
- offsets = compute_offsets_ga(oldoffsets,oligospace,mask);
-
- /* Sort positions in each block */
- if (snps_root) {
- oligok = 0;
- snpoffsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
- offsets_ptr = 0U;
- snpoffsets[oligok++] = offsets_ptr;
- }
- if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(oldoffsets,oligoi,oldoffsetsmeta,oldoffsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
fprintf(stderr,".");
}
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- /* qsort(&(positions8[block_start]),npositions,sizeof(UINT8),UINT8_compare); */
- sort_8mers(&(positions8_high[block_start]),&(positions8_low[block_start]),npositions);
- if (snps_root == NULL) {
- /* FWRITE_UINT8S(&(positions8[block_start]),npositions,positions_fp); */
- FWRITE_CHARS(&(positions8_high[block_start]),npositions,positions_high_fp);
- FWRITE_UINTS(&(positions8_low[block_start]),npositions,positions_low_fp);
-
- } else {
- /* FWRITE_UINT8(positions8[block_start],positions_fp); */
- FWRITE_CHAR(positions8_high[block_start],positions_high_fp);
- FWRITE_UINT(positions8_low[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions8_high[j] == positions8_high[j-1] && positions8_low[j] == positions8_low[j-1]) {
- npositions--;
- } else {
- /* FWRITE_UINT8(positions8[j],positions_fp); */
- FWRITE_CHAR(positions8_high[j],positions_high_fp);
- FWRITE_UINT(positions8_low[j],positions_low_fp);
- }
- }
- offsets_ptr += npositions;
+ block_start = oldoffsets[ii];
+ block_end = oldoffsets[ii+1];
+#ifdef WORDS_BIGENDIAN
+ reduced = Cmet_reduce_ga(oligoi + ii) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = Bigendian_convert_uint(block_start); j < Bigendian_convert_uint(block_end); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[pointers[reduced]/*++*/] = Bigendian_convert_uint8(oldpositions8[j]) >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[pointers[reduced]++] = Bigendian_convert_uint8(oldpositions8[j]) & POSITIONS8_LOW_MASK;
+ }
+ } else {
+ for (j = Bigendian_convert_uint(oldoffsets[oligoi]); j < Bigendian_convert_uint(oldoffsets[oligoi+1]); j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[pointers[reduced]++] = Bigendian_convert_uint(oldpositions4[j]);
}
}
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
- }
- }
- } else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- if (oligoi % MONITOR_INTERVAL == 0) {
- fprintf(stderr,".");
- }
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 0) {
- qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
- if (snps_root == NULL) {
- FWRITE_UINTS(&(positions4[block_start]),npositions,positions_low_fp);
+#else
+ if (block_end > block_start) {
+ reduced = Cmet_reduce_ga(oligoi + ii) & mask;
+ offset = Bitpack64_read_one(reduced,newoffsetsmeta,newoffsetsstrm) + Bitpack64_access(reduced,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions8[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions8_high[offset] = oldpositions8[j] >> POSITIONS8_HIGH_SHIFT;
+ positions8_low[offset] = oldpositions8[j] & POSITIONS8_LOW_MASK;
+ offset++;
+ }
} else {
- FWRITE_UINT(positions4[block_start],positions_low_fp);
- for (j = block_start+1; j < block_end; j++) {
- if (positions4[j] == positions4[j-1]) {
- npositions--;
- } else {
- FWRITE_UINT(positions4[j],positions_low_fp);
- }
+ for (j = block_start; j < block_end; j++) {
+ debug(nt1 = shortoligo_nt(oligoi,index1part);
+ nt2 = shortoligo_nt(reduced,index1part);
+ printf("Oligo %s => %s: copying position %u to location %u\n",
+ nt1,nt2,oldpositions4[j],pointers[oligoi]);
+ FREE(nt2);
+ FREE(nt1);
+ );
+ positions4[offset] = oldpositions4[j];
+ offset++;
}
- offsets_ptr += npositions;
}
- }
- if (snps_root) {
- snpoffsets[oligok++] = offsets_ptr;
+ Bitpack64_add(reduced,countermeta,counterstrm,block_end - block_start);
}
}
+#endif
}
+
+ FREE(counterstrm);
+ FREE(countermeta);
fprintf(stderr,"done\n");
+
+ fprintf(stderr,"Sorting GA positions...");
if (snps_root == NULL) {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,offsets,oligospace);
- } else {
- abort();
- }
+ ptrsfile = compfile = (char *) NULL;
} else {
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/pointers_filename,/*compfile*/offsets_filename,snpoffsets,oligospace);
- } else {
- abort();
- }
- FREE(snpoffsets);
+ ptrsfile = (char *) MALLOC((strlen(new_pointers_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(ptrsfile,"%s.temp",new_pointers_filename);
+ compfile = (char *) MALLOC((strlen(new_offsets_filename) + strlen(".temp") + 1) * sizeof(char));
+ sprintf(compfile,"%s.temp",new_offsets_filename);
}
- FREE(offsets);
+ sort_positions(ptrsfile,compfile,positions_high_fp,positions_low_fp,
+ positions8_high,positions8_low,positions4,
+ newoffsetsmeta,newoffsetsstrm,oligospace,coord_values_8p);
+
+/* Clean up */
+#ifdef HAVE_MMAP
+ munmap((void *) newoffsetsmeta,offsetsmeta_len);
+ munmap((void *) newoffsetsstrm,offsetsstrm_len);
+ close(offsetsmeta_fd);
+ close(offsetsstrm_fd);
+#else
+ FREE(newoffsetsmeta);
+ FREE(newoffsetsstrm);
+#endif
+
if (coord_values_8p == true) {
FREE(positions8_high);
FREE(positions8_low);
@@ -748,6 +983,15 @@ compute_ga (char *pointers_filename, char *offsets_filename,
FREE(positions4);
}
+ if (snps_root) {
+ rename(ptrsfile,new_pointers_filename);
+ rename(compfile,new_offsets_filename);
+ FREE(ptrsfile);
+ FREE(compfile);
+ }
+
+ fprintf(stderr,"done\n");
+
return;
}
@@ -762,16 +1006,15 @@ main (int argc, char *argv[]) {
Filenames_T filenames;
char *new_pointers_filename, *new_offsets_filename;
Univ_IIT_T chromosome_iit;
- Positionsptr_T *ref_offsets;
+ UINT4 *ref_offsetsmeta, *ref_offsetsstrm;
size_t totalcounts, i;
- Storedoligomer_T mask;
+ Oligospace_T mask;
unsigned char *ref_positions8_high;
UINT4 *ref_positions8_low;
UINT8 *ref_positions8;
UINT4 *ref_positions4;
Oligospace_T oligospace;
bool coord_values_8p;
- int shmid;
/* For suffix array */
Univcoord_T genomelength;
@@ -781,19 +1024,25 @@ main (int argc, char *argv[]) {
char *indexijptrsfile, *indexijcompfile;
Genome_T genomecomp;
unsigned char *gbuffer;
- UINT4 *SA, *lcp, *child;
+ UINT4 *SA;
UINT4 nbytes;
unsigned char *discrim_chars;
unsigned char *lcp_bytes;
- UINT4 *lcp_guide, *lcp_exceptions;
- int n_lcp_exceptions;
+ UINT4 *lcp_guide, *lcp_exceptions, n_lcp_exceptions;
+
+ unsigned char *child_bytes;
+ UINT4 *child_exceptions, n_child_exceptions;
int sa_fd;
- size_t sa_len, lcpguide_len, lcpexc_len;
+ Access_T lcpguide_access;
+ size_t sa_len, lcpguide_len;
double seconds;
+ int offsetsmeta_fd, offsetsstrm_fd;
+ size_t offsetsmeta_len, offsetsstrm_len;
+
FILE *positions_high_fp, *positions_low_fp;
int ref_positions_high_fd, ref_positions_low_fd;
size_t ref_positions_high_len, ref_positions_low_len;
@@ -848,6 +1097,10 @@ main (int argc, char *argv[]) {
argc -= (optind - 1);
argv += (optind - 1);
+#ifdef MEMUSAGE
+ Mem_usage_init();
+#endif
+
if (dbroot == NULL) {
fprintf(stderr,"Missing name of genome database. Must specify with -d flag.\n");
fprintf(stderr,"Usage: cmetindex -d <genome>\n");
@@ -877,15 +1130,27 @@ main (int argc, char *argv[]) {
required_index1part,required_interval,
/*offsets_only_p*/false);
- mask = ~(~0UL << 2*index1part);
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
+#else
+ mask = ~(~0U << 2*index1part);
+#endif
oligospace = power(4,index1part);
/* Read offsets */
- if (compression_type == BITPACK64_COMPRESSION) {
- ref_offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part);
- } else {
- abort();
- }
+#ifdef MEMUSAGE
+ printf("%lu\n",Mem_usage_report_std_heap()); /* 421 */
+#endif
+#ifdef HAVE_MMAP
+ ref_offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,filenames->pointers_filename,/*randomp*/false);
+ ref_offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,filenames->offsets_filename,/*randomp*/false);
+#else
+ ref_offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,filenames->pointers_filename,sizeof(UINT4));
+ ref_offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,filenames->offsets_filename,sizeof(UINT4));
+#endif
+#ifdef MEMUSAGE
+ printf("%lu\n",Mem_usage_report_std_heap()); /* 4,294,967,721 */
+#endif
/* Read positions */
#if 0
@@ -900,15 +1165,14 @@ main (int argc, char *argv[]) {
if (coord_values_8p == true) {
#ifdef HAVE_MMAP
ref_positions8_high = (unsigned char *) Access_mmap(&ref_positions_high_fd,&ref_positions_high_len,
- filenames->positions_high_filename,sizeof(unsigned char),/*randomp*/false);
+ filenames->positions_high_filename,/*randomp*/false);
ref_positions8_low = (UINT4 *) Access_mmap(&ref_positions_low_fd,&ref_positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->positions_low_filename,/*randomp*/false);
#else
- ref_positions8_high = (unsigned char *) Access_allocate(&shmid,&ref_positions_high_len,&seconds,
- filenames->positions_high_filename,sizeof(unsigned char),
- /*sharedp*/false);
- ref_positions8_low = (UINT4 *) Access_allocate(&shmid,&ref_positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),/*sharedp*/false);
+ ref_positions8_high = (unsigned char *) Access_allocate_private(&ref_positions_high_access,&ref_positions_high_len,&seconds,
+ filenames->positions_high_filename,sizeof(unsigned char));
+ ref_positions8_low = (UINT4 *) Access_allocate_private(&ref_positions_low_access,&ref_positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
#endif
/* Unpack */
totalcounts = ref_positions_high_len/sizeof(unsigned char);
@@ -933,10 +1197,10 @@ main (int argc, char *argv[]) {
} else {
#ifdef HAVE_MMAP
ref_positions4 = (UINT4 *) Access_mmap(&ref_positions_low_fd,&ref_positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->positions_low_filename,/*randomp*/false);
#else
- ref_positions4 = (UINT4 *) Access_allocate(&shmid,&ref_positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),/*sharedp*/false);
+ ref_positions4 = (UINT4 *) Access_allocate_private(&ref_positions_low_access,&ref_positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
#endif
}
@@ -983,16 +1247,22 @@ main (int argc, char *argv[]) {
/* Compute and write CT files */
if (build_suffix_array_p == true) {
+#ifdef MEMUSAGE
+ printf("Before building suffix array: %lu\n",Mem_usage_report_std_heap()); /* 4,294,967,891 */
+#endif
fprintf(stderr,"Building suffix array for CT\n");
sarrayfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.sarray")+1,sizeof(char));
sprintf(sarrayfile,"%s/%s.metct.sarray",destdir,fileroot);
genomecomp = Genome_new(sourcedir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_OLIGOS,
/*uncompressedp*/false,/*access*/USE_MMAP_ONLY,/*sharedp*/false);
- gbuffer = (unsigned char *) CALLOC(genomelength+1,sizeof(unsigned char));
+ gbuffer = (unsigned char *) CALLOC(genomelength+1,sizeof(unsigned char)); /* Adds 3 GB */
Genome_fill_buffer_int_string(genomecomp,/*left*/0,/*length*/genomelength,gbuffer,ct_conversion);
gbuffer[genomelength] = 0; /* Tried N/X, but SACA_K fails */
Sarray_write_array_from_genome(sarrayfile,gbuffer,genomelength);
+#ifdef MEMUSAGE
+ printf("After writing suffix array: %lu\n",Mem_usage_report_std_heap()); /* 7,390,678,634 */
+#endif
/* Bucket array */
indexijptrsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.saindex64meta")+1,sizeof(char));
@@ -1004,7 +1274,7 @@ main (int argc, char *argv[]) {
FREE(indexijcompfile);
FREE(indexijptrsfile);
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/false);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
#if 0
/* Not needed if we already have gbuffer */
@@ -1016,7 +1286,14 @@ main (int argc, char *argv[]) {
/*mode*/CMET_STRANDED);
#endif
- lcp = Sarray_compute_lcp_from_genome(SA,gbuffer,/*n*/genomelength);
+#ifdef MEMUSAGE
+ printf("Before lcp: %lu\n",Mem_usage_report_std_heap()); /* 7,390,678,634 */
+#endif
+ lcp_bytes = Sarray_compute_lcp_bytes_from_genome(&lcp_exceptions,&n_lcp_exceptions,SA,gbuffer,/*n*/genomelength);
+#ifdef MEMUSAGE
+ printf("After lcp: %lu\n",Mem_usage_report_std_heap()); /* lcp: 19,773,520,854. lcp step requires 12 GB. lcp_bytes: 18,711,482,949. Using cells: 12,542,531,581 */
+#endif
+
munmap((void *) SA,sa_len);
close(sa_fd);
FREE(gbuffer);
@@ -1024,66 +1301,99 @@ main (int argc, char *argv[]) {
Genome_free(&genomebits);
#endif
- /* Write lcp exceptions/guide, but return lcp_bytes */
+ /* Write lcp exceptions/guide */
lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.salcpexc")+1,sizeof(char));
sprintf(lcpexcfile,"%s/%s.metct.salcpexc",destdir,fileroot);
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.metct.salcpguide1024",destdir,fileroot);
-
- lcp_bytes = Bytecoding_write_exceptions_only(lcpexcfile,lcpguidefile,lcp,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,lcpexcfile,lcpguidefile,lcp_bytes,lcp_exceptions,n_lcp_exceptions,
+ genomelength,/*guide_interval*/1024);
+#ifdef MEMUSAGE
+ printf("Creating lcp_bytes: %lu\n",Mem_usage_report_std_heap()); /* 19,773,521,016. Using cells: 9,446,821,188 */
+#endif
FREE(lcpguidefile);
FREE(lcpexcfile);
- FREE(lcp); /* Use lcp_bytes, which are more memory-efficient than lcp */
-
+#ifdef MEMUSAGE
+ printf("After free of lcp: %lu\n",Mem_usage_report_std_heap()); /* 7,390,678,634 */
+#endif
/* DC array */
- /* Assume we have lcp_bytes already in memory. Don't need to use guide for speed. */
+ /* Assume we have lcp_bytes and lcp_exceptions already in memory. Don't need to use guide for speed. */
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.metct.salcpguide1024",destdir,fileroot);
- lcp_guide = (UINT4 *) Access_allocate(&shmid,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4),/*sharedp*/false);
+ lcp_guide = (UINT4 *) Access_allocate_private(&lcpguide_access,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4));
FREE(lcpguidefile);
- lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.salcpexc")+1,sizeof(char));
- sprintf(lcpexcfile,"%s/%s.metct.salcpexc",destdir,fileroot);
- lcp_exceptions = (UINT4 *) Access_allocate(&shmid,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4),/*sharedp*/false);
- n_lcp_exceptions = lcpexc_len/(sizeof(UINT4) + sizeof(UINT4));
- FREE(lcpexcfile);
-
/* Compute discriminating chars (DC) array */
+#ifdef MEMUSAGE
+ printf("Before computing discrim_chars: %lu\n",Mem_usage_report_std_heap()); /* 9,458,913,650 */
+#endif
discrim_chars = Sarray_discriminating_chars(&nbytes,sarrayfile,genomecomp,lcp_bytes,lcp_guide,
lcp_exceptions,/*guide_interval*/1024,/*n*/genomelength,
CT_CHARTABLE);
+#ifdef MEMUSAGE
+ printf("After computing discrim_chars: %lu\n",Mem_usage_report_std_heap()); /* 11,006,768,928 */
+#endif
FREE(sarrayfile);
+#ifdef MEMUSAGE
+ printf("Before computing child array: %lu\n",Mem_usage_report_std_heap()); /* 11,006,768,852 */
+#endif
fprintf(stderr,"Building child array\n");
/* Compute child array (relative values) */
- child = Sarray_compute_child(lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
+ child_bytes = Sarray_compute_child_bytes(&child_exceptions,&n_child_exceptions,lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
+#ifdef MEMUSAGE
+ printf("After computing child array: %lu\n",Mem_usage_report_std_heap()); /* 23,389,611,072 *** */
+#endif
FREE(lcp_exceptions);
FREE(lcp_guide);
- /* Write combined lcpchilddc file */
- lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.salcpchilddc")+1,sizeof(char));
- sprintf(lcpchilddcfile,"%s/%s.metct.salcpchilddc",destdir,fileroot);
childexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.sachildexc")+1,sizeof(char));
sprintf(childexcfile,"%s/%s.metct.sachildexc",destdir,fileroot);
childguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.sachildguide1024")+1,sizeof(char));
sprintf(childguidefile,"%s/%s.metct.sachildguide1024",destdir,fileroot);
- Bytecoding_write_lcpchilddc(lcpchilddcfile,childexcfile,childguidefile,child,
- discrim_chars,lcp_bytes,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,childexcfile,childguidefile,child_bytes,child_exceptions,n_child_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(childguidefile);
FREE(childexcfile);
+ FREE(child_exceptions);
+
+ /* Write combined lcpchilddc file */
+ lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metct.salcpchilddc")+1,sizeof(char));
+ sprintf(lcpchilddcfile,"%s/%s.metct.salcpchilddc",destdir,fileroot);
+ Bytecoding_interleave_lcpchilddc(lcpchilddcfile,child_bytes,discrim_chars,lcp_bytes,genomelength);
FREE(lcpchilddcfile);
- FREE(child);
+ FREE(child_bytes);
FREE(discrim_chars);
FREE(lcp_bytes);
+#ifdef MEMUSAGE
+ printf("At end of suffix array: %lu\n",Mem_usage_report_std_heap()); /* 4,294,968,003 */
+#endif
}
+ /* Read offsets */
+ /* ref_offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part); */
+#ifdef HAVE_MMAP
+ ref_offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,filenames->pointers_filename,/*randomp*/false);
+ ref_offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,filenames->offsets_filename,/*randomp*/false);
+#else
+ ref_offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,filenames->pointers_filename,sizeof(UINT4));
+ ref_offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,filenames->offsets_filename,sizeof(UINT4));
+#endif
+
+#ifdef MEMUSAGE
+ printf("Before compute_ct: %lu\n",Mem_usage_report_std_heap()); /* 4,294,968,003 */
+#endif
compute_ct(new_pointers_filename,new_offsets_filename,
- positions_high_fp,positions_low_fp,ref_offsets,ref_positions8,ref_positions4,
+ positions_high_fp,positions_low_fp,
+ ref_offsetsmeta,ref_offsetsstrm,ref_positions8,ref_positions4,
oligospace,mask,coord_values_8p);
+#ifdef MEMUSAGE
+ printf("After compute_ct: %lu\n",Mem_usage_report_std_heap()); /* 4,294,968,003 */
+#endif
if (coord_values_8p == true) {
fclose(positions_high_fp);
}
@@ -1144,7 +1454,7 @@ main (int argc, char *argv[]) {
FREE(indexijcompfile);
FREE(indexijptrsfile);
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/false);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
#if 0
/* Not needed if we already have gbuffer */
@@ -1156,7 +1466,7 @@ main (int argc, char *argv[]) {
/*mode*/CMET_STRANDED);
#endif
- lcp = Sarray_compute_lcp_from_genome(SA,gbuffer,/*n*/genomelength);
+ lcp_bytes = Sarray_compute_lcp_bytes_from_genome(&lcp_exceptions,&n_lcp_exceptions,SA,gbuffer,/*n*/genomelength);
munmap((void *) SA,sa_len);
close(sa_fd);
FREE(gbuffer);
@@ -1164,33 +1474,25 @@ main (int argc, char *argv[]) {
Genome_free(&genomebits);
#endif
- /* Write lcp exceptions/guide, but return lcp_bytes */
+ /* Write lcp exceptions/guide */
lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.salcpexc")+1,sizeof(char));
sprintf(lcpexcfile,"%s/%s.metga.salcpexc",destdir,fileroot);
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.metga.salcpguide1024",destdir,fileroot);
-
- lcp_bytes = Bytecoding_write_exceptions_only(lcpexcfile,lcpguidefile,lcp,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,lcpexcfile,lcpguidefile,lcp_bytes,lcp_exceptions,n_lcp_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(lcpguidefile);
FREE(lcpexcfile);
- FREE(lcp); /* Use lcp_bytes, which are more memory-efficient than lcp */
-
/* DC array */
- /* Assume we have lcp_bytes already in memory. Don't need to use guide for speed. */
+ /* Assume we have lcp_bytes and lcp_exceptions already in memory. Don't need to use guide for speed. */
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.metga.salcpguide1024",destdir,fileroot);
- lcp_guide = (UINT4 *) Access_allocate(&shmid,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4),/*sharedp*/false);
+ lcp_guide = (UINT4 *) Access_allocate_private(&lcpguide_access,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4));
FREE(lcpguidefile);
- lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.salcpexc")+1,sizeof(char));
- sprintf(lcpexcfile,"%s/%s.metga.salcpexc",destdir,fileroot);
- lcp_exceptions = (UINT4 *) Access_allocate(&shmid,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4),/*sharedp*/false);
- n_lcp_exceptions = lcpexc_len/(sizeof(UINT4) + sizeof(UINT4));
- FREE(lcpexcfile);
-
/* Compute discriminating chars (DC) array */
discrim_chars = Sarray_discriminating_chars(&nbytes,sarrayfile,genomecomp,lcp_bytes,lcp_guide,
lcp_exceptions,/*guide_interval*/1024,/*n*/genomelength,
@@ -1199,24 +1501,27 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Building child array\n");
/* Compute child array (relative values) */
- child = Sarray_compute_child(lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
+ child_bytes = Sarray_compute_child_bytes(&child_exceptions,&n_child_exceptions,lcp_bytes,lcp_guide,lcp_exceptions,/*n*/genomelength);
FREE(lcp_exceptions);
FREE(lcp_guide);
- /* Write combined lcpchilddc file */
- lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.salcpchilddc")+1,sizeof(char));
- sprintf(lcpchilddcfile,"%s/%s.metga.salcpchilddc",destdir,fileroot);
childexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.sachildexc")+1,sizeof(char));
sprintf(childexcfile,"%s/%s.metga.sachildexc",destdir,fileroot);
childguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.sachildguide1024")+1,sizeof(char));
sprintf(childguidefile,"%s/%s.metga.sachildguide1024",destdir,fileroot);
- Bytecoding_write_lcpchilddc(lcpchilddcfile,childexcfile,childguidefile,child,
- discrim_chars,lcp_bytes,genomelength,/*guide_interval*/1024);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,childexcfile,childguidefile,child_bytes,child_exceptions,n_child_exceptions,
+ genomelength,/*guide_interval*/1024);
FREE(childguidefile);
FREE(childexcfile);
+ FREE(child_exceptions);
+
+ /* Write combined lcpchilddc file */
+ lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".metga.salcpchilddc")+1,sizeof(char));
+ sprintf(lcpchilddcfile,"%s/%s.metga.salcpchilddc",destdir,fileroot);
+ Bytecoding_interleave_lcpchilddc(lcpchilddcfile,child_bytes,discrim_chars,lcp_bytes,genomelength);
FREE(lcpchilddcfile);
- FREE(child);
+ FREE(child_bytes);
FREE(discrim_chars);
FREE(lcp_bytes);
@@ -1224,7 +1529,8 @@ main (int argc, char *argv[]) {
}
compute_ga(new_pointers_filename,new_offsets_filename,
- positions_high_fp,positions_low_fp,ref_offsets,ref_positions8,ref_positions4,
+ positions_high_fp,positions_low_fp,
+ ref_offsetsmeta,ref_offsetsstrm,ref_positions8,ref_positions4,
oligospace,mask,coord_values_8p);
if (coord_values_8p == true) {
fclose(positions_high_fp);
@@ -1236,7 +1542,15 @@ main (int argc, char *argv[]) {
/* Clean up */
- FREE(ref_offsets);
+#ifdef HAVE_MMAP
+ munmap((void *) ref_offsetsmeta,offsetsmeta_len);
+ munmap((void *) ref_offsetsstrm,offsetsstrm_len);
+ close(offsetsmeta_fd);
+ close(offsetsstrm_fd);
+#else
+ FREE(ref_offsetsmeta);
+ FREE(ref_offsetsstrm);
+#endif
if (coord_values_8p == true) {
FREE(ref_positions8);
diff --git a/src/compile b/src/compile
new file mode 100644
index 0000000..51522be
--- /dev/null
+++ b/src/compile
@@ -0,0 +1,165 @@
+-*- mode: compilation; default-directory: "~/bioinfo/gmap/trunk/src/" -*-
+Compilation started at Mon Dec 14 14:13:20
+
+make -k gsnap.sse42
+/gne/home/twu/bin/gcc -DHAVE_CONFIG_H -I. -pthread -DTARGET=\"x86_64-unknown-linux-gnu\" -DGMAPDB=\"/gne/research/data/bioinfo/gmap/data/genomes\" -DMAX_READLENGTH=300 -DGSNAP=1 -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mpopcnt -g -Wall -Wextra -DCHECK_ASSERTIONS=1 -MT gsnap_sse42-dynprog_simd.o -MD -MP -MF .deps/gsnap_sse42-dynprog_simd.Tpo -c -o gsnap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c
+dynprog_simd.c: In function ‘Dynprog_simd_8’:
+dynprog_simd.c:2143:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:2143:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2144:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:2144:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2347:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:2347:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2348:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:2348:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:1942:33: warning: variable ‘extend_ladder’ set but not used [-Wunused-but-set-variable]
+ __m128i gap_open, gap_extend, extend_ladder, complement_dummy;
+ ^
+dynprog_simd.c: In function ‘Dynprog_simd_8_upper’:
+dynprog_simd.c:2770:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:2770:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2771:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:2771:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2896:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:2896:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2897:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:2897:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:2632:8: warning: unused variable ‘na2_single’ [-Wunused-variable]
+ char na2_single;
+ ^
+dynprog_simd.c:2626:70: warning: unused variable ‘pairscore’ [-Wunused-variable]
+ Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore;
+ ^
+dynprog_simd.c: In function ‘Dynprog_simd_8_lower’:
+dynprog_simd.c:3238:3: error: ‘extend_ladder’ undeclared (first use in this function)
+ extend_ladder = _mm_setr_epi8(0,extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*ext
+ ^
+dynprog_simd.c:3238:3: note: each undeclared identifier is reported only once for each function it appears in
+dynprog_simd.c:3267:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ ^
+dynprog_simd.c:3267:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:3389:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ ^
+dynprog_simd.c:3389:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:3089:8: warning: unused variable ‘na2_single’ [-Wunused-variable]
+ char na2_single;
+ ^
+dynprog_simd.c:3083:45: warning: unused variable ‘pairscore’ [-Wunused-variable]
+ Score8_T *pairscores[5], *pairscores_ptr, pairscore;
+ ^
+dynprog_simd.c: In function ‘Dynprog_simd_16’:
+dynprog_simd.c:3739:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:3739:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:3740:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:3740:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:3923:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:3923:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:3924:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:3924:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:3563:33: warning: variable ‘extend_ladder’ set but not used [-Wunused-but-set-variable]
+ __m128i gap_open, gap_extend, extend_ladder, complement_dummy;
+ ^
+dynprog_simd.c: In function ‘Dynprog_simd_16_upper’:
+dynprog_simd.c:4259:3: error: ‘extend_ladder’ undeclared (first use in this function)
+ extend_ladder = _mm_setr_epi16(0,extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*ex
+ ^
+dynprog_simd.c:4284:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:4284:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:4285:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:4285:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:4381:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ ^
+dynprog_simd.c:4381:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:4382:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1
+ ^
+dynprog_simd.c:4382:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:4158:8: warning: unused variable ‘na2_single’ [-Wunused-variable]
+ char na2_single;
+ ^
+dynprog_simd.c:4152:71: warning: unused variable ‘pairscore’ [-Wunused-variable]
+ Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore;
+ ^
+dynprog_simd.c: In function ‘Dynprog_simd_16_lower’:
+dynprog_simd.c:4675:3: error: ‘extend_ladder’ undeclared (first use in this function)
+ extend_ladder = _mm_setr_epi16(0,extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*ex
+ ^
+dynprog_simd.c:4699:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ ^
+dynprog_simd.c:4699:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:4792:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ ^
+dynprog_simd.c:4792:4: warning: array subscript has type ‘char’ [-Wchar-subscripts]
+dynprog_simd.c:4542:8: warning: unused variable ‘na2_single’ [-Wunused-variable]
+ char na2_single;
+ ^
+dynprog_simd.c:4536:46: warning: unused variable ‘pairscore’ [-Wunused-variable]
+ Score16_T *pairscores[5], *pairscores_ptr, pairscore;
+ ^
+dynprog_simd.c: In function ‘Dynprog_traceback_8_lower’:
+dynprog_simd.c:5278:8: warning: unused variable ‘add_dashes_p’ [-Wunused-variable]
+ bool add_dashes_p;
+ ^
+dynprog_simd.c:5275:11: warning: unused parameter ‘cdna_direction’ [-Wunused-parameter]
+ int cdna_direction, bool watsonp, int dynprogindex) {
+ ^
+dynprog_simd.c: In function ‘Dynprog_traceback_16_lower’:
+dynprog_simd.c:5662:8: warning: unused variable ‘add_dashes_p’ [-Wunused-variable]
+ bool add_dashes_p;
+ ^
+dynprog_simd.c:5659:12: warning: unused parameter ‘cdna_direction’ [-Wunused-parameter]
+ int cdna_direction, bool watsonp, int dynprogindex) {
+ ^
+dynprog_simd.c: At top level:
+dynprog_simd.c:1:13: warning: ‘rcsid’ defined but not used [-Wunused-variable]
+ static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
+ ^
+dynprog_simd.c:510:1: warning: ‘Directions8_print’ defined but not used [-Wunused-function]
+ Directions8_print (Direction8_T **directions_nogap, Direction8_T **directions_Egap, Directi
+ ^
+dynprog_simd.c:604:1: warning: ‘Directions8_print_ud’ defined but not used [-Wunused-function]
+ Directions8_print_ud (Direction8_T **directions_nogap, Direction8_T **directions_Egap,
+ ^
+dynprog_simd.c:713:1: warning: ‘Directions16_print’ defined but not used [-Wunused-function]
+ Directions16_print (Direction16_T **directions_nogap, Direction16_T **directions_Egap, Dire
+ ^
+dynprog_simd.c:807:1: warning: ‘Directions16_print_ud’ defined but not used [-Wunused-function]
+ Directions16_print_ud (Direction16_T **directions_nogap, Direction16_T **directions_Egap,
+ ^
+make: *** [gsnap_sse42-dynprog_simd.o] Error 1
+make: Target `gsnap.sse42' not remade because of errors.
+
+Compilation exited abnormally with code 2 at Mon Dec 14 14:13:23
diff --git a/src/compress-write.c b/src/compress-write.c
index c726331..94cd23a 100644
--- a/src/compress-write.c
+++ b/src/compress-write.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: compress-write.c 153955 2014-11-24 17:54:45Z twu $";
+static char rcsid[] = "$Id: compress-write.c 180699 2015-12-10 19:10:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -70,9 +70,10 @@ fill_buffer (int *Buffer, Genomecomp_T high, Genomecomp_T low, Genomecomp_T flag
} else if (Buffer[i] == 'T') {
Buffer[i] = 'X';
} else {
- printf("Parsing error; saw non-ACGT flag plus %c at position %llu\n",
- Buffer[i],(unsigned long long) position+i);
- exit(9);
+ printf("Parsing error; saw non-ACGT flag plus %c at position %llu = %llu + %d\n",
+ Buffer[i],(unsigned long long) position+i,position,i);
+ printf("flags: %08X\n",flags);
+ abort();
}
}
flags >>= 1;
@@ -116,18 +117,18 @@ Compress_get_char (FILE *sequence_fp, Univcoord_T position, bool uncompressedp)
* Compression and uncompression of the genome
************************************************************************/
-/* 87654321 */
-#define LEFT_A 0x00000000
-#define LEFT_C 0x40000000
-#define LEFT_G 0x80000000
-#define LEFT_T 0xC0000000
-#define LEFT_BIT 0x80000000
+/* 87654321 */
+#define UINT4_LEFT_A 0x00000000
+#define UINT4_LEFT_C 0x40000000
+#define UINT4_LEFT_G 0x80000000
+#define UINT4_LEFT_T 0xC0000000
+#define UINT4_LEFT_BIT 0x80000000
-/* 87654321 */
-#define LEFT_0 0x00000000
-#define LEFT_1 0x40000000
-#define LEFT_2 0x80000000
-#define LEFT_3 0xC0000000
+/* 87654321 */
+#define UINT4_LEFT_0 0x00000000
+#define UINT4_LEFT_1 0x40000000
+#define UINT4_LEFT_2 0x80000000
+#define UINT4_LEFT_3 0xC0000000
/* Genomecomp format */
@@ -140,9 +141,9 @@ Compress_get_char (FILE *sequence_fp, Univcoord_T position, bool uncompressedp)
*/
-/* 87654321 */
-#define LEFT_SET 0x80000000
-#define LEFT_CLEAR 0x00000000
+/* 87654321 */
+#define UINT4_LEFT_SET 0x80000000
+#define UINT4_LEFT_CLEAR 0x00000000
/* Genome128 format */
@@ -233,19 +234,19 @@ write_compressed_one (FILE *fp, int *nbadchars, char Buffer[], Univcoord_T posit
flags >>= 1;
switch (carry) {
case 0U: break;
- case 1U: low |= LEFT_C; break;
- case 2U: low |= LEFT_G; break;
- case 3U: low |= LEFT_T; break;
+ case 1U: low |= UINT4_LEFT_C; break;
+ case 2U: low |= UINT4_LEFT_G; break;
+ case 3U: low |= UINT4_LEFT_T; break;
default: abort();
}
switch (uppercaseCode[(int) Buffer[i]]) {
case 'A': break;
- case 'C': high |= LEFT_C; break;
- case 'G': high |= LEFT_G; break;
- case 'T': high |= LEFT_T; break;
- case 'N': flags |= LEFT_BIT; break;
- case 'X': high |= LEFT_T; flags |= LEFT_BIT; break;
+ case 'C': high |= UINT4_LEFT_C; break;
+ case 'G': high |= UINT4_LEFT_G; break;
+ case 'T': high |= UINT4_LEFT_T; break;
+ case 'N': flags |= UINT4_LEFT_BIT; break;
+ case 'X': high |= UINT4_LEFT_T; flags |= UINT4_LEFT_BIT; break;
default:
(*nbadchars) += 1;
if (*nbadchars < MAX_BADCHAR_MESSAGES) {
@@ -256,7 +257,7 @@ write_compressed_one (FILE *fp, int *nbadchars, char Buffer[], Univcoord_T posit
} else if ((*nbadchars) % BADCHAR_INTERVAL == 0) {
fprintf(stderr,"A total of %d non-ACGTNX characters seen so far.\n",*nbadchars);
}
- flags |= LEFT_BIT;
+ flags |= UINT4_LEFT_BIT;
break;
}
}
@@ -281,19 +282,19 @@ put_compressed_one (Genomecomp_T *sectioncomp, int *nbadchars, char Buffer[], Un
flags >>= 1;
switch (carry) {
case 0U: break;
- case 1U: low |= LEFT_C; break;
- case 2U: low |= LEFT_G; break;
- case 3U: low |= LEFT_T; break;
+ case 1U: low |= UINT4_LEFT_C; break;
+ case 2U: low |= UINT4_LEFT_G; break;
+ case 3U: low |= UINT4_LEFT_T; break;
default: abort();
}
switch (uppercaseCode[(int) Buffer[i]]) {
case 'A': break;
- case 'C': high |= LEFT_C; break;
- case 'G': high |= LEFT_G; break;
- case 'T': high |= LEFT_T; break;
- case 'N': flags |= LEFT_BIT; break;
- case 'X': high |= LEFT_T; flags |= LEFT_BIT; break;
+ case 'C': high |= UINT4_LEFT_C; break;
+ case 'G': high |= UINT4_LEFT_G; break;
+ case 'T': high |= UINT4_LEFT_T; break;
+ case 'N': flags |= UINT4_LEFT_BIT; break;
+ case 'X': high |= UINT4_LEFT_T; flags |= UINT4_LEFT_BIT; break;
default:
(*nbadchars) += 1;
if (*nbadchars < MAX_BADCHAR_MESSAGES) {
@@ -304,7 +305,7 @@ put_compressed_one (Genomecomp_T *sectioncomp, int *nbadchars, char Buffer[], Un
} else if ((*nbadchars) % BADCHAR_INTERVAL == 0) {
fprintf(stderr,"A total of %d non-ACGTNX characters seen so far.\n",*nbadchars);
}
- flags |= LEFT_BIT;
+ flags |= UINT4_LEFT_BIT;
break;
}
}
diff --git a/src/compress.c b/src/compress.c
index 8dc44ad..cf3eab9 100644
--- a/src/compress.c
+++ b/src/compress.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: compress.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: compress.c 184457 2016-02-18 00:05:15Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -198,11 +198,10 @@ Compress_print_blocks (Genomecomp_T *blocks, int nshift, int pos5, int pos3) {
void
Compress_print_blocks (Genomecomp_T *blocks, int nshift, int pos5, int pos3) {
int ptr, endptr;
- int startcolumni, endcolumni;
+ /* int startcolumni, endcolumni; */
-
- startcolumni = ((nshift + pos5) % 128) / 32;
- endcolumni = ((nshift + pos3) % 128) / 32;
+ /* startcolumni = ((nshift + pos5) % 128) / 32; */
+ /* endcolumni = ((nshift + pos3) % 128) / 32; */
endptr = (nshift + pos3)/128U*12;
ptr = (nshift + pos5)/128U*12;
@@ -239,30 +238,36 @@ Compress_print_blocks (Genomecomp_T *blocks, int nshift, int pos5, int pos3) {
write_chars(blocks[ptr],blocks[ptr+4],blocks[ptr+8]);
printf("\n");
+#if 0
if (0 && endcolumni == 0) {
printf("\n");
return;
}
+#endif
printf("high: %08X low: %08X flags: %08X\t",
blocks[ptr+1],blocks[ptr+5],blocks[ptr+9]);
write_chars(blocks[ptr+1],blocks[ptr+5],blocks[ptr+9]);
printf("\n");
+#if 0
if (0 && endcolumni == 1) {
printf("\n");
return;
}
+#endif
printf("high: %08X low: %08X flags: %08X\t",
blocks[ptr+2],blocks[ptr+6],blocks[ptr+10]);
write_chars(blocks[ptr+2],blocks[ptr+6],blocks[ptr+10]);
printf("\n");
+#if 0
if (0 && endcolumni == 2) {
printf("\n");
return;
}
+#endif
printf("high: %08X low: %08X flags: %08X\t",
blocks[ptr+3],blocks[ptr+7],blocks[ptr+11]);
@@ -1712,8 +1717,13 @@ Compress32_shift (T this, int nshift) {
void
Compress_get_16mer_left (UINT4 *high, UINT4 *low, UINT4 *flags, T this, int pos3) {
int leftshift, rightshift;
- int columni, blocki;
+ int blocki;
Genomecomp_T *ptr, curr_high, curr_low, curr_flags, prev_high, prev_low, prev_flags;
+#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
+#else
+ int columni;
+#endif
+
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
/* query is stored as 3 x 32-bit words */
@@ -1787,8 +1797,13 @@ Compress_get_16mer_left (UINT4 *high, UINT4 *low, UINT4 *flags, T this, int pos3
void
Compress_get_16mer_right (UINT4 *high, UINT4 *low, UINT4 *flags, T this, int pos5) {
int leftshift, rightshift;
- int columni, blocki;
+ int blocki;
Genomecomp_T *ptr, curr_high, curr_low, curr_flags, next_high, next_low, next_flags;
+#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
+#else
+ int columni;
+#endif
+
#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)
/* query is stored as 3 x 32-bit words */
diff --git a/src/config.h.in b/src/config.h.in
index 07cbd67..167409e 100644
--- a/src/config.h.in
+++ b/src/config.h.in
@@ -22,29 +22,16 @@
*/
#undef HAVE_ALLOCA_H
-/* Define to 1 if you support Altivec instructions */
-#undef HAVE_ALTIVEC
-
/* Define to 1 if bsr command is available in assembly */
#undef HAVE_ASM_BSR
-/* Define to 1 if you support AVX (Advanced Vector Extensions) instructions */
-#undef HAVE_AVX
-
-/* Define to 1 if you support AVX2 (Advanced Vector Extensions 2) instructions
- */
-#undef HAVE_AVX2
-
-/* Define to 1 if you support BMI2 (Bit Manipulation Instruction set 2) */
-#undef HAVE_BMI2
-
/* Define to 1 if __builtin_clz works. */
#undef HAVE_BUILTIN_CLZ
/* Define to 1 if __builtin_ctz works. */
#undef HAVE_BUILTIN_CTZ
-/* Define to 1 if __builtin_popcount works. */
+/* Define to 1 if __builtin_popcount works */
#undef HAVE_BUILTIN_POPCOUNT
/* Define to 1 if you have a working bzlib library. */
@@ -132,9 +119,6 @@
/* Define to 1 if MAP_VARIABLE available for mmap. */
#undef HAVE_MMAP_MAP_VARIABLE
-/* Define to 1 if you support MMX instructions */
-#undef HAVE_MMX
-
/* Define to 1 if you support Intel intrinsic _mm_popcnt_u32/64 instructions
*/
#undef HAVE_MM_POPCNT
@@ -148,6 +132,9 @@
/* Define to 1 if you have the <ndir.h> header file, and it defines `DIR'. */
#undef HAVE_NDIR_H
+/* Define to 1 if you support Intel intrinsic _pext instruction */
+#undef HAVE_PEXT
+
/* Define to 1 if you support Intel intrinsic _popcnt instruction */
#undef HAVE_POPCNT
@@ -187,29 +174,6 @@
/* Define to 1 if you have the `sigaction' function. */
#undef HAVE_SIGACTION
-/* Define to 1 if you support SSE (Streaming SIMD Extensions) instructions */
-#undef HAVE_SSE
-
-/* Define to 1 if you support SSE2 (Streaming SIMD Extensions 2) instructions
- */
-#undef HAVE_SSE2
-
-/* Define to 1 if you support SSE3 (Streaming SIMD Extensions 3) instructions
- */
-#undef HAVE_SSE3
-
-/* Define to 1 if you support SSE4.1 (Streaming SIMD Extensions 4.1)
- instructions */
-#undef HAVE_SSE4_1
-
-/* Define to 1 if you support SSE4.2 (Streaming SIMD Extensions 4.2)
- instructions */
-#undef HAVE_SSE4_2
-
-/* Define to 1 if you support SSSE3 (Supplemental Streaming SIMD Extensions 3)
- instructions */
-#undef HAVE_SSSE3
-
/* Define to 1 if you have the `stat64' function. */
#undef HAVE_STAT64
diff --git a/src/cpuid.c b/src/cpuid.c
new file mode 100644
index 0000000..121842d
--- /dev/null
+++ b/src/cpuid.c
@@ -0,0 +1,107 @@
+#include "cpuid.h"
+#include "bool.h"
+#include <stdio.h>
+
+
+#if defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 1300)
+
+#include <immintrin.h>
+
+void
+CPUID_support (bool *sse2_support_p, bool *ssse3_support_p, bool *sse4_1_support_p, bool *sse4_2_support_p, bool *avx2_support_p) {
+ *sse2_support_p = _may_i_use_cpu_feature(_FEATURE_SSE2);
+ *ssse3_support_p = _may_i_use_cpu_feature(_FEATURE_SSSE3);
+ *sse4_1_support_p = _may_i_use_cpu_feature(_FEATURE_SSE4_1);
+ *sse4_2_support_p = _may_i_use_cpu_feature(_FEATURE_SSE4_2);
+ *avx2_support_p = _may_i_use_cpu_feature(_FEATURE_AVX2 | _FEATURE_FMA | _FEATURE_BMI | _FEATURE_LZCNT | _FEATURE_MOVBE);
+
+ return;
+}
+
+
+#else /* non-Intel compiler */
+
+#define EAX 0
+#define EBX 1
+#define ECX 2
+#define EDX 3
+
+#include <stdint.h>
+#if defined(_MSC_VER)
+#include <intrin.h>
+#endif
+
+static void
+run_cpuid (uint32_t eax, uint32_t ecx, uint32_t *abcd) {
+#if defined(_MSC_VER)
+ __cpuidex(abcd, eax, ecx);
+#else
+ uint32_t ebx, edx;
+#if defined(__i386__) && defined(__PIC__)
+ /* in case of PIC under 32-bit, EBX cannot be clobbered */
+ __asm__ ("movl %%ebx, %%edi \n\t cpuid \n\t xchgl %%ebx, %%edi"
+ : "=D" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
+#else
+ __asm__ ("cpuid" : "+b" (ebx), "+a" (eax), "+c" (ecx), "=d" (edx));
+#endif
+ abcd[EAX] = eax, abcd[EBX] = ebx, abcd[ECX] = ecx, abcd[EDX] = edx;
+#endif
+}
+
+static int
+check_xcr0_ymm () {
+ uint32_t xcr0;
+#if defined(_MSC_VER)
+ xcr0 = (uint32_t)_xgetbv(0); /* min VS2010 SP1 compiler is required */
+#else
+ __asm__ ("xgetbv" : "=a" (xcr0) : "c" (0) : "%edx");
+#endif
+ return ((xcr0 & 6) == 6); /* checking if xmm and ymm state are enabled in XCR0 */
+}
+
+void
+CPUID_support (bool *sse2_support_p, bool *ssse3_support_p, bool *sse4_1_support_p, bool *sse4_2_support_p, bool *avx2_support_p) {
+ uint32_t abcd[4];
+ uint32_t sse2_mask = (1 << 26); /* edx */
+ uint32_t ssse3_mask = (1 << 9); /* ecx */
+ uint32_t sse4_1_mask = (1 << 19); /* ecx */
+ uint32_t sse4_2_mask = (1 << 20); /* ecx */
+#if 0
+ uint32_t popcnt_mask = (1 << 23); /* ecx */
+#endif
+ uint32_t fma_movbe_osxsave_mask = ((1 << 12) | (1 << 22) | (1 << 27)); /* ecx */
+ uint32_t avx2_bmi12_mask = ((1 << 5) | (1 << 3) | (1 << 8)); /* ebx */
+ uint32_t lzcnt_mask = (1 << 5); /* ecx */
+
+
+ run_cpuid(1, 0, abcd);
+ *sse2_support_p = ((abcd[EDX] & sse2_mask) == sse2_mask) ? true : false;
+ *ssse3_support_p = ((abcd[ECX] & ssse3_mask) == ssse3_mask) ? true : false;
+ *sse4_1_support_p = ((abcd[ECX] & sse4_1_mask) == sse4_1_mask) ? true : false;
+ *sse4_2_support_p = ((abcd[ECX] & sse4_2_mask) == sse4_2_mask) ? true : false;
+ /* *popcnt_support_p = ((abcd[ECX] & popcnt_mask) == popcnt_mask); */
+
+ if ((abcd[ECX] & fma_movbe_osxsave_mask) != fma_movbe_osxsave_mask) {
+ *avx2_support_p = false;
+ } else if (!check_xcr0_ymm()) {
+ *avx2_support_p = false;
+ } else {
+ run_cpuid(7, 0, abcd);
+ if ((abcd[EBX] & avx2_bmi12_mask) != avx2_bmi12_mask) {
+ *avx2_support_p = false;
+ } else {
+ run_cpuid(0x80000001, 0, abcd);
+ if ((abcd[ECX] & lzcnt_mask) != lzcnt_mask) {
+ *avx2_support_p = false;
+ } else {
+ *avx2_support_p = true;
+ }
+ }
+ }
+
+ return;
+}
+
+#endif /* non-Intel compiler */
+
+
diff --git a/src/cpuid.h b/src/cpuid.h
new file mode 100644
index 0000000..97048ab
--- /dev/null
+++ b/src/cpuid.h
@@ -0,0 +1,10 @@
+/* $Id: cpuid.h 171614 2015-08-10 23:27:29Z twu $ */
+#ifndef CPUID_INCLUDED
+#define CPUID_INCLUDED
+#include "bool.h"
+
+extern void
+CPUID_support (bool *sse2_support_p, bool *ssse3_support_p, bool *sse4_1_support_p, bool *sse4_2_support_p, bool *avx2_support_p);
+
+#endif
+
diff --git a/src/datadir.c b/src/datadir.c
index 42874c1..579f2d1 100644
--- a/src/datadir.c
+++ b/src/datadir.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: datadir.c 73988 2012-09-13 23:55:05Z twu $";
+static char rcsid[] = "$Id: datadir.c 175304 2015-09-24 17:47:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -6,7 +6,7 @@ static char rcsid[] = "$Id: datadir.c 73988 2012-09-13 23:55:05Z twu $";
#include "datadir.h"
#include <stdio.h>
#include <stdlib.h> /* For getenv */
-#include <string.h>
+#include <string.h> /* For strlen */
#include <strings.h> /* For rindex */
#include <pwd.h>
#ifdef HAVE_SYS_TYPES_H
@@ -122,13 +122,13 @@ find_fileroot (char *genomesubdir, char *genomedir, char *dbroot) {
static char *
get_dbversion (char *filename) {
- char *dbversion = NULL, Buffer[100], *p;
+ char *dbversion = NULL, Buffer[1024], *p;
FILE *fp;
fp = FOPEN_READ_TEXT(filename);
if (!fp) {
return NULL;
- } else if (fgets(Buffer,100,fp) == NULL) {
+ } else if (fgets(Buffer,1024,fp) == NULL) {
fclose(fp);
return NULL;
} else {
@@ -138,7 +138,7 @@ get_dbversion (char *filename) {
fclose(fp);
}
- dbversion = (char *) CALLOC(strlen(Buffer)+1,sizeof(char));
+ dbversion = (char *) MALLOC((strlen(Buffer)+1)*sizeof(char));
strcpy(dbversion,Buffer);
return dbversion;
}
diff --git a/src/dynprog.c b/src/dynprog.c
index 9e4cc2b..48a7dff 100644
--- a/src/dynprog.c
+++ b/src/dynprog.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: dynprog.c 184440 2016-02-17 21:03:49Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -73,11 +73,11 @@ static char rcsid[] = "$Id: dynprog.c 145990 2014-08-25 21:47:32Z twu $";
#define debug12a(x)
#endif
-/* Comparing SIMD with standard code */
-#ifdef DEBUG14
-#define debug14(x) x
+/* Comparing SIMD with standard code. Define in dynprog.h */
+#ifdef DEBUG_SIMD
+#define debug_simd(x) x
#else
-#define debug14(x)
+#define debug_simd(x)
#endif
@@ -85,7 +85,7 @@ static char rcsid[] = "$Id: dynprog.c 145990 2014-08-25 21:47:32Z twu $";
#define RIGHTANGLE 1
*/
-#if defined(DEBUG2) || defined(DEBUG14)
+#if defined(DEBUG2) || defined(DEBUG_SIMD)
#define NEG_INFINITY_DISPLAY (-99)
#endif
@@ -111,6 +111,7 @@ static char rcsid[] = "$Id: dynprog.c 145990 2014-08-25 21:47:32Z twu $";
#define T Dynprog_T
+
char *
Dynprog_endalign_string (Endalign_T endalign) {
switch (endalign) {
@@ -143,6 +144,7 @@ Dynprog_score (int matches, int mismatches, int qopens, int qindels, int topens,
}
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
static char complCode[128] = COMPLEMENT_LC;
static char
@@ -210,13 +212,14 @@ get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T
return complCode[(int) c2];
}
}
+#endif
/************************************************************************
* Matrix
************************************************************************/
-#if !defined(HAVE_SSE2) || defined(DEBUG14)
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
/* Makes a matrix of dimensions 0..glength x 0..rlength inclusive */
static Score32_T **
Matrix32_alloc (int rlength, int glength, Score32_T **ptrs, Score32_T *space) {
@@ -242,9 +245,9 @@ Matrix32_alloc (int rlength, int glength, Score32_T **ptrs, Score32_T *space) {
#endif
-#ifdef DEBUG2
+#if defined(DEBUG2) || defined(DEBUG_SIMD)
void
-Matrix32_print (Score32_T **matrix, int rlength, int glength, char *rsequence,
+Dynprog_Matrix32_print (Score32_T **matrix, int rlength, int glength, char *rsequence,
char *gsequence, char *gsequencealt,
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh,
bool watsonp, bool revp, int lband, int uband) {
@@ -497,7 +500,7 @@ Matrix3_print (struct Int3_T **matrix, int rlength, int glength, char *rsequence
/* Directions */
/************************************************************************/
-#if !defined(HAVE_SSE2) || defined(DEBUG14)
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
/* Makes a matrix of dimensions 0..glength x 0..rlength inclusive */
static Direction32_T **
Directions32_alloc (int rlength, int glength, Direction32_T **ptrs, Direction32_T *space) {
@@ -518,12 +521,12 @@ Directions32_alloc (int rlength, int glength, Direction32_T **ptrs, Direction32_
-#ifdef DEBUG2
+#if defined(DEBUG2) || defined(DEBUG_SIMD)
void
-Directions32_print (Direction32_T **directions_nogap, Direction32_T **directions_Egap, Direction32_T **directions_Fgap,
- int rlength, int glength, char *rsequence, char *gsequence, char *gsequence_alt,
- int goffset, Univcoord_T chroffset, Univcoord_T chrhigh,
- bool watsonp, bool revp, int lband, int uband) {
+Dynprog_Directions32_print (Direction32_T **directions_nogap, Direction32_T **directions_Egap, Direction32_T **directions_Fgap,
+ int rlength, int glength, char *rsequence, char *gsequence, char *gsequence_alt,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh,
+ bool watsonp, bool revp, int lband, int uband) {
int i, j;
char g_alt;
@@ -659,7 +662,7 @@ Dynprog_new (int maxlookback, int extraquerygap, int maxpeelback,
new->matrix3_ptrs = (struct Int3_T **) CALLOC(max_glength+1,sizeof(struct Int3_T *));
new->matrix3_space = (struct Int3_T *) CALLOC((max_glength+1)*(max_rlength+1),sizeof(struct Int3_T));
#endif
-#if !defined(HAVE_SSE2) || defined(DEBUG14)
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
new->matrix_ptrs = (Score32_T **) CALLOC(max_glength+1,sizeof(Score32_T *));
new->matrix_space = (Score32_T *) CALLOC((max_glength+1)*(max_glength+1),sizeof(Score32_T));
new->directions_ptrs_0 = (Direction32_T **) CALLOC(max_glength+1,sizeof(Direction32_T *));
@@ -673,30 +676,62 @@ Dynprog_new (int maxlookback, int extraquerygap, int maxpeelback,
/* Use SIMD_NCHARS > SIMD_NSHORTS and sizeof(Score16_T) > sizeof(Score8_T) */
if (doublep == true) {
new->aligned.two.upper_matrix_ptrs = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.two.upper_matrix_space = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.two.upper_matrix_space = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.two.upper_directions_ptrs_0 = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.two.upper_directions_space_0 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.two.upper_directions_space_0 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.two.upper_directions_ptrs_1 = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.two.upper_directions_space_1 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.two.upper_directions_space_1 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.two.lower_matrix_ptrs = (void **) CALLOC(max_rlength+1,sizeof(void *));
- new->aligned.two.lower_matrix_space = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.two.lower_matrix_space = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.two.lower_directions_ptrs_0 = (void **) CALLOC(max_rlength+1,sizeof(void *));
- new->aligned.two.lower_directions_space_0 = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.two.lower_directions_space_0 = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.two.lower_directions_ptrs_1 = (void **) CALLOC(max_rlength+1,sizeof(void *));
- new->aligned.two.lower_directions_space_1 = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.two.lower_directions_space_1 = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->nspaces = 2;
} else {
new->aligned.one.matrix_ptrs = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.one.matrix_space = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.one.matrix_space = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.one.directions_ptrs_0 = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.one.directions_space_0 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.one.directions_space_0 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.one.directions_ptrs_1 = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.one.directions_space_1 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.one.directions_space_1 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->aligned.one.directions_ptrs_2 = (void **) CALLOC(max_glength+1,sizeof(void *));
- new->aligned.one.directions_space_2 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),16);
+ new->aligned.one.directions_space_2 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+
+ new->nspaces = 1;
+ }
+#endif
+#if defined(DEBUG_AVX2)
+ /* Use SIMD_NCHARS > SIMD_NSHORTS and sizeof(Score16_T) > sizeof(Score8_T) */
+ if (doublep == true) {
+ new->aligned_std.two.upper_matrix_ptrs = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.two.upper_matrix_space = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.two.upper_directions_ptrs_0 = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.two.upper_directions_space_0 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.two.upper_directions_ptrs_1 = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.two.upper_directions_space_1 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+
+ new->aligned_std.two.lower_matrix_ptrs = (void **) CALLOC(max_rlength+1,sizeof(void *));
+ new->aligned_std.two.lower_matrix_space = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.two.lower_directions_ptrs_0 = (void **) CALLOC(max_rlength+1,sizeof(void *));
+ new->aligned_std.two.lower_directions_space_0 = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.two.lower_directions_ptrs_1 = (void **) CALLOC(max_rlength+1,sizeof(void *));
+ new->aligned_std.two.lower_directions_space_1 = (void *) _mm_malloc((max_rlength+1)*(max_glength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+
+ new->nspaces = 2;
+
+ } else {
+ new->aligned_std.one.matrix_ptrs = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.one.matrix_space = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.one.directions_ptrs_0 = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.one.directions_space_0 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.one.directions_ptrs_1 = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.one.directions_space_1 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
+ new->aligned_std.one.directions_ptrs_2 = (void **) CALLOC(max_glength+1,sizeof(void *));
+ new->aligned_std.one.directions_space_2 = (void *) _mm_malloc((max_glength+1)*(max_rlength+SIMD_NCHARS+SIMD_NCHARS)*sizeof(Score16_T),ALIGN_SIZE);
new->nspaces = 1;
}
@@ -712,7 +747,7 @@ Dynprog_free (T *old) {
FREE((*old)->matrix3_ptrs);
FREE((*old)->matrix3_space);
#endif
-#if !defined(HAVE_SSE2) || defined(DEBUG14)
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
FREE((*old)->matrix_ptrs);
FREE((*old)->matrix_space);
FREE((*old)->directions_ptrs_2);
@@ -748,6 +783,32 @@ Dynprog_free (T *old) {
_mm_free((*old)->aligned.two.lower_directions_space_0);
}
#endif
+#if defined(DEBUG_AVX2)
+ if ((*old)->nspaces == 1) {
+ FREE((*old)->aligned_std.one.matrix_ptrs);
+ _mm_free((*old)->aligned_std.one.matrix_space);
+ FREE((*old)->aligned_std.one.directions_ptrs_2);
+ _mm_free((*old)->aligned_std.one.directions_space_2);
+ FREE((*old)->aligned_std.one.directions_ptrs_1);
+ _mm_free((*old)->aligned_std.one.directions_space_1);
+ FREE((*old)->aligned_std.one.directions_ptrs_0);
+ _mm_free((*old)->aligned_std.one.directions_space_0);
+ } else {
+ FREE((*old)->aligned_std.two.upper_matrix_ptrs);
+ _mm_free((*old)->aligned_std.two.upper_matrix_space);
+ FREE((*old)->aligned_std.two.upper_directions_ptrs_1);
+ _mm_free((*old)->aligned_std.two.upper_directions_space_1);
+ FREE((*old)->aligned_std.two.upper_directions_ptrs_0);
+ _mm_free((*old)->aligned_std.two.upper_directions_space_0);
+
+ FREE((*old)->aligned_std.two.lower_matrix_ptrs);
+ _mm_free((*old)->aligned_std.two.lower_matrix_space);
+ FREE((*old)->aligned_std.two.lower_directions_ptrs_1);
+ _mm_free((*old)->aligned_std.two.lower_directions_space_1);
+ FREE((*old)->aligned_std.two.lower_directions_ptrs_0);
+ _mm_free((*old)->aligned_std.two.lower_directions_space_0);
+ }
+#endif
FREE(*old);
}
@@ -757,42 +818,6 @@ Dynprog_free (T *old) {
/************************************************************************/
-#ifdef PMAP
-/* Same as in boyer-moore.c */
-/* Handle only cases in iupac table in sequence.c */
-static bool matchtable[26][26] =
-/* A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z */
- {{1,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,0,0,0,0,1,0,0,0}, /* A */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* B */
- {0,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,0,0,0,0,0,1,0}, /* C */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* D */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* E */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* F */
- {0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0,0,0,0}, /* G */
- {1,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,1,1,0,0,1,0,1,0}, /* H = [ACT] */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* I */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* J */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* K */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* L */
- {1,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,1,0,0,0,1,0,1,0}, /* M = [AC] */
- {1,0,1,0,0,0,1,1,0,0,0,0,1,1,0,0,0,1,1,1,0,0,1,0,1,0}, /* N = [ACGT] */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* O */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* P */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* Q */
- {1,0,0,0,0,0,1,1,0,0,0,0,1,1,0,0,0,1,1,0,0,0,1,0,0,0}, /* R = [AG] */
- {0,0,1,0,0,0,1,1,0,0,0,0,1,1,0,0,0,1,1,0,0,0,0,0,1,0}, /* S = [CG] */
- {0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,1,0}, /* T */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* U */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* V */
- {1,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,0,1,0,0,1,0,1,0}, /* W = [AT] */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* X */
- {0,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,1,0,0,1,0,1,0}, /* Y = [CT] */
- {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}}; /* Z */
-#endif
-
-
-/************************************************************************/
-
/* These are extern arrays, used by all dynprog procedures */
Pairdistance_T **pairdistance_array[NMISMATCHTYPES];
#ifndef HAVE_SSE4_1
@@ -1087,14 +1112,16 @@ Dynprog_compute_bands (int *lband, int *uband, int rlength, int glength, int ext
}
-#if !defined(HAVE_SSE2) || defined(DEBUG14)
+/* For upper triangular, we allow horizontal (E) jumps. For lower triangular, we allow vertical (F) jumps */
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
Score32_T **
Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions_Egap, Direction32_T ***directions_Fgap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
Mismatchtype_T mismatchtype, Score32_T open, Score32_T extend,
- int lband, int uband, bool jump_late_p, bool revp, int saturation) {
+ int lband, int uband, bool jump_late_p, bool revp, int saturation,
+ bool upperp, bool lowerp) {
#ifdef DEBUG12
Score32_T bestscore;
Direction32_T bestdir;
@@ -1120,6 +1147,22 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
*directions_Fgap = Directions32_alloc(rlength,glength,this->directions_ptrs_2,this->directions_space_2);
/* (*directions_nogap)[0][0] = STOP; -- Check for r > 0 && c > 0 instead */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ /* Row 0 initialization */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ matrix[c][0] = 0;
+ (*directions_Egap)[c][0] = HORIZ;
+ (*directions_nogap)[c][0] = HORIZ;
+ }
+
+ /* Column 0 initialization */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ matrix[0][r] = 0;
+ (*directions_Fgap)[0][r] = VERT;
+ (*directions_nogap)[0][r] = VERT;
+ }
+
+#else
/* Row 0 initialization */
penalty = open;
for (c = 1; c <= uband && c <= glength; c++) {
@@ -1145,10 +1188,22 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
/* Already initialized to DIAG */
(*directions_Fgap)[0][1] = DIAG; /* previously used STOP */
#endif
+#endif
r_gap = (Score32_T *) MALLOCA((rlength+1) * sizeof(Score32_T));
nogap = (Score32_T *) MALLOCA((rlength+1) * sizeof(Score32_T));
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ nogap[0] = 0;
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ r_gap[r] = NEG_INFINITY_32;
+ nogap[r] = 0;
+ }
+ for ( ; r <= rlength; r++) {
+ r_gap[r] = NEG_INFINITY_32;
+ nogap[r] = NEG_INFINITY_32;
+ }
+#else
nogap[0] = 0;
penalty = open;
for (r = 1; r <= lband && r <= rlength; r++) {
@@ -1160,6 +1215,7 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
r_gap[r] = NEG_INFINITY_32;
nogap[r] = NEG_INFINITY_32;
}
+#endif
#ifdef DEBUG12
@@ -1204,14 +1260,27 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
if (c == 1) {
rlo = 1;
prev_nogap = 0; /* was nogap[rlo-1] */
- last_nogap = penalty;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ last_nogap = 0;
+#else
+ last_nogap = NEG_INFINITY_32 - open + 1; /* making c_gap < last_nogap + open */
+#endif
} else if ((rlo = c - uband) < 1) {
rlo = 1;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ prev_nogap = 0;
+ last_nogap = 0;
+#else
prev_nogap = penalty;
penalty += extend;
last_nogap = penalty;
+#endif
} else if (rlo == 1) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ prev_nogap = 0;
+#else
prev_nogap = penalty;
+#endif
/* penalty += extend; */
last_nogap = NEG_INFINITY_32;
#ifdef DEBUG12
@@ -1262,7 +1331,7 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
assert(matrix3[c][r-1].Fgap == c_gap);
#endif
debug3(printf("std Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",r,c,c_gap + extend,last_nogap + open + extend));
- if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
+ if (lowerp == true && c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
c_gap += extend;
(*directions_Fgap)[c][r] = VERT;
} else {
@@ -1294,7 +1363,7 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
assert(matrix3[c-1][r].Egap == r_gap[r]);
#endif
/* debug3(printf("Egap at r %d, c %d: r_gap[r] %d vs nogap[r] + open %d\n",r,c,r_gap[r],nogap[r]+open)); */
- if (r_gap[r] /* + extend */ >= (score = nogap[r] + open /* + extend */)) { /* Use >= for jump late */
+ if (upperp == true && r_gap[r] /* + extend */ >= (score = nogap[r] + open /* + extend */)) { /* Use >= for jump late */
r_gap[r] += extend;
(*directions_Egap)[c][r] = HORIZ;
} else {
@@ -1340,11 +1409,11 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
/* bestdir2 = DIAG; -- Already initialized to DIAG */
/* debug3(printf("assign nogap at r %d, c %d: H + pairscore %d vs r_horiz + extend %d vs vert + extend %d\n",
r,c,last_nogap,r_gap[r],c_gap)); */
- if (r_gap[r] >= last_nogap) { /* Use >= for jump late */
+ if (upperp == true && r_gap[r] >= last_nogap) { /* Use >= for jump late */
last_nogap = r_gap[r];
(*directions_nogap)[c][r] = HORIZ;
}
- if (c_gap >= last_nogap) { /* Use >= for jump late */
+ if (lowerp == true && c_gap >= last_nogap) { /* Use >= for jump late */
last_nogap = c_gap;
(*directions_nogap)[c][r] = VERT;
}
@@ -1378,14 +1447,27 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
if (c == 1) {
rlo = 1;
prev_nogap = 0; /* was nogap[rlo-1] */
- last_nogap = penalty;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ last_nogap = 0;
+#else
+ last_nogap = NEG_INFINITY_32 - open + 1; /* making c_gap < last_nogap + open */
+#endif
} else if ((rlo = c - uband) < 1) {
rlo = 1;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ prev_nogap = 0;
+ last_nogap = 0;
+#else
prev_nogap = penalty;
penalty += extend;
last_nogap = penalty;
+#endif
} else if (rlo == 1) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ prev_nogap = 0;
+#else
prev_nogap = penalty;
+#endif
/* penalty += extend; */
last_nogap = NEG_INFINITY_32;
#ifdef DEBUG12
@@ -1436,7 +1518,7 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
assert(matrix3[c][r-1].Fgap == c_gap);
#endif
debug3(printf("std Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",r,c,c_gap + extend,last_nogap + open + extend));
- if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
+ if (lowerp == true && c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
c_gap += extend;
(*directions_Fgap)[c][r] = VERT;
} else {
@@ -1468,7 +1550,7 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
assert(matrix3[c-1][r].Egap == r_gap[r]);
#endif
/* debug3(printf("Egap at r %d, c %d: r_gap[r] %d vs nogap[r] + open %d\n",r,c,r_gap[r],nogap[r]+open)); */
- if (r_gap[r] /* + extend */ > (score = nogap[r] + open /* + extend */)) { /* Use > for jump early */
+ if (upperp == true && r_gap[r] /* + extend */ > (score = nogap[r] + open /* + extend */)) { /* Use > for jump early */
r_gap[r] += extend;
(*directions_Egap)[c][r] = HORIZ;
} else {
@@ -1514,11 +1596,11 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
/* bestdir2 = DIAG; -- Already initialized to DIAG */
/* debug3(printf("assign nogap at r %d, c %d: H + pairscore %d vs r_horiz + extend %d vs vert + extend %d\n",
r,c,last_nogap,r_gap[r],c_gap)); */
- if (r_gap[r] > last_nogap) { /* Use > for jump early */
+ if (upperp == true && r_gap[r] > last_nogap) { /* Use > for jump early */
last_nogap = r_gap[r];
(*directions_nogap)[c][r] = HORIZ;
}
- if (c_gap > last_nogap) { /* Use > for jump early */
+ if (lowerp == true && c_gap > last_nogap) { /* Use > for jump early */
last_nogap = c_gap;
(*directions_nogap)[c][r] = VERT;
}
@@ -1536,11 +1618,11 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
}
}
- debug2(Matrix32_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp,lband,uband));
- debug2(Directions32_print(*directions_nogap,*directions_Egap,*directions_Fgap,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp,lband,uband));
+ debug2(Dynprog_Matrix32_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp,lband,uband));
+ debug2(Dynprog_Directions32_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp,lband,uband));
debug12a(Matrix3_print(matrix3,rlength,glength,rsequence,gsequence,gsequence_alt,
goffset,chroffset,chrhigh,watsonp,revp));
@@ -1562,14 +1644,13 @@ Dynprog_traceback_std (List_T pairs, int *nmatches, int *nmismatches, int *nopen
Direction32_T **directions_nogap, Direction32_T **directions_Egap, Direction32_T **directions_Fgap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
int querycoord, genomecoord;
Direction32_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG_SIMD
char c2_single;
#endif
@@ -1591,10 +1672,9 @@ Dynprog_traceback_std (List_T pairs, int *nmatches, int *nmismatches, int *nopen
#endif
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -1635,7 +1715,7 @@ Dynprog_traceback_std (List_T pairs, int *nmatches, int *nmismatches, int *nopen
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG_SIMD
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -1694,10 +1774,9 @@ Dynprog_traceback_std (List_T pairs, int *nmatches, int *nmismatches, int *nopen
assert(r == 0);
dist = c;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
diff --git a/src/dynprog.h b/src/dynprog.h
index b4b134c..a9be567 100644
--- a/src/dynprog.h
+++ b/src/dynprog.h
@@ -1,10 +1,24 @@
-/* $Id: dynprog.h 157225 2015-01-22 18:47:23Z twu $ */
+/* $Id: dynprog.h 184430 2016-02-17 19:56:26Z twu $ */
#ifndef DYNPROG_INCLUDED
#define DYNPROG_INCLUDED
#ifdef HAVE_CONFIG_H
#include <config.h> /* For HAVE_SSE2, HAVE_SSE4_1 */
#endif
+
+/* #define DEBUG_SIMD 1 */
+/* #define DEBUG_AVX2 1 */
+
+/* Used by dynprog_simd.c and dynprog.c when comparing using DEBUG_SIMD or DEBUG_AVX2 */
+/* #define ZERO_INITIAL_GAP_PENALTY 1 */ /* Needed for bam_indelfix */
+#define INFINITE_INITIAL_GAP_PENALTY 1 /* Prevents any gaps on row 0 or column 0 */
+
+/* Note: If we select neither ZERO_INITIAL_GAP_PENALTY or
+ INFINITE_INITIAL_GAP_PENALTY, we have standard behavior, which
+ allows open+extend on row 0 or column 0 */
+
+
+
/* BEST_LOCAL is a local alignment, whereas QUERYEND_INDELS and
QUERYEND_NOGAPS are global. QUERYEND_GAP allows an intron at the
end */
@@ -81,14 +95,39 @@ typedef int Direction32_T;
/* We can allow -128 and -32768 for NEG_INFINITY in SIMD procedures,
because we are using saturation */
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#ifdef HAVE_AVX2
+#define ALIGN_SIZE 32
#define ONE_CHAR 1
-#define LAST_CHAR 15
+#define MID_CHAR_INSERT 16
+#define LAST_CHAR_INSERT 0
+#define SIMD_NCHARS 32 /* 32 8-bit chars in 256 bits */
+
+#define ONE_SHORT 2
+#define MID_SHORT_INSERT 8
+#define LAST_SHORT_INSERT 0
+#define SIMD_NSHORTS 16 /* 16 16-bit shorts in 256 bits */
+
+#define LAST_CHAR_NONAVX2 15 /* For DEBUG_AVX2 */
+#define LAST_SHORT_NONAVX2 14 /* For DEBUG_AVX2. (8 - 1) * 2 */
+
+#ifdef DEBUG_AVX2
+#define SIMD_NCHARS_NONAVX2 16
+#define SIMD_NSHORTS_NONAVX2 8
+#endif
+
+#elif defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#define ALIGN_SIZE 16
+#define ONE_CHAR 1
+#define LAST_CHAR_SHIFT 15
#define SIMD_NCHARS 16 /* 16 8-bit chars in 128 bits */
#define ONE_SHORT 2
-#define LAST_SHORT 14 /* (8 - 1) * 2 */
+#define LAST_SHORT_SHIFT 14 /* (8 - 1) * 2 */
#define SIMD_NSHORTS 8 /* 8 16-bit shorts in 128 bits */
+
+#define LAST_CHAR_NONAVX2 15 /* For DEBUG_SIMD */
+#define LAST_SHORT_NONAVX2 14 /* For DEBUG_SIMD */
+
#endif
/* Can allow -32768 in non-SIMD procedures, because we are using ints */
@@ -134,7 +173,7 @@ struct T {
struct Int3_T **matrix3_ptrs, *matrix3_space;
#endif
-#if !defined(HAVE_SSE2) || defined(DEBUG14)
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
Score32_T **matrix_ptrs, *matrix_space;
Direction32_T **directions_ptrs_0, *directions_space_0;
Direction32_T **directions_ptrs_1, *directions_space_1;
@@ -145,6 +184,12 @@ struct T {
struct Space_single_T one;
struct Space_double_T two;
} aligned;
+#ifdef DEBUG_AVX2
+ union {
+ struct Space_single_T one;
+ struct Space_double_T two;
+ } aligned_std;
+#endif
#endif
int nspaces;
};
@@ -194,15 +239,15 @@ Dynprog_standard (Direction32_T ***directions_nogap, Direction32_T ***directions
int rlength, int glength,
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
Mismatchtype_T mismatchtype, Score32_T open, Score32_T extend,
- int lband, int uband, bool jump_late_p, bool revp, int saturation);
+ int lband, int uband, bool jump_late_p, bool revp, int saturation,
+ bool upperp, bool lowerp);
extern List_T
Dynprog_traceback_std (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction32_T **directions_nogap, Direction32_T **directions_Egap, Direction32_T **directions_Fgap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex);
#undef T
diff --git a/src/dynprog_cdna.c b/src/dynprog_cdna.c
index d3d6592..7e0ee13 100644
--- a/src/dynprog_cdna.c
+++ b/src/dynprog_cdna.c
@@ -1,20 +1,14 @@
-static char rcsid[] = "$Id: dynprog_cdna.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: dynprog_cdna.c 184458 2016-02-18 00:06:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#include "dynprog_genome.h"
+#include "dynprog_cdna.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h> /* For ceil, log, pow */
#include <ctype.h> /* For tolower */
-#ifdef HAVE_SSE2
-#include <emmintrin.h>
-#endif
-#ifdef HAVE_SSE4_1
-#include <smmintrin.h>
-#endif
#include "bool.h"
@@ -141,7 +135,7 @@ get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T
}
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Columns are always genomic. Rows are always query. Bridging across common columns */
static void
bridge_cdna_gap_8_ud (int *finalscore, int *bestcL, int *bestcR, int *bestrL, int *bestrR,
@@ -150,7 +144,7 @@ bridge_cdna_gap_8_ud (int *finalscore, int *bestcL, int *bestcR, int *bestrL, in
int glength, int rlengthL, int rlengthR,
int lbandL, int ubandL, int lbandR, int ubandR,
int open, int extend, int leftoffset, int rightoffset, bool jump_late_p) {
- int bestscore = NEG_INFINITY_16, score, scoreL, scoreR, pen, end_reward = 0;
+ int bestscore = NEG_INFINITY_8, score, scoreL, scoreR, pen, end_reward = 0;
int rL, rR, cL, cR;
int rloL, rhighL;
int rloR, rhighR;
@@ -405,7 +399,7 @@ bridge_cdna_gap_8_ud (int *finalscore, int *bestcL, int *bestcR, int *bestrL, in
}
#endif
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Columns are always genomic. Rows are always query. Bridging across common columns */
static void
bridge_cdna_gap_16_ud (int *finalscore, int *bestcL, int *bestcR, int *bestrL, int *bestrR,
@@ -819,14 +813,14 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
int rlengthL, int rlengthR, int glength,
int roffsetL, int rev_roffsetR, int goffset,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_paired, double defect_rate) {
List_T pairs = NULL;
char *gsequence, *gsequence_alt, *rev_gsequence, *rev_gsequence_alt;
Mismatchtype_T mismatchtype;
int lbandL, ubandL, lbandR, ubandR;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
Score8_T **matrix8L_upper, **matrix8L_lower, **matrix8R_upper, **matrix8R_lower;
Direction8_T **directions8L_upper_nogap, **directions8L_upper_Egap,
**directions8L_lower_nogap, **directions8L_lower_Egap,
@@ -927,7 +921,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
debug(printf("At query offset %d-%d, %.*s\n",rev_roffsetR-rlengthR+1,rev_roffsetR,rlengthR,&(rev_rsequenceR[-rlengthR+1])));
debug(printf("Whole piece at query offset %d-%d, %.*s\n",roffsetL,rev_roffsetR,rev_roffsetR-roffsetL+1,rsequenceL));
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (glength <= SIMD_MAXLENGTH_EPI8 || (rlengthL <= SIMD_MAXLENGTH_EPI8 && rlengthR <= SIMD_MAXLENGTH_EPI8)) {
use8p = true;
@@ -962,19 +956,19 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
}
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
if (use8p == true) {
Dynprog_compute_bands(&lbandL,&ubandL,rlengthL,glength,extraband_paired,/*widebandp*/true);
matrix8L_upper = Dynprog_simd_8_upper(&directions8L_upper_nogap,&directions8L_upper_Egap,dynprogL,
rsequenceL,gsequence,gsequence_alt,rlengthL,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
matrix8L_lower = Dynprog_simd_8_lower(&directions8L_lower_nogap,&directions8L_lower_Egap,dynprogL,
rsequenceL,gsequence,gsequence_alt,rlengthL,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
@@ -984,7 +978,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
matrix8R_upper = Dynprog_simd_8_upper(&directions8R_upper_nogap,&directions8R_upper_Egap,dynprogR,
rev_rsequenceR,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlengthR,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -992,7 +986,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
matrix8R_lower = Dynprog_simd_8_lower(&directions8R_lower_nogap,&directions8R_lower_Egap,dynprogR,
rev_rsequenceR,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlengthR,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -1010,14 +1004,14 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
bestrR,bestcR,rev_rsequenceR,rev_rsequence_ucR,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffsetR,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_8_lower(NULL,&nmatches,&nmismatches,&nopens,&nindels,
directions8R_lower_nogap,directions8R_lower_Egap,
bestrR,bestcR,rev_rsequenceR,rev_rsequence_ucR,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffsetR,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
pairs = List_reverse(pairs);
@@ -1067,13 +1061,13 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
directions8L_upper_nogap,directions8L_upper_Egap,
bestrL,bestcL,rsequenceL,rsequence_ucL,
gsequence,gsequence_alt,roffsetL,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_8_lower(pairs,&nmatches,&nmismatches,&nopens,&nindels,
directions8L_lower_nogap,directions8L_lower_Egap,
bestrL,bestcL,rsequenceL,rsequence_ucL,
gsequence,gsequence_alt,roffsetL,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
if (List_length(pairs) == 1) {
@@ -1096,14 +1090,14 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
Dynprog_compute_bands(&lbandL,&ubandL,rlengthL,glength,extraband_paired,/*widebandp*/true);
matrix16L_upper = Dynprog_simd_16_upper(&directions16L_upper_nogap,&directions16L_upper_Egap,dynprogL,
rsequenceL,gsequence,gsequence_alt,rlengthL,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
matrix16L_lower = Dynprog_simd_16_lower(&directions16L_lower_nogap,&directions16L_lower_Egap,dynprogL,
rsequenceL,gsequence,gsequence_alt,rlengthL,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
@@ -1112,7 +1106,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
matrix16R_upper = Dynprog_simd_16_upper(&directions16R_upper_nogap,&directions16R_upper_Egap,dynprogR,
rev_rsequenceR,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlengthR,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -1120,7 +1114,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
matrix16R_lower = Dynprog_simd_16_lower(&directions16R_lower_nogap,&directions16R_lower_Egap,dynprogR,
rev_rsequenceR,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlengthR,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -1138,14 +1132,14 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
bestrR,bestcR,rev_rsequenceR,rev_rsequence_ucR,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffsetR,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_16_lower(NULL,&nmatches,&nmismatches,&nopens,&nindels,
directions16R_lower_nogap,directions16R_lower_Egap,
bestrR,bestcR,rev_rsequenceR,rev_rsequence_ucR,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffsetR,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
pairs = List_reverse(pairs);
@@ -1195,13 +1189,13 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
directions16L_upper_nogap,directions16L_upper_Egap,
bestrL,bestcL,rsequenceL,rsequence_ucL,
gsequence,gsequence_alt,roffsetL,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_16_lower(pairs,&nmatches,&nmismatches,&nopens,&nindels,
directions16L_lower_nogap,directions16L_lower_Egap,
bestrL,bestcL,rsequenceL,rsequence_ucL,
gsequence,gsequence_alt,roffsetL,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
if (List_length(pairs) == 1) {
@@ -1227,14 +1221,16 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
rsequenceL,gsequence,gsequence_alt,rlengthL,glength,
goffset,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lbandL,ubandL,
- jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT);
+ jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
Dynprog_compute_bands(&lbandR,&ubandR,rlengthR,glength,extraband_paired,/*widebandp*/true);
matrixR = Dynprog_standard(&directionsR_nogap,&directionsR_Egap,&directionsR_Fgap,dynprogR,
rev_rsequenceR,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlengthR,glength,rev_goffset,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lbandL,ubandR,
- /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT);
+ /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
nmatches = nmismatches = nopens = nindels = 0;
@@ -1247,7 +1243,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
rev_rsequenceR,rev_rsequence_ucR,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffsetR,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
pairs = List_reverse(pairs);
@@ -1295,7 +1291,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
directionsL_nogap,directionsL_Egap,directionsL_Fgap,bestrL,bestcL,
rsequenceL,rsequence_ucL,
gsequence,gsequence_alt,roffsetL,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
if (List_length(pairs) == 1) {
/* Only a gap added */
diff --git a/src/dynprog_cdna.h b/src/dynprog_cdna.h
index ffd77ed..4351d98 100644
--- a/src/dynprog_cdna.h
+++ b/src/dynprog_cdna.h
@@ -1,4 +1,4 @@
-/* $Id: dynprog_cdna.h 132731 2014-04-08 21:19:57Z twu $ */
+/* $Id: dynprog_cdna.h 184440 2016-02-17 21:03:49Z twu $ */
#ifndef DYNPROG_CDNA_INCLUDED
#define DYNPROG_CDNA_INCLUDED
@@ -23,7 +23,7 @@ Dynprog_cdna_gap (int *dynprogindex, int *finalscore, bool *incompletep,
int rlengthL, int rlengthR, int glength,
int roffsetL, int rev_roffsetR, int goffset,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_paired, double defect_rate);
diff --git a/src/dynprog_end.c b/src/dynprog_end.c
index fd8c2bc..34361e3 100644
--- a/src/dynprog_end.c
+++ b/src/dynprog_end.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_end.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: dynprog_end.c 184458 2016-02-18 00:06:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -9,12 +9,6 @@ static char rcsid[] = "$Id: dynprog_end.c 145990 2014-08-25 21:47:32Z twu $";
#include <string.h>
#include <math.h> /* For ceil, log, pow */
#include <ctype.h> /* For tolower */
-#ifdef HAVE_SSE2
-#include <emmintrin.h>
-#endif
-#ifdef HAVE_SSE4_1
-#include <smmintrin.h>
-#endif
#include "bool.h"
@@ -137,7 +131,7 @@ Dynprog_end_setup (Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in,
}
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
static void
find_best_endpoint_8 (int *finalscore, int *bestr, int *bestc, Score8_T **matrix_upper,
Score8_T **matrix_lower, int rlength, int glength,
@@ -213,6 +207,7 @@ find_best_endpoint_8 (int *finalscore, int *bestr, int *bestc, Score8_T **matrix
}
#endif
+#if defined(HAVE_SSE2)
static void
find_best_endpoint_16 (int *finalscore, int *bestr, int *bestc,
Score16_T **matrix_upper, Score16_T **matrix_lower,
@@ -286,7 +281,10 @@ find_best_endpoint_16 (int *finalscore, int *bestr, int *bestc,
*finalscore = (int) bestscore;
return;
}
+#endif
+
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
static void
find_best_endpoint_std (int *finalscore, int *bestr, int *bestc, Score32_T **matrix,
int rlength, int glength, int lband, int uband,
@@ -345,8 +343,10 @@ find_best_endpoint_std (int *finalscore, int *bestr, int *bestc, Score32_T **mat
*finalscore = (int) bestscore;
return;
}
+#endif
+
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
static void
find_best_endpoint_to_queryend_indels_8 (int *finalscore, int *bestr, int *bestc,
Score8_T **matrix_upper, Score8_T **matrix_lower,
@@ -424,6 +424,7 @@ find_best_endpoint_to_queryend_indels_8 (int *finalscore, int *bestr, int *bestc
#endif
+#if defined(HAVE_SSE2)
static void
find_best_endpoint_to_queryend_indels_16 (int *finalscore, int *bestr, int *bestc,
Score16_T **matrix_upper, Score16_T **matrix_lower,
@@ -498,8 +499,10 @@ find_best_endpoint_to_queryend_indels_16 (int *finalscore, int *bestr, int *best
*finalscore = (int) bestscore;
return;
}
+#endif
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
static void
find_best_endpoint_to_queryend_indels_std (int *finalscore, int *bestr, int *bestc, Score32_T **matrix,
int rlength, int glength, int lband, int uband,
@@ -559,6 +562,7 @@ find_best_endpoint_to_queryend_indels_std (int *finalscore, int *bestr, int *bes
*finalscore = (int) bestscore;
return;
}
+#endif
static void
@@ -575,6 +579,78 @@ find_best_endpoint_to_queryend_nogaps (int *bestr, int *bestc, int rlength, int
}
+static char complCode[128] = COMPLEMENT_LC;
+
+#if 0
+static char
+get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh,
+ bool watsonp) {
+ char c2, c2_alt;
+ Univcoord_T pos;
+
+#if 0
+ /* If the read has a deletion, then we will extend beyond 0 or genomiclength, so do not restrict. */
+ if (genomicpos < 0) {
+ return '*';
+
+ } else if (genomicpos >= genomiclength) {
+ return '*';
+
+ }
+#endif
+
+ if (watsonp) {
+ if ((pos = chroffset + genomicpos) < chroffset) { /* Must be <, and not <=, or dynamic programming will fail */
+ *g_alt = '*';
+ return '*';
+
+ } else if (pos >= chrhigh) {
+ *g_alt = '*';
+ return '*';
+
+#if 0
+ } else if (genome) {
+ /* Not necessary, because Genome_get_char_blocks should work */
+ debug8(printf("At %u, genomicnt is %c\n",
+ genomicpos,Genome_get_char(genome,pos)));
+ return Genome_get_char(genome,pos);
+#endif
+
+ } else {
+ /* GMAP with user-supplied genomic segment */
+ debug8(printf("At %u, genomicnt is %c\n",
+ genomicpos,Genome_get_char_blocks(pos)));
+ return Genome_get_char_blocks(&(*g_alt),pos);
+ }
+
+ } else {
+ if ((pos = chrhigh - genomicpos) < chroffset) { /* Must be <, and not <=, or dynamic programming will fail */
+ *g_alt = '*';
+ return '*';
+
+ } else if (pos >= chrhigh) {
+ *g_alt = '*';
+ return '*';
+
+#if 0
+ } else if (genome) {
+ /* Not necessary, because Genome_get_char_blocks should work */
+ c2 = Genome_get_char(genome,pos);
+#endif
+
+ } else {
+ /* GMAP with user-supplied genomic segment */
+ c2 = Genome_get_char_blocks(&c2_alt,pos);
+ }
+ debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2]));
+ *g_alt = complCode[(int) c2_alt];
+ return complCode[(int) c2];
+ }
+}
+#endif
+
+
+
/* revp means both rev1p and rev2p, which must have equal values */
/* Iterative version */
static List_T
@@ -582,13 +658,13 @@ traceback_nogaps (List_T pairs, int *nmatches, int *nmismatches,
int r, int c, char *rsequence, char *rsequenceuc,
char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
bool revp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int querycoord, genomecoord;
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
char c2_single;
#endif
@@ -609,7 +685,7 @@ traceback_nogaps (List_T pairs, int *nmatches, int *nmismatches,
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -652,16 +728,15 @@ traceback_nogaps (List_T pairs, int *nmatches, int *nmismatches,
}
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Want to keep pointers to r and c because traceback is interrupted */
static List_T
traceback_local_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction8_T **directions_nogap, Direction8_T **directions_Egap,
int *r, int *c, int endc, char *rsequence, char *rsequenceuc,
- char *genomesequence, char *genomesequenceuc, char *genomesequencealt,
+ char *genomesequence, char *genomesequencealt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
@@ -683,10 +758,9 @@ traceback_local_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *nop
/* assert(*c != endc); */
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,
- genomesequence,genomesequenceuc,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,genomesequence,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/true);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -739,10 +813,9 @@ traceback_local_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *nop
} else {
dist = (*c) - endc;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/**r*/0+LAZY_INDEL,*c,dist,genomesequence,genomesequenceuc,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/**r*/0+LAZY_INDEL,*c,dist,genomesequence,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,
- /*use_genomicseg_p*/true);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -755,15 +828,14 @@ traceback_local_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *nop
#endif
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
static List_T
traceback_local_8_lower (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction8_T **directions_nogap, Direction8_T **directions_Egap,
int *r, int *c, int endc, char *rsequence, char *rsequenceuc,
- char *genomesequence, char *genomesequenceuc, char *genomesequencealt,
+ char *genomesequence, char *genomesequencealt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
int querycoord, genomecoord;
@@ -851,14 +923,14 @@ traceback_local_8_lower (List_T pairs, int *nmatches, int *nmismatches, int *nop
#endif
+#if defined(HAVE_SSE2)
static List_T
traceback_local_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction16_T **directions_nogap, Direction16_T **directions_Egap,
int *r, int *c, int endc, char *rsequence, char *rsequenceuc,
- char *genomesequence, char *genomesequenceuc, char *genomesequencealt,
+ char *genomesequence, char *genomesequencealt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
@@ -878,10 +950,9 @@ traceback_local_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *no
}
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,
- genomesequence,genomesequenceuc,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,genomesequence,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/true);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -935,10 +1006,9 @@ traceback_local_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *no
/* Must be HORIZ */
dist = (*c) - endc;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/**r*/0+LAZY_INDEL,*c,dist,genomesequence,genomesequenceuc,
- queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,
- /*use_genomicseg_p*/true);
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/**r*/0+LAZY_INDEL,*c,dist,genomesequence,
+ queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -948,16 +1018,17 @@ traceback_local_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *no
return pairs;
}
+#endif
+#if defined(HAVE_SSE2)
static List_T
traceback_local_16_lower (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction16_T **directions_nogap, Direction16_T **directions_Egap,
int *r, int *c, int endc, char *rsequence, char *rsequenceuc,
- char *genomesequence, char *genomesequenceuc, char *genomesequencealt,
+ char *genomesequence, char *genomesequencealt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
int querycoord, genomecoord;
@@ -1042,16 +1113,17 @@ traceback_local_16_lower (List_T pairs, int *nmatches, int *nmismatches, int *no
return pairs;
}
+#endif
+#if !defined(HAVE_SSE2) || defined(DEBUG_SIMD)
static List_T
traceback_local_std (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction32_T **directions_nogap, Direction32_T **directions_Egap, Direction32_T **directions_Fgap,
int *r, int *c, int endc, char *rsequence, char *rsequenceuc,
- char *genomesequence, char *genomesequenceuc, char *genomesequencealt,
+ char *genomesequence, char *genomesequencealt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
@@ -1078,9 +1150,9 @@ traceback_local_std (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
/* dir = directions_nogap[*c][*r]; */
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,genomesequence,genomesequenceuc,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,genomesequence,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/true);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -1158,10 +1230,9 @@ traceback_local_std (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
/* dir = directions_nogap[*c][*r]; */
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,genomesequence,genomesequenceuc,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,*r,(*c)+dist,dist,genomesequence,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,
- /*use_genomicseg_p*/true);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -1191,7 +1262,7 @@ traceback_local_std (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
return pairs;
}
-
+#endif
List_T
@@ -1200,7 +1271,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
char *rev_rsequence, char *rev_rsequenceuc,
int rlength, int glength, int rev_roffset, int rev_goffset,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, Endalign_T endalign) {
List_T pairs = NULL;
char *rev_gsequence, *rev_gsequence_alt;
@@ -1208,7 +1279,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
Mismatchtype_T mismatchtype;
int bestr, bestc, lband, uband;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
bool use8p = false;
Score8_T **matrix8_upper, **matrix8_lower;
Direction8_T **directions8_upper_nogap, **directions8_upper_Egap,
@@ -1296,14 +1367,14 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
if (endalign == QUERYEND_GAP || endalign == BEST_LOCAL) {
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_end,/*widebandp*/true);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || glength <= SIMD_MAXLENGTH_EPI8) {
use8p = true;
matrix8_upper = Dynprog_simd_8_upper(&directions8_upper_nogap,&directions8_upper_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1311,7 +1382,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix8_lower = Dynprog_simd_8_lower(&directions8_lower_nogap,&directions8_lower_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1324,7 +1395,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix16_upper = Dynprog_simd_16_upper(&directions16_upper_nogap,&directions16_upper_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1332,7 +1403,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix16_lower = Dynprog_simd_16_lower(&directions16_lower_nogap,&directions16_lower_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1348,14 +1419,15 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,rev_goffset,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lband,uband,
- /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT);
+ /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
find_best_endpoint_std(&(*finalscore),&bestr,&bestc,matrix,rlength,glength,lband,uband,
!jump_late_p);
#endif
} else if (endalign == QUERYEND_INDELS) {
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_end,/*widebandp*/true);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achive a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || glength <= SIMD_MAXLENGTH_EPI8) {
@@ -1364,7 +1436,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix8_upper = Dynprog_simd_8_upper(&directions8_upper_nogap,&directions8_upper_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1372,7 +1444,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix8_lower = Dynprog_simd_8_lower(&directions8_lower_nogap,&directions8_lower_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1385,7 +1457,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix16_upper = Dynprog_simd_16_upper(&directions16_upper_nogap,&directions16_upper_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1393,7 +1465,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix16_lower = Dynprog_simd_16_lower(&directions16_lower_nogap,&directions16_lower_Egap,dynprog,
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1409,7 +1481,8 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
rev_rsequence,&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rlength,glength,rev_goffset,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lband,uband,
- /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT);
+ /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
find_best_endpoint_to_queryend_indels_std(&(*finalscore),&bestr,&bestc,matrix,rlength,glength,lband,uband,
!jump_late_p);
/* *finalscore = 0 -- Splicetrie procedures need to know finalscore */
@@ -1445,13 +1518,13 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
rev_rsequence,rev_rsequenceuc,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffset,rev_goffset,pairpool,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
chroffset,chrhigh,watsonp,
#endif
/*revp*/true,*dynprogindex);
*finalscore = (*nmatches)*FULLMATCH + (*nmismatches)*MISMATCH_ENDQ;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
} else if (use8p == true) {
if (bestc >= bestr) {
pairs = Dynprog_traceback_8_upper(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
@@ -1459,14 +1532,14 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
bestr,bestc,rev_rsequence,rev_rsequenceuc,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffset,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_8_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_lower_nogap,directions8_lower_Egap,
bestr,bestc,rev_rsequence,rev_rsequenceuc,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffset,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
} else {
@@ -1476,14 +1549,14 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
bestr,bestc,rev_rsequence,rev_rsequenceuc,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffset,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_16_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_lower_nogap,directions16_lower_Egap,
bestr,bestc,rev_rsequence,rev_rsequenceuc,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffset,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
#else
@@ -1493,7 +1566,7 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
rev_rsequence,rev_rsequenceuc,
&(rev_gsequence[glength-1]),&(rev_gsequence_alt[glength-1]),
rev_roffset,rev_goffset,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
#endif
}
@@ -1531,17 +1604,17 @@ List_T
Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
int *nmatches, int *nmismatches, int *nopens, int *nindels, T dynprog,
char *rev_rsequence, char *rev_rsequenceuc,
- char *rev_gsequence, char *rev_gsequence_uc, char *rev_gsequence_alt,
+ char *rev_gsequence, char *rev_gsequence_alt,
int rlength, int glength, int rev_roffset, int rev_goffset_anchor, int rev_goffset_far,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, int contlength) {
List_T pairs = NULL;
Pair_T pair;
Mismatchtype_T mismatchtype;
int bestr, bestc, lband, uband;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
bool use8p = false;
Score8_T **matrix8_upper, **matrix8_lower;
Direction8_T **directions8_upper_nogap, **directions8_upper_Egap,
@@ -1610,22 +1683,22 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
#endif
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_end,/*widebandp*/true);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || glength <= SIMD_MAXLENGTH_EPI8) {
use8p = true;
matrix8_upper = Dynprog_simd_8_upper(&directions8_upper_nogap,&directions8_upper_Egap,dynprog,
- rev_rsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_rsequence,rev_gsequence,rev_gsequence_alt,
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,/*for revp true*/!jump_late_p,/*revp*/true);
matrix8_lower = Dynprog_simd_8_lower(&directions8_lower_nogap,&directions8_lower_Egap,dynprog,
- rev_rsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_rsequence,rev_gsequence,rev_gsequence_alt,
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1636,17 +1709,17 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
} else {
matrix16_upper = Dynprog_simd_16_upper(&directions16_upper_nogap,&directions16_upper_Egap,dynprog,
- rev_rsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_rsequence,rev_gsequence,rev_gsequence_alt,
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,/*for revp true*/!jump_late_p,/*revp*/true);
matrix16_lower = Dynprog_simd_16_lower(&directions16_lower_nogap,&directions16_lower_Egap,dynprog,
- rev_rsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_rsequence,rev_gsequence,rev_gsequence_alt,
rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1661,7 +1734,8 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
rev_rsequence,rev_gsequence,rev_gsequence_alt,
rlength,glength,/*goffset*/0,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lband,uband,
- /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT);
+ /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
find_best_endpoint_to_queryend_indels_std(&(*finalscore),&bestr,&bestc,matrix,rlength,glength,lband,uband,
!jump_late_p);
#endif
@@ -1672,22 +1746,21 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
} else {
*nmatches = *nmismatches = *nopens = *nindels = 0;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
if (use8p == true) {
if (bestc >= bestr) {
pairs = traceback_local_8_upper(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_upper_nogap,directions8_upper_Egap,&bestr,&bestc,/*endc*/contlength,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_gsequence,rev_gsequence_alt,
rev_roffset,rev_goffset_far,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_8_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_lower_nogap,directions8_lower_Egap,&bestr,&bestc,/*endc*/contlength,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
- rev_roffset,rev_goffset_far,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rev_gsequence,rev_gsequence_alt,
+ rev_roffset,rev_goffset_far,pairpool,/*revp*/true,*dynprogindex);
}
pairs = Pairpool_push_gapholder(pairs,pairpool,/*queryjump*/0,/*genomejump*/rev_goffset_anchor - rev_goffset_far,
@@ -1697,16 +1770,15 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
pairs = traceback_local_8_upper(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_upper_nogap,directions8_upper_Egap,&bestr,&bestc,/*endc*/0,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_gsequence,rev_gsequence_alt,
rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_8_lower(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_lower_nogap,directions8_lower_Egap,&bestr,&bestc,/*endc*/0,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
- rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rev_gsequence,rev_gsequence_alt,
+ rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,*dynprogindex);
}
} else {
@@ -1714,16 +1786,15 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
pairs = traceback_local_16_upper(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_upper_nogap,directions16_upper_Egap,&bestr,&bestc,/*endc*/contlength,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_gsequence,rev_gsequence_alt,
rev_roffset,rev_goffset_far,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_16_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_lower_nogap,directions16_lower_Egap,&bestr,&bestc,/*endc*/contlength,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
- rev_roffset,rev_goffset_far,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rev_gsequence,rev_gsequence_alt,
+ rev_roffset,rev_goffset_far,pairpool,/*revp*/true,*dynprogindex);
}
pairs = Pairpool_push_gapholder(pairs,pairpool,/*queryjump*/0,/*genomejump*/rev_goffset_anchor - rev_goffset_far,
@@ -1733,16 +1804,15 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
pairs = traceback_local_16_upper(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_upper_nogap,directions16_upper_Egap,&bestr,&bestc,/*endc*/0,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_gsequence,rev_gsequence_alt,
rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_16_lower(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_lower_nogap,directions16_lower_Egap,&bestr,&bestc,/*endc*/0,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
- rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rev_gsequence,rev_gsequence_alt,
+ rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,*dynprogindex);
}
}
@@ -1750,9 +1820,9 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
pairs = traceback_local_std(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions_nogap,directions_Egap,directions_Fgap,&bestr,&bestc,/*endc*/contlength,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_gsequence,rev_gsequence_alt,
rev_roffset,rev_goffset_far,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
pairs = Pairpool_push_gapholder(pairs,pairpool,/*queryjump*/0,/*genomejump*/rev_goffset_anchor - rev_goffset_far,
/*leftpair*/NULL,/*rightpair*/NULL,/*knownp*/true);
@@ -1760,9 +1830,9 @@ Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
pairs = traceback_local_std(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions_nogap,directions_Egap,directions_Fgap,&bestr,&bestc,/*endc*/0,
rev_rsequence,rev_rsequenceuc,
- rev_gsequence,rev_gsequence_uc,rev_gsequence_alt,
+ rev_gsequence,rev_gsequence_alt,
rev_roffset,rev_goffset_anchor,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
#endif
@@ -1795,7 +1865,7 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
char *rsequence, char *rsequenceuc,
int rlength, int glength, int roffset, int goffset,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, Endalign_T endalign) {
List_T pairs = NULL;
char *gsequence, *gsequence_alt;
@@ -1803,7 +1873,7 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
Mismatchtype_T mismatchtype;
int bestr, bestc, lband, uband;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
bool use8p = false;
Score8_T **matrix8_upper, **matrix8_lower;
Direction8_T **directions8_upper_nogap, **directions8_upper_Egap,
@@ -1887,20 +1957,20 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
if (endalign == QUERYEND_GAP || endalign == BEST_LOCAL) {
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_end,/*widebandp*/true);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || glength <= SIMD_MAXLENGTH_EPI8) {
use8p = true;
matrix8_upper = Dynprog_simd_8_upper(&directions8_upper_nogap,&directions8_upper_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,jump_late_p,/*revp*/false);
matrix8_lower = Dynprog_simd_8_lower(&directions8_lower_nogap,&directions8_lower_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1911,14 +1981,14 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
} else {
matrix16_upper = Dynprog_simd_16_upper(&directions16_upper_nogap,&directions16_upper_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,jump_late_p,/*revp*/false);
matrix16_lower = Dynprog_simd_16_lower(&directions16_lower_nogap,&directions16_lower_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1932,27 +2002,28 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix = Dynprog_standard(&directions_nogap,&directions_Egap,&directions_Fgap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
goffset,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
- lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT);
+ lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
find_best_endpoint_std(&(*finalscore),&bestr,&bestc,matrix,rlength,glength,lband,uband,
jump_late_p);
#endif
} else if (endalign == QUERYEND_INDELS) {
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_end,/*widebandp*/true);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || glength <= SIMD_MAXLENGTH_EPI8) {
use8p = true;
matrix8_upper = Dynprog_simd_8_upper(&directions8_upper_nogap,&directions8_upper_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,jump_late_p,/*revp*/false);
matrix8_lower = Dynprog_simd_8_lower(&directions8_lower_nogap,&directions8_lower_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1964,14 +2035,14 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
} else {
matrix16_upper = Dynprog_simd_16_upper(&directions16_upper_nogap,&directions16_upper_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,jump_late_p,/*revp*/false);
matrix16_lower = Dynprog_simd_16_lower(&directions16_lower_nogap,&directions16_lower_Egap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -1986,7 +2057,8 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
matrix = Dynprog_standard(&directions_nogap,&directions_Egap,&directions_Fgap,dynprog,
rsequenceuc,gsequence,gsequence_alt,rlength,glength,
goffset,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
- lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT);
+ lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
find_best_endpoint_to_queryend_indels_std(&(*finalscore),&bestr,&bestc,matrix,rlength,glength,lband,uband,
jump_late_p);
/* *finalscore = 0; -- Splicetrie procedures need to know finalscore */
@@ -2018,26 +2090,26 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
pairs = traceback_nogaps(NULL,&(*nmatches),&(*nmismatches),bestr,bestc,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
chroffset,chrhigh,watsonp,
#endif
/*revp*/false,*dynprogindex);
*finalscore = (*nmatches)*FULLMATCH + (*nmismatches)*MISMATCH_ENDQ;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
} else if (use8p == true) {
if (bestc >= bestr) {
pairs = Dynprog_traceback_8_upper(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_upper_nogap,directions8_upper_Egap,bestr,bestc,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_8_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_lower_nogap,directions8_lower_Egap,bestr,bestc,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
} else {
@@ -2046,13 +2118,13 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
directions16_upper_nogap,directions16_upper_Egap,bestr,bestc,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_16_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_lower_nogap,directions16_lower_Egap,bestr,bestc,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
#else
@@ -2061,7 +2133,7 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
directions_nogap,directions_Egap,directions_Fgap,bestr,bestc,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
#endif
}
@@ -2098,17 +2170,17 @@ List_T
Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
int *nmatches, int *nmismatches, int *nopens, int *nindels, T dynprog,
char *rsequence, char *rsequenceuc,
- char *gsequence, char *gsequence_uc, char *gsequence_alt,
+ char *gsequence, char *gsequence_alt,
int rlength, int glength, int roffset, int goffset_anchor, int goffset_far,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, int contlength) {
List_T pairs = NULL;
Pair_T pair;
Mismatchtype_T mismatchtype;
int bestr, bestc, lband, uband;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
bool use8p = false;
Score8_T **matrix8_upper, **matrix8_lower;
Direction8_T **directions8_upper_nogap, **directions8_upper_Egap,
@@ -2181,20 +2253,20 @@ Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
#endif
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_end,/*widebandp*/true);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || glength <= SIMD_MAXLENGTH_EPI8) {
use8p = true;
matrix8_upper = Dynprog_simd_8_upper(&directions8_upper_nogap,&directions8_upper_Egap,dynprog,
- rsequenceuc,gsequence_uc,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+ rsequenceuc,gsequence,gsequence_alt,rlength,glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,jump_late_p,/*revp*/false);
matrix8_lower = Dynprog_simd_8_lower(&directions8_lower_nogap,&directions8_lower_Egap,dynprog,
- rsequenceuc,gsequence_uc,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+ rsequenceuc,gsequence,gsequence_alt,rlength,glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -2206,15 +2278,15 @@ Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
} else {
matrix16_upper = Dynprog_simd_16_upper(&directions16_upper_nogap,&directions16_upper_Egap,dynprog,
- rsequenceuc,gsequence_uc,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+ rsequenceuc,gsequence,gsequence_alt,rlength,glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
uband,jump_late_p,/*revp*/false);
matrix16_lower = Dynprog_simd_16_lower(&directions16_lower_nogap,&directions16_lower_Egap,dynprog,
- rsequenceuc,gsequence_uc,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+ rsequenceuc,gsequence,gsequence_alt,rlength,glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
/*goffset*/0,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -2227,9 +2299,10 @@ Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
#else
/* Non-SIMD methods */
matrix = Dynprog_standard(&directions_nogap,&directions_Egap,&directions_Fgap,dynprog,
- rsequenceuc,gsequence_uc,gsequence_alt,rlength,glength,
+ rsequenceuc,gsequence,gsequence_alt,rlength,glength,
/*goffset*/0,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
- lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT);
+ lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
find_best_endpoint_to_queryend_indels_std(&(*finalscore),&bestr,&bestc,matrix,rlength,glength,lband,uband,
jump_late_p);
#endif
@@ -2240,65 +2313,61 @@ Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
} else {
*nmatches = *nmismatches = *nopens = *nindels = 0;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
if (use8p == true) {
if (bestc >= bestr) {
pairs = traceback_local_8_upper(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_upper_nogap,directions8_upper_Egap,&bestr,&bestc,/*endc*/contlength,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
roffset,goffset_far,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_8_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_lower_nogap,directions8_lower_Egap,&bestr,&bestc,/*endc*/contlength,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
- roffset,goffset_far,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
+ roffset,goffset_far,pairpool,/*revp*/false,*dynprogindex);
}
pairs = Pairpool_push_gapholder(pairs,pairpool,/*queryjump*/0,/*genomejump*/goffset_far - goffset_anchor,
/*leftpair*/NULL,/*rightpair*/NULL,/*knownp*/true);
if (bestc >= bestr) {
pairs = traceback_local_8_upper(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_upper_nogap,directions8_upper_Egap,&bestr,&bestc,/*endc*/0,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
roffset,goffset_anchor,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_8_lower(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8_lower_nogap,directions8_lower_Egap,&bestr,&bestc,/*endc*/0,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
- roffset,goffset_anchor,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
+ roffset,goffset_anchor,pairpool,/*revp*/false,*dynprogindex);
}
} else {
if (bestc >= bestr) {
pairs = traceback_local_16_upper(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_upper_nogap,directions16_upper_Egap,&bestr,&bestc,/*endc*/contlength,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
roffset,goffset_far,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_16_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_lower_nogap,directions16_lower_Egap,&bestr,&bestc,/*endc*/contlength,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
- roffset,goffset_far,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
+ roffset,goffset_far,pairpool,/*revp*/false,*dynprogindex);
}
pairs = Pairpool_push_gapholder(pairs,pairpool,/*queryjump*/0,/*genomejump*/goffset_far - goffset_anchor,
/*leftpair*/NULL,/*rightpair*/NULL,/*knownp*/true);
if (bestc >= bestr) {
pairs = traceback_local_16_upper(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_upper_nogap,directions16_upper_Egap,&bestr,&bestc,/*endc*/0,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
roffset,goffset_anchor,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = traceback_local_16_lower(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16_lower_nogap,directions16_lower_Egap,&bestr,&bestc,/*endc*/0,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
- roffset,goffset_anchor,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
+ roffset,goffset_anchor,pairpool,/*revp*/false,*dynprogindex);
}
}
@@ -2306,18 +2375,18 @@ Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
/* Non-SIMD methods */
pairs = traceback_local_std(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions_nogap,directions_Egap,directions_Fgap,&bestr,&bestc,/*endc*/contlength,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
roffset,goffset_far,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
pairs = Pairpool_push_gapholder(pairs,pairpool,/*queryjump*/0,/*genomejump*/goffset_far - goffset_anchor,
/*leftpair*/NULL,/*rightpair*/NULL,/*knownp*/true);
pairs = traceback_local_std(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions_nogap,directions_Egap,directions_Fgap,&bestr,&bestc,/*endc*/0,
- rsequence,rsequenceuc,gsequence,gsequence_uc,gsequence_alt,
+ rsequence,rsequenceuc,gsequence,gsequence_alt,
roffset,goffset_anchor,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
#endif
/* Score compared with perfect score, so heavy weight on mismatches may not be necessary */
@@ -2342,8 +2411,6 @@ Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
}
-static char complCode[128] = COMPLEMENT_LC;
-
static void
make_complement_inplace (char *sequence, unsigned int length) {
char temp;
@@ -2430,7 +2497,7 @@ Dynprog_make_splicejunction_5 (char *splicejunction, char *splicejunction_alt, U
} else if (far_splicetype == ANTIDONOR) {
Genome_fill_buffer_blocks_noterm(splicecoord,splicelength,distal,distal_alt);
- } else if (splicecoord <= splicelength) {
+ } else if (splicecoord <= (Univcoord_T) splicelength) {
return false;
} else if (far_splicetype == ANTIACCEPTOR) {
@@ -2531,7 +2598,7 @@ Dynprog_make_splicejunction_3 (char *splicejunction, char *splicejunction_alt, U
} else if (far_splicetype == ACCEPTOR) {
Genome_fill_buffer_blocks_noterm(splicecoord,splicelength,distal,distal_alt);
- } else if (splicecoord <= splicelength) {
+ } else if (splicecoord <= (Univcoord_T) splicelength) {
return false;
} else if (far_splicetype == DONOR) {
@@ -2650,7 +2717,7 @@ Dynprog_end5_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
best_pairs = Dynprog_end5_gap(&(*dynprogindex),&(*finalscore),&(*nmatches),&(*nmismatches),
&(*nopens),&(*nindels),dynprog,rev_rsequence,rev_rsequenceuc,
rlength,glength,rev_roffset,rev_goffset,chroffset,chrhigh,
- cdna_direction,watsonp,jump_late_p,pairpool,
+ watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS);
if (*finalscore < 0) {
orig_score = 0;
@@ -2810,7 +2877,7 @@ Dynprog_end5_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
orig_pairs = Dynprog_end5_gap(&(*dynprogindex),&(*finalscore),&(*nmatches),&(*nmismatches),
&(*nopens),&(*nindels),dynprog,rev_rsequence,rev_rsequenceuc,
rlength,glength,rev_roffset,rev_goffset,chroffset,chrhigh,
- cdna_direction,watsonp,jump_late_p,pairpool,
+ watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,/*endalign*/BEST_LOCAL);
debug7(Pair_dump_list(orig_pairs,/*zerobasedp*/true));
debug7(printf("End of dynprog end5 known\n"));
@@ -2839,7 +2906,7 @@ Dynprog_end5_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
*ambig_end_length = 0;
debug7(printf("End of dynprog end5 known\n"));
if (*knownsplicep == true) {
- return Pair_protect_end5(best_pairs,pairpool);
+ return Pair_protect_end5(best_pairs);
} else {
return best_pairs;
}
@@ -2907,7 +2974,7 @@ Dynprog_end3_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
best_pairs = Dynprog_end3_gap(&(*dynprogindex),&(*finalscore),&(*nmatches),&(*nmismatches),
&(*nopens),&(*nindels),dynprog,rsequence,rsequenceuc,
rlength,glength,roffset,goffset,chroffset,chrhigh,
- cdna_direction,watsonp,jump_late_p,pairpool,
+ watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,/*endalign*/QUERYEND_NOGAPS);
if (*finalscore < 0) {
orig_score = 0;
@@ -3067,7 +3134,7 @@ Dynprog_end3_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
orig_pairs = Dynprog_end3_gap(&(*dynprogindex),&(*finalscore),&(*nmatches),&(*nmismatches),
&(*nopens),&(*nindels),dynprog,rsequence,rsequenceuc,
rlength,glength,roffset,goffset,chroffset,chrhigh,
- cdna_direction,watsonp,jump_late_p,pairpool,
+ watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,/*endalign*/BEST_LOCAL);
debug7(Pair_dump_list(orig_pairs,/*zerobasedp*/true));
*knownsplicep = false;
@@ -3094,7 +3161,7 @@ Dynprog_end3_known (bool *knownsplicep, int *dynprogindex, int *finalscore,
*ambig_end_length = 0;
debug7(printf("End of dynprog end3 known\n"));
if (*knownsplicep == true) {
- return Pair_protect_end3(best_pairs,pairpool);
+ return Pair_protect_end3(best_pairs);
} else {
return best_pairs;
}
diff --git a/src/dynprog_end.h b/src/dynprog_end.h
index 027bc14..72380fb 100644
--- a/src/dynprog_end.h
+++ b/src/dynprog_end.h
@@ -1,4 +1,4 @@
-/* $Id: dynprog_end.h 132731 2014-04-08 21:19:57Z twu $ */
+/* $Id: dynprog_end.h 184458 2016-02-18 00:06:33Z twu $ */
#ifndef DYNPROG_END_INCLUDED
#define DYNPROG_END_INCLUDED
@@ -26,17 +26,17 @@ Dynprog_end5_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
char *revsequence1, char *revsequenceuc1,
int length1, int length2, int revoffset1, int revoffset2,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, Endalign_T endalign);
extern List_T
Dynprog_end5_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
int *nmatches, int *nmismatches, int *nopens, int *nindels, T dynprog,
- char *revsequence1, char *revsequenceuc1,
- char *revsequence2, char *revsequenceuc2, char *revsequencealt2,
+ char *rev_rsequence, char *rev_rsequenceuc,
+ char *rev_gsequence, char *rev_gsequence_alt,
int length1, int length2, int revoffset1, int revoffset2_anchor, int revoffset2_far,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, int contlength);
extern List_T
@@ -45,17 +45,17 @@ Dynprog_end3_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmisma
char *sequence1, char *sequenceuc1,
int length1, int length2, int offset1, int offset2,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, Endalign_T endalign);
extern List_T
Dynprog_end3_splicejunction (int *dynprogindex, int *finalscore, int *missscore,
int *nmatches, int *nmismatches, int *nopens, int *nindels, T dynprog,
- char *sequence1, char *sequenceuc1,
- char *sequence2, char *sequenceuc2, char *sequencealt2,
+ char *rsequence, char *rsequenceuc,
+ char *gsequence, char *gsequence_alt,
int length1, int length2, int offset1, int offset2_anchor, int offset2_far,
Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
int extraband_end, double defect_rate, int contlength);
extern bool
diff --git a/src/dynprog_genome.c b/src/dynprog_genome.c
index 5687b0f..e8b6f39 100644
--- a/src/dynprog_genome.c
+++ b/src/dynprog_genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_genome.c 182795 2016-01-21 19:51:16Z twu $";
+static char rcsid[] = "$Id: dynprog_genome.c 184458 2016-02-18 00:06:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -9,12 +9,6 @@ static char rcsid[] = "$Id: dynprog_genome.c 182795 2016-01-21 19:51:16Z twu $";
#include <string.h>
#include <math.h> /* For ceil, log, pow */
#include <ctype.h> /* For tolower */
-#ifdef HAVE_SSE2
-#include <emmintrin.h>
-#endif
-#ifdef HAVE_SSE4_1
-#include <smmintrin.h>
-#endif
#include "bool.h"
@@ -550,8 +544,7 @@ get_known_splicesites (int *left_known, int *right_known, int glengthL, int glen
}
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
-
+#if defined(HAVE_SSE2)
/* Returns finalscore */
static int
bridge_intron_gap_8_intron_level (int *bestrL, int *bestrR, int *bestcL, int *bestcR,
@@ -1476,7 +1469,7 @@ bridge_intron_gap_8_ud (int *bestrL, int *bestrR, int *bestcL, int *bestcR,
char *gsequenceL, char *gsequenceL_alt, char *rev_gsequenceR, char *rev_gsequenceR_alt,
int goffsetL, int rev_goffsetR, int rlength, int glengthL, int glengthR,
int cdna_direction, bool watsonp, int lbandL, int ubandL, int lbandR, int ubandR,
- double defect_rate, int canonical_reward, int leftoffset, int rightoffset,
+ int canonical_reward, int leftoffset, int rightoffset,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
bool halfp, bool finalp, bool jump_late_p) {
int finalscore;
@@ -2487,7 +2480,7 @@ bridge_intron_gap_16_ud (int *bestrL, int *bestrR, int *bestcL, int *bestcR,
char *gsequenceL, char *gsequenceL_alt, char *rev_gsequenceR, char *rev_gsequenceR_alt,
int goffsetL, int rev_goffsetR, int rlength, int glengthL, int glengthR,
int cdna_direction, bool watsonp, int lbandL, int ubandL, int lbandR, int ubandR,
- double defect_rate, int canonical_reward, int leftoffset, int rightoffset,
+ int canonical_reward, int leftoffset, int rightoffset,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
bool halfp, bool finalp, bool jump_late_p) {
int finalscore;
@@ -3132,7 +3125,7 @@ bridge_intron_gap (int *bestrL, int *bestrR, int *bestcL, int *bestcR,
Direction32_T **directionsL_nogap, Direction32_T **directionsR_nogap,
char *gsequenceL, char *gsequenceL_alt, char *rev_gsequenceR, char *rev_gsequenceR_alt,
int goffsetL, int rev_goffsetR, int rlength, int glengthL, int glengthR,
- int cdna_direction, bool watsonp, int extraband_paired, double defect_rate, int canonical_reward,
+ int cdna_direction, bool watsonp, int extraband_paired, int canonical_reward,
int leftoffset, int rightoffset,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
bool halfp, bool finalp, bool jump_late_p) {
@@ -3509,7 +3502,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
int rev_roffset, bestrL = -1, bestrR, bestcL, bestcR;
int lbandL, ubandL, lbandR, ubandR;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
Score8_T **matrix8L_upper, **matrix8L_lower, **matrix8R_upper, **matrix8R_lower;
Direction8_T **directions8L_upper_nogap, **directions8L_upper_Egap,
**directions8L_lower_nogap, **directions8L_lower_Egap,
@@ -3707,7 +3700,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
}
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
if (rlength <= SIMD_MAXLENGTH_EPI8 || (glengthL <= SIMD_MAXLENGTH_EPI8 && glengthR <= SIMD_MAXLENGTH_EPI8)) {
use8p = true;
@@ -3716,13 +3709,13 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
}
#endif
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
if (use8p == true) {
Dynprog_compute_bands(&lbandL,&ubandL,rlength,glengthL,extraband_paired,/*widebandp*/true);
debug3(printf("Computing matrix8L_upper\n"));
matrix8L_upper = Dynprog_simd_8_upper(&directions8L_upper_nogap,&directions8L_upper_Egap,dynprogL,
rsequence,gsequenceL,gsequenceL_alt,rlength,glengthL,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffsetL,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
@@ -3730,7 +3723,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
debug3(printf("Computing matrix8L_lower\n"));
matrix8L_lower = Dynprog_simd_8_lower(&directions8L_lower_nogap,&directions8L_lower_Egap,dynprogL,
rsequence,gsequenceL,gsequenceL_alt,rlength,glengthL,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffsetL,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
@@ -3741,7 +3734,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
matrix8R_upper = Dynprog_simd_8_upper(&directions8R_upper_nogap,&directions8R_upper_Egap,dynprogR,
rev_rsequence,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rlength,glengthR,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffsetR,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -3750,7 +3743,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
matrix8R_lower = Dynprog_simd_8_lower(&directions8R_lower_nogap,&directions8R_lower_Egap,dynprogR,
rev_rsequence,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rlength,glengthR,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffsetR,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -3762,7 +3755,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
directions8R_upper_nogap,directions8R_lower_nogap,
gsequenceL,gsequenceL_alt,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
goffsetL,rev_goffsetR,rlength,glengthL,glengthR,
- cdna_direction,watsonp,lbandL,ubandL,lbandR,ubandR,defect_rate,
+ cdna_direction,watsonp,lbandL,ubandL,lbandR,ubandR,
canonical_reward,goffsetL,rev_goffsetR,
chrnum,chroffset,chrhigh,halfp,finalp,jump_late_p)) < 0) {
FREEA(rev_gsequenceR_alt);
@@ -3785,14 +3778,14 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
bestrR,bestcR,rev_rsequence,rev_rsequenceuc,
&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rev_roffset,rev_goffsetR,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_8_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8R_lower_nogap,directions8R_lower_Egap,
bestrR,bestcR,rev_rsequence,rev_rsequenceuc,
&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rev_roffset,rev_goffsetR,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
pairs = List_reverse(pairs);
@@ -3820,13 +3813,13 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
directions8L_upper_nogap,directions8L_upper_Egap,
bestrL,bestcL,rsequence,rsequenceuc,gsequenceL,gsequenceL_alt,
roffset,goffsetL,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_8_lower(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions8L_lower_nogap,directions8L_lower_Egap,
bestrL,bestcL,rsequence,rsequenceuc,gsequenceL,gsequenceL_alt,
roffset,goffsetL,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
if (List_length(pairs) == 1) {
@@ -3857,7 +3850,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
debug3(printf("Computing matrix16L_upper\n"));
matrix16L_upper = Dynprog_simd_16_upper(&directions16L_upper_nogap,&directions16L_upper_Egap,dynprogL,
rsequence,gsequenceL,gsequenceL_alt,rlength,glengthL,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffsetL,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandL,jump_late_p,/*revp*/false);
@@ -3865,7 +3858,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
debug3(printf("Computing matrix16L_lower\n"));
matrix16L_lower = Dynprog_simd_16_lower(&directions16L_lower_nogap,&directions16L_lower_Egap,dynprogL,
rsequence,gsequenceL,gsequenceL_alt,rlength,glengthL,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffsetL,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandL,jump_late_p,/*revp*/false);
@@ -3875,7 +3868,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
matrix16R_upper = Dynprog_simd_16_upper(&directions16R_upper_nogap,&directions16R_upper_Egap,dynprogR,
rev_rsequence,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rlength,glengthR,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffsetR,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,ubandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -3884,7 +3877,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
matrix16R_lower = Dynprog_simd_16_lower(&directions16R_lower_nogap,&directions16R_lower_Egap,dynprogR,
rev_rsequence,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rlength,glengthR,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
rev_goffsetR,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,lbandR,/*for revp true*/!jump_late_p,/*revp*/true);
@@ -3896,7 +3889,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
directions16R_upper_nogap,directions16R_lower_nogap,
gsequenceL,gsequenceL_alt,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
goffsetL,rev_goffsetR,rlength,glengthL,glengthR,
- cdna_direction,watsonp,lbandL,ubandL,lbandR,ubandR,defect_rate,
+ cdna_direction,watsonp,lbandL,ubandL,lbandR,ubandR,
canonical_reward,goffsetL,rev_goffsetR,
chrnum,chroffset,chrhigh,halfp,finalp,jump_late_p)) < 0) {
@@ -3920,14 +3913,14 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
bestrR,bestcR,rev_rsequence,rev_rsequenceuc,
&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rev_roffset,rev_goffsetR,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_16_lower(NULL,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16R_lower_nogap,directions16R_lower_Egap,
bestrR,bestcR,rev_rsequence,rev_rsequenceuc,
&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rev_roffset,rev_goffsetR,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
pairs = List_reverse(pairs);
@@ -3954,13 +3947,13 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
directions16L_upper_nogap,directions16L_upper_Egap,
bestrL,bestcL,rsequence,rsequenceuc,
gsequenceL,gsequenceL_alt,roffset,goffsetL,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
pairs = Dynprog_traceback_16_lower(pairs,&(*nmatches),&(*nmismatches),&(*nopens),&(*nindels),
directions16L_lower_nogap,directions16L_lower_Egap,
bestrL,bestcL,rsequence,rsequenceuc,
gsequenceL,gsequenceL_alt,roffset,goffsetL,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ *dynprogindex);
}
if (List_length(pairs) == 1) {
@@ -3995,7 +3988,8 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
rsequence,gsequenceL,gsequenceL_alt,rlength,glengthL,
goffsetL,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lbandL,ubandL,
- jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT);
+ jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
Dynprog_compute_bands(&lbandR,&ubandR,rlength,glengthR,extraband_paired,/*widebandp*/true);
debug3(printf("Computing matrixR\n"));
@@ -4003,14 +3997,15 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
rev_rsequence,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rlength,glengthR,rev_goffsetR,chroffset,chrhigh,watsonp,
mismatchtype,open,extend,lbandL,ubandR,
- /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT);
+ /*for revp true*/!jump_late_p,/*revp*/true,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
if ((*finalscore = bridge_intron_gap(&bestrL,&bestrR,&bestcL,&bestcR,
&(*introntype),&(*left_prob),&(*right_prob),
matrixL,matrixR,directionsL_nogap,directionsR_nogap,
gsequenceL,gsequenceL_alt,&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
goffsetL,rev_goffsetR,rlength,glengthL,glengthR,
- cdna_direction,watsonp,extraband_paired,defect_rate,
+ cdna_direction,watsonp,extraband_paired,
canonical_reward,goffsetL,rev_goffsetR,
chrnum,chroffset,chrhigh,halfp,finalp,jump_late_p)) < 0) {
@@ -4033,7 +4028,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
rev_rsequence,rev_rsequenceuc,
&(rev_gsequenceR[glengthR-1]),&(rev_gsequenceR_alt[glengthR-1]),
rev_roffset,rev_goffsetR,pairpool,/*revp*/true,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
pairs = List_reverse(pairs);
/* queryjump = (rev_roffset-bestrR) - (roffset+bestrL) + 1; */
@@ -4058,7 +4053,7 @@ Dynprog_genome_gap (int *dynprogindex, int *finalscore, int *new_leftgenomepos,
directionsL_nogap,directionsL_Egap,directionsL_Fgap,bestrL,bestcL,
rsequence,rsequenceuc,
gsequenceL,gsequenceL_alt,roffset,goffsetL,pairpool,/*revp*/false,
- chroffset,chrhigh,cdna_direction,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
if (List_length(pairs) == 1) {
/* Only a gap inserted */
diff --git a/src/dynprog_simd.c b/src/dynprog_simd.c
index e8a8f53..fed4ff9 100644
--- a/src/dynprog_simd.c
+++ b/src/dynprog_simd.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
+static char rcsid[] = "$Id: dynprog_simd.c 184440 2016-02-17 21:03:49Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -9,19 +9,76 @@ static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
#include <string.h>
#include <math.h> /* For ceil, log, pow */
#include <ctype.h> /* For tolower */
+
#ifdef HAVE_SSE2
#include <emmintrin.h>
#endif
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
+#ifdef HAVE_AVX2
+#include <immintrin.h>
+#endif
#include "mem.h"
#include "comp.h"
#include "assert.h"
-/* #define NO_INITIAL_GAP_PENALTY 1 -- Needed for bam_indelfix */
+#ifdef HAVE_AVX2
+#define _MM_ADD_EPI8(x,y) _mm256_add_epi8(x,y)
+#define _MM_ADDS_EPI8(x,y) _mm256_adds_epi8(x,y)
+#define _MM_SUBS_EPI8(x,y) _mm256_subs_epi8(x,y)
+#define _MM_CMPGT_EPI8(x,y) _mm256_cmpgt_epi8(x,y)
+#define _MM_CMPLT_EPI8(x,y) _mm256_cmpgt_epi8(y,x) /* No _mm256_cmplt commands */
+#define _MM_MAX_EPI8(x,y) _mm256_max_epi8(x,y)
+#define _MM_MIN_EPI8(x,y) _mm256_min_epi8(x,y)
+#define _MM_SET1_EPI8(x) _mm256_set1_epi8(x)
+
+#define _MM_ADD_EPI16(x,y) _mm256_add_epi16(x,y)
+#define _MM_ADDS_EPI16(x,y) _mm256_adds_epi16(x,y)
+#define _MM_SUBS_EPI16(x,y) _mm256_subs_epi16(x,y)
+#define _MM_CMPGT_EPI16(x,y) _mm256_cmpgt_epi16(x,y)
+#define _MM_CMPLT_EPI16(x,y) _mm256_cmpgt_epi16(y,x) /* No _mm256_cmplt commands */
+#define _MM_MAX_EPI16(x,y) _mm256_max_epi16(x,y)
+#define _MM_MIN_EPI16(x,y) _mm256_min_epi16(x,y)
+#define _MM_SET1_EPI16(x) _mm256_set1_epi16(x)
+
+#define _MM_SETZERO_SI _mm256_setzero_si256
+/* #define _MM_SLLI_SI(x,y) _mm256_slli_si256(x,y) -- 256-bit version works within 128-bit lanes */
+/* #define _MM_SRLI_SI(x,y) _mm256_srli_si256(x,y) -- 256-bit version works within 128-bit lanes */
+#define _MM_ANDNOT_SI(x,y) _mm256_andnot_si256(x,y)
+#define _MM_OR_SI(x,y) _mm256_or_si256(x,y)
+#define _MM_AND_SI(x,y) _mm256_and_si256(x,y)
+
+#elif defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#define _MM_ADD_EPI8(x,y) _mm_add_epi8(x,y)
+#define _MM_ADDS_EPI8(x,y) _mm_adds_epi8(x,y)
+#define _MM_SUBS_EPI8(x,y) _mm_subs_epi8(x,y)
+#define _MM_CMPGT_EPI8(x,y) _mm_cmpgt_epi8(x,y)
+#define _MM_CMPLT_EPI8(x,y) _mm_cmplt_epi8(x,y)
+#define _MM_MAX_EPI8(x,y) _mm_max_epi8(x,y)
+#define _MM_MIN_EPI8(x,y) _mm_min_epi8(x,y)
+#define _MM_SET1_EPI8(x) _mm_set1_epi8(x)
+
+#define _MM_ADD_EPI16(x,y) _mm_add_epi16(x,y)
+#define _MM_ADDS_EPI16(x,y) _mm_adds_epi16(x,y)
+#define _MM_SUBS_EPI16(x,y) _mm_subs_epi16(x,y)
+#define _MM_CMPGT_EPI16(x,y) _mm_cmpgt_epi16(x,y)
+#define _MM_CMPLT_EPI16(x,y) _mm_cmplt_epi16(x,y)
+#define _MM_MAX_EPI16(x,y) _mm_max_epi16(x,y)
+#define _MM_MIN_EPI16(x,y) _mm_min_epi16(x,y)
+#define _MM_SET1_EPI16(x) _mm_set1_epi16(x)
+
+#define _MM_SETZERO_SI _mm_setzero_si128
+/* #define _MM_SLLI_SI(x,y) _mm_slli_si128(x,y) -- 256-bit version works within 128-bit lanes */
+/* #define _MM_SRLI_SI(x,y) _mm_srli_si128(x,y) -- 256-bit version works within 128-bit lanes */
+#define _MM_ANDNOT_SI(x,y) _mm_andnot_si128(x,y)
+#define _MM_OR_SI(x,y) _mm_or_si128(x,y)
+#define _MM_AND_SI(x,y) _mm_and_si128(x,y)
+#endif
+
+
#define LAZY_INDEL 1 /* Don't advance to next coordinate on final indel, since could go over chromosome bounds. */
@@ -59,10 +116,11 @@ static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
#define debug8(x)
#endif
-#ifdef DEBUG14
-#define debug14(x) x
+/* Compare SIMD with non-SIMD. Define in dynprog.h */
+#ifdef DEBUG_SIMD
+#define debug_simd(x) x
#else
-#define debug14(x)
+#define debug_simd(x)
#endif
#ifdef DEBUG15
@@ -71,6 +129,20 @@ static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
#define debug15(x)
#endif
+/* Compare AVX2 with SSE42. Define in dynprog.h */
+#ifdef DEBUG_AVX2
+#define debug_avx2(x) x
+#else
+#define debug_avx2(x)
+#endif
+
+/* Checking genomic nt in traceback procedures */
+#ifdef DEBUG17
+#define debug17(x) x
+#else
+#define debug17(x)
+#endif
+
#include "complement.h"
@@ -83,6 +155,33 @@ static char rcsid[] = "$Id: dynprog_simd.c 146623 2014-09-02 21:31:32Z twu $";
#ifdef DEBUG15
/* For debugging of SIMD procedures*/
+#ifdef HAVE_AVX2
+static void
+print_vector_8 (__m256i x, int r, int c, char *label) {
+ __m256i a[1];
+ Score8_T *s = a;
+
+ _mm_lfence(); /* Needed to print correct values */
+ _mm256_store_si256(a,x);
+ printf("%d,%d %s: %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d\n",
+ r,c,label,s[0],s[1],s[2],s[3],s[4],s[5],s[6],s[7],s[8],s[9],s[10],s[11],s[12],s[13],s[14],s[15],
+ s[16],s[17],s[18],s[19],s[20],s[21],s[22],s[23],s[24],s[25],s[26],s[27],s[28],s[29],s[30],s[31]);
+ return;
+}
+
+static void
+print_vector_16 (__m256i x, int r, int c, char *label) {
+ __m256i a[1];
+ Score16_T *s = a;
+
+ _mm_lfence(); /* Needed to print correct values */
+ _mm256_store_si256(a,x);
+ printf("%d,%d %s: %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d %d\n",
+ r,c,label,s[0],s[1],s[2],s[3],s[4],s[5],s[6],s[7],s[8],s[9],s[10],s[11],s[12],s[13],s[14],s[15]);
+ return;
+}
+
+#else
static void
print_vector_8 (__m128i x, int r, int c, char *label) {
__m128i a[1];
@@ -106,9 +205,10 @@ print_vector_16 (__m128i x, int r, int c, char *label) {
return;
}
#endif
+#endif
-#if defined(DEBUG14) || defined(DEBUG2)
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD) || defined(DEBUG2)
static void
Matrix8_print (Score8_T **matrix, int rlength, int glength, char *rsequence,
char *gsequence, char *gsequencealt,
@@ -498,7 +598,7 @@ Matrix16_print_ud (Score16_T **matrix, int rlength, int glength, char *rsequence
}
#endif
-#if defined(DEBUG14) || defined(DEBUG2)
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD) || defined(DEBUG2)
static void
Directions8_print (Direction8_T **directions_nogap, Direction8_T **directions_Egap, Direction8_T **directions_Fgap,
int rlength, int glength, char *rsequence, char *gsequence, char *gsequencealt,
@@ -907,10 +1007,15 @@ Directions16_print_ud (Direction16_T **directions_nogap, Direction16_T **directi
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
static void
-banded_matrix8_compare (Score8_T **matrix1, Score32_T **matrix2, int rlength, int glength,
- int lband, int uband, char *rsequence, char *gsequence, char *gsequence_alt,
+banded_matrix8_compare (Score8_T **matrix1,
+#ifdef DEBUG_AVX2
+ Score8_T **matrix2,
+#else
+ Score32_T **matrix2,
+#endif
+ int rlength, int glength, int lband, int uband, char *rsequence, char *gsequence, char *gsequence_alt,
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
bool revp) {
int r, c, rlo, rhigh;
@@ -926,25 +1031,135 @@ banded_matrix8_compare (Score8_T **matrix1, Score32_T **matrix2, int rlength, in
for (r = rlo; r <= rhigh; r++) {
if (matrix1[c][r] <= NEG_INFINITY_8 + 30 && matrix2[c][r] <= NEG_INFINITY_8 + 30) {
- /* Okay */
+ /* Okay: both essentially negative infinity */
} else if (matrix1[c][r] != matrix2[c][r]) {
printf("At %d,%d, value %d != value %d\n",r,c,matrix1[c][r],matrix2[c][r]);
Matrix8_print(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
revp,lband,uband);
+#ifdef DEBUG_AVX2
+ Matrix8_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+#elif defined(DEBUG_SIMD)
Dynprog_Matrix32_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
goffset,chroffset,chrhigh,watsonp,revp,lband,uband);
- exit(9);
+#endif
+ abort();
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_matrix8_compare_upper (Score8_T **matrix1,
+#ifdef DEBUG_AVX2
+ Score8_T **matrix2,
+#else
+ Score32_T **matrix2,
+#endif
+ int rlength, int glength,
+ int uband, char *rsequence, char *gsequence, char *gsequence_alt,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ bool revp) {
+ int r, c, rlo, rhigh;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c) > rlength) {
+ rhigh = rlength;
+ }
+
+ for (r = rlo; r <= rhigh; r++) {
+ if (matrix1[c][r] <= NEG_INFINITY_8 + 30 && matrix2[c][r] <= NEG_INFINITY_8 + 30) {
+ /* Okay */
+ } else if (matrix1[c][r] != matrix2[c][r]) {
+ printf("At %d,%d, value %d != value %d\n",r,c,matrix1[c][r],matrix2[c][r]);
+
+ Matrix8_print_ud(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+#ifdef DEBUG_AVX2
+ Matrix8_print_ud(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+#else
+ Dynprog_Matrix32_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp,/*lband*/0,uband);
+#endif
+ abort();
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_matrix8_compare_lower (Score8_T **matrix1,
+#ifdef DEBUG_AVX2
+ Score8_T **matrix2,
+#else
+ Score32_T **matrix2,
+#endif
+ int rlength, int glength,
+ int lband, char *rsequence, char *gsequence, char *gsequence_alt,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ bool revp) {
+ int r, c, rlo, rhigh;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c + lband) > rlength) {
+ rhigh = rlength;
+ }
+
+ for (r = rlo; r <= rhigh; r++) {
+#ifdef DEBUG_AVX2
+ if (matrix1[r][c] <= NEG_INFINITY_8 + 30 && matrix2[r][c] <= NEG_INFINITY_8 + 30) {
+ /* Okay */
+ } else if (matrix1[r][c] != matrix2[r][c]) {
+ printf("At %d,%d, value %d != value %d\n",r,c,matrix1[r][c],matrix2[r][c]);
+
+ Matrix8_print_ud(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Matrix8_print_ud(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ abort();
+ }
+#else
+ if (matrix1[r][c] <= NEG_INFINITY_8 + 30 && matrix2[c][r] <= NEG_INFINITY_8 + 30) {
+ /* Okay */
+ } else if (matrix1[r][c] != matrix2[c][r]) {
+ printf("At %d,%d, value %d != value %d\n",r,c,matrix1[r][c],matrix2[c][r]);
+
+ Matrix8_print_ud(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Dynprog_Matrix32_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp,lband,/*uband*/0);
+ abort();
}
+#endif
}
}
return;
}
+
static void
-banded_matrix16_compare (Score16_T **matrix1, Score32_T **matrix2, int rlength, int glength,
- int lband, int uband, char *rsequence, char *gsequence, char *gsequence_alt,
+banded_matrix16_compare (Score16_T **matrix1,
+#ifdef DEBUG_AVX2
+ Score16_T **matrix2,
+#elif defined(DEBUG_SIMD)
+ Score32_T **matrix2,
+#endif
+ int rlength, int glength, int lband, int uband, char *rsequence, char *gsequence, char *gsequence_alt,
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
bool revp) {
int r, c, rlo, rhigh;
@@ -960,26 +1175,136 @@ banded_matrix16_compare (Score16_T **matrix1, Score32_T **matrix2, int rlength,
for (r = rlo; r <= rhigh; r++) {
if (matrix1[c][r] <= NEG_INFINITY_16 + 30 && matrix2[c][r] <= NEG_INFINITY_16 + 30) {
- /* Okay */
+ /* Okay: both essentially negative infinity */
} else if (matrix1[c][r] != matrix2[c][r]) {
printf("At %d,%d, value %d != value %d\n",r,c,matrix1[c][r],matrix2[c][r]);
Matrix16_print(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp,lband,uband);
+ revp,lband,uband);
+#ifdef DEBUG_AVX2
+ Matrix16_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+#elif defined(DEBUG_SIMD)
Dynprog_Matrix32_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
goffset,chroffset,chrhigh,watsonp,revp,lband,uband);
- exit(9);
+#endif
+ abort();
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_matrix16_compare_upper (Score16_T **matrix1,
+#ifdef DEBUG_AVX2
+ Score16_T **matrix2,
+#else
+ Score32_T **matrix2,
+#endif
+ int rlength, int glength,
+ int uband, char *rsequence, char *gsequence, char *gsequence_alt,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ bool revp) {
+ int r, c, rlo, rhigh;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c) > rlength) {
+ rhigh = rlength;
+ }
+
+ for (r = rlo; r <= rhigh; r++) {
+ if (matrix1[c][r] <= NEG_INFINITY_16 + 30 && matrix2[c][r] <= NEG_INFINITY_16 + 30) {
+ /* Okay */
+ } else if (matrix1[c][r] != matrix2[c][r]) {
+ printf("At %d,%d, value %d != value %d\n",r,c,matrix1[c][r],matrix2[c][r]);
+
+ Matrix16_print_ud(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+#ifdef DEBUG_AVX2
+ Matrix16_print_ud(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+#else
+ Dynprog_Matrix32_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp,/*lband*/0,uband);
+#endif
+ abort();
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_matrix16_compare_lower (Score16_T **matrix1,
+#ifdef DEBUG_AVX2
+ Score16_T **matrix2,
+#else
+ Score32_T **matrix2,
+#endif
+ int rlength, int glength,
+ int lband, char *rsequence, char *gsequence, char *gsequence_alt,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ bool revp) {
+ int r, c, rlo, rhigh;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c + lband) > rlength) {
+ rhigh = rlength;
+ }
+
+ for (r = rlo; r <= rhigh; r++) {
+#ifdef DEBUG_AVX2
+ if (matrix1[r][c] <= NEG_INFINITY_16 + 30 && matrix2[r][c] <= NEG_INFINITY_16 + 30) {
+ /* Okay */
+ } else if (matrix1[r][c] != matrix2[r][c]) {
+ printf("At %d,%d, value %d != value %d\n",r,c,matrix1[r][c],matrix2[r][c]);
+
+ Matrix16_print_ud(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Matrix16_print_ud(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ abort();
+ }
+#else
+ if (matrix1[r][c] <= NEG_INFINITY_16 + 30 && matrix2[c][r] <= NEG_INFINITY_16 + 30) {
+ /* Okay */
+ } else if (matrix1[r][c] != matrix2[c][r]) {
+ printf("At %d,%d, value %d != value %d\n",r,c,matrix1[r][c],matrix2[c][r]);
+
+ Matrix16_print_ud(matrix1,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Dynprog_Matrix32_print(matrix2,rlength,glength,rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp,lband,/*uband*/0);
+ abort();
}
+#endif
}
}
return;
}
+
#endif
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
static void
-banded_directions8_compare_nogap (Score8_T **matrix, Direction8_T **directions1, Direction32_T **directions2,
+banded_directions8_compare_nogap (Score8_T **matrix, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#elif defined(DEBUG_SIMD)
+ Direction32_T **directions2,
+#endif
int rlength, int glength, int lband, int uband) {
int r, c, rlo, rhigh;
@@ -1000,20 +1325,20 @@ banded_directions8_compare_nogap (Score8_T **matrix, Direction8_T **directions1,
if (directions2[c][r] == 0) {
} else {
printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ abort();
}
} else if (directions1[c][r] == 1) {
if (directions2[c][r] == 1) {
} else {
printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ abort();
}
} else {
if (directions2[c][r] == 0 || directions2[c][r] == 0) {
printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ abort();
}
}
}
@@ -1022,10 +1347,14 @@ banded_directions8_compare_nogap (Score8_T **matrix, Direction8_T **directions1,
return;
}
-
static void
-banded_directions16_compare_nogap (Direction16_T **directions1, Direction32_T **directions2,
- int rlength, int glength, int lband, int uband) {
+banded_directions8_compare_nogap_upper (Score8_T **matrix, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#elif defined(DEBUG_SIMD)
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int uband) {
int r, c, rlo, rhigh;
for (c = 1; c <= glength; c++) {
@@ -1033,29 +1362,32 @@ banded_directions16_compare_nogap (Direction16_T **directions1, Direction32_T **
rlo = 1;
};
- if ((rhigh = c + lband) > rlength) {
+ if ((rhigh = c) > rlength) {
rhigh = rlength;
}
for (r = rlo; r <= rhigh; r++) {
- if (directions1[c][r] == 0) {
+ if (matrix[c][r] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
+
+ } else if (directions1[c][r] == 0) {
if (directions2[c][r] == 0) {
} else {
printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ abort();
}
} else if (directions1[c][r] == 1) {
if (directions2[c][r] == 1) {
} else {
printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ abort();
}
} else {
if (directions2[c][r] == 0 || directions2[c][r] == 0) {
printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ abort();
}
}
}
@@ -1063,101 +1395,125 @@ banded_directions16_compare_nogap (Direction16_T **directions1, Direction32_T **
return;
}
-#endif
-#ifdef DEBUG14
static void
-banded_directions8_compare_Egap (Score8_T **matrix1, Direction8_T **directions1, Direction32_T **directions2,
- int rlength, int glength, int lband, int uband) {
- int r, c, rlo, rhigh, last_check;
+banded_directions8_compare_nogap_lower (Score8_T **matrix, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#elif defined(DEBUG_SIMD)
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband) {
+ int r, c, rlo, rhigh;
for (c = 1; c <= glength; c++) {
- if ((rlo = c - uband) < 1) {
+ if ((rlo = c) < 1) {
rlo = 1;
};
- if ((rhigh = c + lband) <= rlength) {
- /* Don't check rhigh. Egap direction derives from a comparison
- of NEG_INFINITY values, and we should never reach here from
- directions_nogap anyway. */
- last_check = rhigh - 1;
-
- } else {
- /* Do check rhigh, which contains instructions for the bottom row */
+ if ((rhigh = c + lband) > rlength) {
rhigh = rlength;
- last_check = rhigh;
}
- for (r = rlo; r <= last_check; r++) {
- if (matrix1[c][r] < NEG_INFINITY_8 + 30) {
+#ifdef DEBUG_AVX2
+ for (r = rlo; r <= rhigh; r++) {
+ if (matrix[c][r] < NEG_INFINITY_8 + 30) {
/* Don't check */
- } else if (directions1[c][r] == 0) {
+ } else if (directions1[r][c] == 0) {
+ if (directions2[r][c] == 0) {
+ } else {
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+
+ } else if (directions1[r][c] == 1) {
+ if (directions2[r][c] == 1) {
+ } else {
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+
+ } else {
+ if (directions2[r][c] == 0 || directions2[r][c] == 0) {
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+ }
+ }
+
+#else
+ for (r = rlo; r <= rhigh; r++) {
+ if (matrix[c][r] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
+
+ } else if (directions1[r][c] == 0) {
if (directions2[c][r] == 0) {
} else {
- printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
}
- } else if (directions1[c][r] == 1) {
+ } else if (directions1[r][c] == 1) {
if (directions2[c][r] == 1) {
} else {
- printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
}
} else {
if (directions2[c][r] == 0 || directions2[c][r] == 0) {
- printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
}
}
}
+#endif
+
}
return;
}
+
static void
-banded_directions16_compare_Egap (Direction16_T **directions1, Direction32_T **directions2,
- int rlength, int glength, int lband, int uband) {
- int r, c, rlo, rhigh, last_check;
+banded_directions16_compare_nogap (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#elif defined(DEBUG_SIMD)
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband, int uband) {
+ int r, c, rlo, rhigh;
for (c = 1; c <= glength; c++) {
if ((rlo = c - uband) < 1) {
rlo = 1;
};
- if ((rhigh = c + lband) <= rlength) {
- /* Don't check rhigh. Egap direction derives from a comparison
- of NEG_INFINITY values, and we should never reach here from
- directions_nogap anyway. */
- last_check = rhigh - 1;
-
- } else {
- /* Do check rhigh, which contains instructions for the bottom row */
+ if ((rhigh = c + lband) > rlength) {
rhigh = rlength;
- last_check = rhigh;
}
- for (r = rlo; r <= last_check; r++) {
+ for (r = rlo; r <= rhigh; r++) {
if (directions1[c][r] == 0) {
if (directions2[c][r] == 0) {
} else {
- printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
}
+
} else if (directions1[c][r] == 1) {
if (directions2[c][r] == 1) {
} else {
- printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
}
} else {
if (directions2[c][r] == 0 || directions2[c][r] == 0) {
- printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
}
}
}
@@ -1165,51 +1521,45 @@ banded_directions16_compare_Egap (Direction16_T **directions1, Direction32_T **d
return;
}
-#endif
-
-#ifdef DEBUG14
static void
-banded_directions8_compare_Fgap (Score8_T **matrix1, Direction8_T **directions1, Direction32_T **directions2,
- int rlength, int glength, int lband, int uband) {
- int r, c, rlo, rhigh, first_check;
+banded_directions16_compare_nogap_upper (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int uband) {
+ int r, c, rlo, rhigh;
for (c = 1; c <= glength; c++) {
if ((rlo = c - uband) < 1) {
- first_check = rlo = 1;
- } else {
- first_check = rlo + 1;
- }
+ rlo = 1;
+ };
- if ((rhigh = c + lband) > rlength) {
+ if ((rhigh = c) > rlength) {
rhigh = rlength;
}
- for (r = first_check; r <= rhigh; r++) {
- if (matrix1[c][r] < NEG_INFINITY_8 + 30) {
- /* Don't check */
-
- } else if (directions1[c][r] == 0) {
+ for (r = rlo; r <= rhigh; r++) {
+ if (directions1[c][r] == 0) {
if (directions2[c][r] == 0) {
} else {
- printf("At %d,%d, Fgap dir %d != dir %d. Score is %d\n",
- r,c,directions1[c][r],directions2[c][r],matrix1[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
}
} else if (directions1[c][r] == 1) {
if (directions2[c][r] == 1) {
} else {
- printf("At %d,%d, Fgap dir %d != dir %d. Score is %d\n",
- r,c,directions1[c][r],directions2[c][r],matrix1[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
}
} else {
if (directions2[c][r] == 0 || directions2[c][r] == 0) {
- printf("At %d,%d, Fgap dir %d != dir %d. Score is %d\n",
- r,c,directions1[c][r],directions2[c][r],matrix1[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
}
}
}
@@ -1219,41 +1569,68 @@ banded_directions8_compare_Fgap (Score8_T **matrix1, Direction8_T **directions1,
}
static void
-banded_directions16_compare_Fgap (Direction16_T **directions1, Direction32_T **directions2,
- int rlength, int glength, int lband, int uband) {
- int r, c, rlo, rhigh, first_check;
+banded_directions16_compare_nogap_lower (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband) {
+ int r, c, rlo, rhigh;
for (c = 1; c <= glength; c++) {
- if ((rlo = c - uband) < 1) {
- first_check = rlo = 1;
- } else {
- first_check = rlo + 1;
- }
+ if ((rlo = c) < 1) {
+ rlo = 1;
+ };
if ((rhigh = c + lband) > rlength) {
rhigh = rlength;
}
- for (r = first_check; r <= rhigh; r++) {
- if (directions1[c][r] == 0) {
+ for (r = rlo; r <= rhigh; r++) {
+#ifdef DEBUG_AVX2
+ if (directions1[r][c] == 0) {
+ if (directions2[r][c] == 0) {
+ } else {
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+
+ } else if (directions1[r][c] == 1) {
+ if (directions2[r][c] == 1) {
+ } else {
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+
+ } else {
+ if (directions2[r][c] == 0 || directions2[r][c] == 0) {
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+ }
+#else
+ if (directions1[r][c] == 0) {
if (directions2[c][r] == 0) {
} else {
- printf("At %d,%d, Fgap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
}
- } else if (directions1[c][r] == 1) {
+
+ } else if (directions1[r][c] == 1) {
if (directions2[c][r] == 1) {
} else {
- printf("At %d,%d, Fgap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
}
} else {
if (directions2[c][r] == 0 || directions2[c][r] == 0) {
- printf("At %d,%d, Fgap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
- exit(9);
+ printf("At %d,%d, nogap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
}
}
+#endif
}
}
@@ -1261,203 +1638,4184 @@ banded_directions16_compare_Fgap (Direction16_T **directions1, Direction32_T **d
}
#endif
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+static void
+banded_directions8_compare_Egap (Score8_T **matrix1, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband, int uband) {
+ int r, c, rlo, rhigh, last_check;
-/************************************************************************
- * End of debugging procedures
- ************************************************************************/
-
-
-
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
-/* Makes a matrix of dimensions 0..rlength x 0..glength inclusive */
-static Score8_T **
-aligned_score8_alloc (int rlength, int glength, void **ptrs, void *space) {
- Score8_T **matrix, *ptr;
- int c;
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ rlo = 1;
+ };
- matrix = (Score8_T **) ptrs;
+ if ((rhigh = c + lband) <= rlength) {
+ /* Don't check rhigh. Egap direction derives from a comparison
+ of NEG_INFINITY values, and we should never reach here from
+ directions_nogap anyway. */
+ last_check = rhigh - 1;
- ptr = (Score8_T *) space;
- matrix[0] = ptr; /* Want aligned row to be r = 0, 16, ... */
- for (c = 1; c <= glength; c++) {
- ptr += rlength;
- matrix[c] = ptr; /* Want aligned row to be r = 0, 16, ... */
- }
-#if defined(DEBUG2) && defined(DEBUG14)
- memset((void *) matrix[0],0,(glength+1)*rlength*sizeof(Score8_T));
-#endif
+ } else {
+ /* Do check rhigh, which contains instructions for the bottom row */
+ rhigh = rlength;
+ last_check = rhigh;
+ }
- return matrix;
-}
+ for (r = rlo; r <= last_check; r++) {
+ if (matrix1[c][r] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
-/* No initialization to DIAG (0), for directions_Egap and directions_nogap */
-static Score8_T **
-aligned_directions8_alloc (int rlength, int glength, void **ptrs, void *space) {
- Score8_T **matrix, *ptr;
- int c;
+ } else if (directions1[c][r] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
- matrix = (Score8_T **) ptrs;
+ } else if (directions1[c][r] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
- ptr = (Score8_T *) space;
- matrix[0] = ptr; /* Want aligned row to be r = 0, 16, ... */
- for (c = 1; c <= glength; c++) {
- ptr += rlength;
- matrix[c] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ }
+ }
}
-#if defined(DEBUG2) && defined(DEBUG14)
- memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score8_T));
-#endif
- return matrix;
+ return;
}
-/* Initialization to DIAG (0), for directions_Fgap */
-static Score8_T **
-aligned_directions8_calloc (int rlength, int glength, void **ptrs, void *space) {
- Score8_T **matrix, *ptr;
- int c;
-
- matrix = (Score8_T **) ptrs;
+static void
+banded_directions8_compare_Egap_upper (Score8_T **matrix1, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int uband) {
+ int r, c, rlo, rhigh, last_check;
- ptr = (Score8_T *) space;
- matrix[0] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ return;
for (c = 1; c <= glength; c++) {
- ptr += rlength;
- matrix[c] = ptr; /* Want aligned row to be r = 0, 16, ... */
- }
- memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score8_T));
+ if ((rlo = c - uband) < 1) {
+ rlo = 1;
+ };
- return matrix;
-}
+ if ((rhigh = c) <= rlength) {
+ /* Don't check rhigh. Egap direction derives from a comparison
+ of NEG_INFINITY values, and we should never reach here from
+ directions_nogap anyway. */
+ last_check = rhigh - 1;
+ } else {
+ /* Do check rhigh, which contains instructions for the bottom row */
+ rhigh = rlength;
+ last_check = rhigh;
+ }
+ for (r = rlo; r <= last_check; r++) {
+ if (matrix1[c][r] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
-/* Makes a matrix of dimensions 0..rlength x 0..glength inclusive */
-static Score16_T **
-aligned_score16_alloc (int rlength, int glength, void **ptrs, void *space) {
- Score16_T **matrix, *ptr;
- int c;
+ } else if (directions1[c][r] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
- matrix = (Score16_T **) ptrs;
+ } else if (directions1[c][r] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
- ptr = (Score16_T *) space;
- matrix[0] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
- for (c = 1; c <= glength; c++) {
- ptr += rlength;
- matrix[c] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ }
+ }
}
-#ifdef DEBUG2
- memset((void *) matrix[0],0,(glength+1)*rlength*sizeof(Score16_T));
-#endif
- return matrix;
+ return;
}
-/* No initialization to DIAG (0), for directions_Egap and directions_nogap */
-static Score16_T **
-aligned_directions16_alloc (int rlength, int glength, void **ptrs, void *space) {
- Score16_T **matrix, *ptr;
- int c;
-
- matrix = (Score16_T **) ptrs;
-
- ptr = (Score16_T *) space;
- matrix[0] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
- for (c = 1; c <= glength; c++) {
- ptr += rlength;
- matrix[c] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
- }
-#ifdef DEBUG2
- memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score16_T));
+static void
+banded_directions8_compare_Egap_lower (Score8_T **matrix1, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#else
+ Direction32_T **directions2,
#endif
+ int rlength, int glength, int lband) {
+ int r, c, rlo, rhigh, last_check;
- return matrix;
-}
+ return;
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c) < 1) {
+ rlo = 1;
+ };
-/* Initialization to DIAG (0), for directions_Fgap */
-static Score16_T **
-aligned_directions16_calloc (int rlength, int glength, void **ptrs, void *space) {
- Score16_T **matrix, *ptr;
- int c;
+ if ((rhigh = c + lband) <= rlength) {
+ /* Don't check rhigh. Egap direction derives from a comparison
+ of NEG_INFINITY values, and we should never reach here from
+ directions_nogap anyway. */
+ last_check = rhigh - 1;
- matrix = (Score16_T **) ptrs;
+ } else {
+ /* Do check rhigh, which contains instructions for the bottom row */
+ rhigh = rlength;
+ last_check = rhigh;
+ }
- ptr = (Score16_T *) space;
- matrix[0] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
- for (c = 1; c <= glength; c++) {
- ptr += rlength;
- matrix[c] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
- }
- memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score16_T));
+ for (r = rlo; r <= last_check; r++) {
+#ifdef DEBUG_AVX2
+ if (matrix1[r][c] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
- return matrix;
-}
-#endif
+ } else if (directions1[r][c] == 0) {
+ if (directions2[r][c] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+ } else if (directions1[r][c] == 1) {
+ if (directions2[r][c] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+
+ } else {
+ if (directions2[r][c] == 0 || directions2[r][c] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+ }
+#else
+ if (matrix1[r][c] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
+
+ } else if (directions1[r][c] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
+ }
+
+ } else if (directions1[r][c] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
+ }
+
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
+ }
+ }
+#endif
+ }
+ }
+
+ return;
+}
+
+
+static void
+banded_directions16_compare_Egap (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband, int uband) {
+ int r, c, rlo, rhigh, last_check;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c + lband) <= rlength) {
+ /* Don't check rhigh. Egap direction derives from a comparison
+ of NEG_INFINITY values, and we should never reach here from
+ directions_nogap anyway. */
+ last_check = rhigh - 1;
+
+ } else {
+ /* Do check rhigh, which contains instructions for the bottom row */
+ rhigh = rlength;
+ last_check = rhigh;
+ }
+
+ for (r = rlo; r <= last_check; r++) {
+ if (directions1[c][r] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ } else if (directions1[c][r] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_directions16_compare_Egap_upper (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int uband) {
+ int r, c, rlo, rhigh, last_check;
+
+ return;
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c) <= rlength) {
+ /* Don't check rhigh. Egap direction derives from a comparison
+ of NEG_INFINITY values, and we should never reach here from
+ directions_nogap anyway. */
+ last_check = rhigh - 1;
+
+ } else {
+ /* Do check rhigh, which contains instructions for the bottom row */
+ rhigh = rlength;
+ last_check = rhigh;
+ }
+
+ for (r = rlo; r <= last_check; r++) {
+ if (directions1[c][r] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ } else if (directions1[c][r] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_directions16_compare_Egap_lower (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband) {
+ int r, c, rlo, rhigh, last_check;
+
+ return;
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c) < 1) {
+ rlo = 1;
+ };
+
+ if ((rhigh = c + lband) <= rlength) {
+ /* Don't check rhigh. Egap direction derives from a comparison
+ of NEG_INFINITY values, and we should never reach here from
+ directions_nogap anyway. */
+ last_check = rhigh - 1;
+
+ } else {
+ /* Do check rhigh, which contains instructions for the bottom row */
+ rhigh = rlength;
+ last_check = rhigh;
+ }
+
+ for (r = rlo; r <= last_check; r++) {
+#ifdef DEBUG_AVX2
+ if (directions1[r][c] == 0) {
+ if (directions2[r][c] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+ } else if (directions1[r][c] == 1) {
+ if (directions2[r][c] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+
+ } else {
+ if (directions2[r][c] == 0 || directions2[r][c] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[r][c]);
+ abort();
+ }
+ }
+#else
+ if (directions1[r][c] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
+ }
+ } else if (directions1[r][c] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
+ }
+
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Egap dir %d != dir %d\n",r,c,directions1[r][c],directions2[c][r]);
+ abort();
+ }
+ }
+#endif
+ }
+ }
+
+ return;
+}
+#endif
+
+
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+static void
+banded_directions8_compare_Fgap (Score8_T **matrix1, Direction8_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction8_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband, int uband) {
+ int r, c, rlo, rhigh, first_check;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ first_check = rlo = 1;
+ } else {
+ first_check = rlo + 1;
+ }
+
+ if ((rhigh = c + lband) > rlength) {
+ rhigh = rlength;
+ }
+
+ for (r = first_check; r <= rhigh; r++) {
+ if (matrix1[c][r] < NEG_INFINITY_8 + 30) {
+ /* Don't check */
+
+ } else if (directions1[c][r] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Fgap dir %d != dir %d. Score is %d\n",
+ r,c,directions1[c][r],directions2[c][r],matrix1[c][r]);
+ abort();
+ }
+
+ } else if (directions1[c][r] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Fgap dir %d != dir %d. Score is %d\n",
+ r,c,directions1[c][r],directions2[c][r],matrix1[c][r]);
+ abort();
+ }
+
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Fgap dir %d != dir %d. Score is %d\n",
+ r,c,directions1[c][r],directions2[c][r],matrix1[c][r]);
+ abort();
+ }
+ }
+ }
+ }
+
+ return;
+}
+
+static void
+banded_directions16_compare_Fgap (Direction16_T **directions1,
+#ifdef DEBUG_AVX2
+ Direction16_T **directions2,
+#else
+ Direction32_T **directions2,
+#endif
+ int rlength, int glength, int lband, int uband) {
+ int r, c, rlo, rhigh, first_check;
+
+ for (c = 1; c <= glength; c++) {
+ if ((rlo = c - uband) < 1) {
+ first_check = rlo = 1;
+ } else {
+ first_check = rlo + 1;
+ }
+
+ if ((rhigh = c + lband) > rlength) {
+ rhigh = rlength;
+ }
+
+ for (r = first_check; r <= rhigh; r++) {
+ if (directions1[c][r] == 0) {
+ if (directions2[c][r] == 0) {
+ } else {
+ printf("At %d,%d, Fgap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ } else if (directions1[c][r] == 1) {
+ if (directions2[c][r] == 1) {
+ } else {
+ printf("At %d,%d, Fgap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+
+ } else {
+ if (directions2[c][r] == 0 || directions2[c][r] == 0) {
+ printf("At %d,%d, Fgap dir %d != dir %d\n",r,c,directions1[c][r],directions2[c][r]);
+ abort();
+ }
+ }
+ }
+ }
+
+ return;
+}
+#endif
+
+
+/************************************************************************
+ * End of debugging procedures
+ ************************************************************************/
+
+
+
+#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+/* Makes a matrix of dimensions 0..rlength x 0..glength inclusive */
+static Score8_T **
+aligned_score8_alloc (int rlength, int glength, void **ptrs, void *space) {
+ Score8_T **matrix, *ptr;
+ int c;
+
+ matrix = (Score8_T **) ptrs;
+
+ ptr = (Score8_T *) space;
+ matrix[0] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ for (c = 1; c <= glength; c++) {
+ ptr += rlength;
+ matrix[c] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ }
+#if defined(DEBUG2) && (defined(DEBUG_AVX2) || defined(DEBUG_SIMD))
+ memset((void *) matrix[0],0,(glength+1)*rlength*sizeof(Score8_T));
+#endif
+
+ return matrix;
+}
+
+/* No initialization to DIAG (0), for directions_Egap and directions_nogap */
+static Score8_T **
+aligned_directions8_alloc (int rlength, int glength, void **ptrs, void *space) {
+ Score8_T **matrix, *ptr;
+ int c;
+
+ matrix = (Score8_T **) ptrs;
+
+ ptr = (Score8_T *) space;
+ matrix[0] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ for (c = 1; c <= glength; c++) {
+ ptr += rlength;
+ matrix[c] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ }
+#if defined(DEBUG2) && (defined(DEBUG_AVX2) || defined(DEBUG_SIMD))
+ memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score8_T));
+#endif
+
+ return matrix;
+}
+
+/* Initialization to DIAG (0), for directions_Fgap */
+static Score8_T **
+aligned_directions8_calloc (int rlength, int glength, void **ptrs, void *space) {
+ Score8_T **matrix, *ptr;
+ int c;
+
+ matrix = (Score8_T **) ptrs;
+
+ ptr = (Score8_T *) space;
+ matrix[0] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ for (c = 1; c <= glength; c++) {
+ ptr += rlength;
+ matrix[c] = ptr; /* Want aligned row to be r = 0, 16, ... */
+ }
+ memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score8_T));
+
+ return matrix;
+}
+
+
+
+/* Makes a matrix of dimensions 0..rlength x 0..glength inclusive */
+static Score16_T **
+aligned_score16_alloc (int rlength, int glength, void **ptrs, void *space) {
+ Score16_T **matrix, *ptr;
+ int c;
+
+ matrix = (Score16_T **) ptrs;
+
+ ptr = (Score16_T *) space;
+ matrix[0] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ for (c = 1; c <= glength; c++) {
+ ptr += rlength;
+ matrix[c] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ }
+#ifdef DEBUG2
+ memset((void *) matrix[0],0,(glength+1)*rlength*sizeof(Score16_T));
+#endif
+
+ return matrix;
+}
+
+/* No initialization to DIAG (0), for directions_Egap and directions_nogap */
+static Score16_T **
+aligned_directions16_alloc (int rlength, int glength, void **ptrs, void *space) {
+ Score16_T **matrix, *ptr;
+ int c;
+
+ matrix = (Score16_T **) ptrs;
+
+ ptr = (Score16_T *) space;
+ matrix[0] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ for (c = 1; c <= glength; c++) {
+ ptr += rlength;
+ matrix[c] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ }
+#ifdef DEBUG2
+ memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score16_T));
+#endif
+
+ return matrix;
+}
+
+/* Initialization to DIAG (0), for directions_Fgap */
+static Score16_T **
+aligned_directions16_calloc (int rlength, int glength, void **ptrs, void *space) {
+ Score16_T **matrix, *ptr;
+ int c;
+
+ matrix = (Score16_T **) ptrs;
+
+ ptr = (Score16_T *) space;
+ matrix[0] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ for (c = 1; c <= glength; c++) {
+ ptr += rlength;
+ matrix[c] = ptr; /* Want aligned row to be r = 0, 8, 16, ... */
+ }
+ memset((void *) matrix[0],/*DIAG*/0,(glength+1)*rlength*sizeof(Score16_T));
+
+ return matrix;
+}
+#endif
+
+
+#define T Dynprog_T
+
+
+#ifdef DEBUG_AVX2
+Score8_T **
+Dynprog_simd_8_nonavx2 (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
+ Direction8_T ***directions_Fgap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, int uband, bool jump_late_p, bool revp) {
+ int c_gap, last_nogap, score, *FF; /* Need to have the ability to go past NEG_INFINITY */
+ Score8_T **matrix, *score_column;
+ __m128i pairscores_std, pairscores_alt;
+#ifndef HAVE_SSE4_1
+ __m128i pairscores_best, all_128;
+#endif
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, T1;
+ __m128i gap_open, gap_extend, extend_ladder, extend_chunk, complement_dummy;
+ __m128i dir_horiz;
+ __m128i ramp, ramp_chunk, lband_vector, filter, ones;
+ int rlength_ceil, lband_ceil, r, c;
+ int rlo, rhigh, rlo_calc, rhigh_calc;
+ int na1, na2, na2_alt;
+ Score8_T *pairscores_col0;
+ Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore, pairscore0;
+ Pairdistance_T **pairdistance_array_type;
+
+
+ debug2(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d, lband %d, uband %d\n",
+ jump_late_p,open,extend,lband,uband));
+
+ rlength_ceil = (int) ((rlength + SIMD_NCHARS_NONAVX2)/SIMD_NCHARS_NONAVX2) * SIMD_NCHARS_NONAVX2;
+
+#ifdef HAVE_SSE4_1
+ pairdistance_array_type = pairdistance_array[mismatchtype];
+#else
+ /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
+ pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
+ all_128 = _mm_set1_epi8(128);
+#endif
+
+ debug(printf("Dynprog_simd_8: "));
+ debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
+ debug(printf("Query length rounded up to %d\n",rlength_ceil));
+
+ matrix = aligned_score8_alloc(rlength_ceil,glength,
+ this->aligned_std.one.matrix_ptrs,this->aligned_std.one.matrix_space);
+ *directions_nogap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned_std.one.directions_ptrs_0,this->aligned_std.one.directions_space_0);
+ *directions_Egap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned_std.one.directions_ptrs_1,this->aligned_std.one.directions_space_1);
+ /* Need to calloc to save time in F loop */
+ *directions_Fgap = aligned_directions8_calloc(rlength_ceil,glength,
+ this->aligned_std.one.directions_ptrs_2,this->aligned_std.one.directions_space_2);
+
+#if 0
+ /* Row 0 initialization */
+ /* penalty = open; */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ /* penalty += extend; */
+ (*directions_Egap)[c][0] = HORIZ;
+ (*directions_nogap)[c][0] = HORIZ;
+ }
+#endif
+#if 0
+ /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ (*directions_Egap)[1][0] = DIAG; /* previously used STOP */
+ (*directions_nogap)[0][0] = DIAG; /* previously used STOP */
+#endif
+
+#if 0
+ /* Column 0 initialization */
+ /* penalty = open; */
+ for (r = 1; r <= SIMD_NCHARS_NONAVX2 && r <= rlength; r++) {
+ /* penalty += extend; */
+ (*directions_nogap)[0][r] = VERT;
+ }
+#endif
+
+
+ /* Load pairscores. Store match - mismatch */
+ pairscores[0] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[1] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[2] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[3] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[4] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+
+ lband_ceil = (int) ((lband + SIMD_NCHARS_NONAVX2)/SIMD_NCHARS_NONAVX2) * SIMD_NCHARS_NONAVX2;
+ pairscores_col0 = (Score8_T *) _mm_malloc(lband_ceil * sizeof(Score8_T),16);
+
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score8_T));
+#endif
+
+ /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
+#ifdef HAVE_SSE4_1
+ pairscores_col0[0] = (Score8_T) 0;
+ /* Initialization just to lband causes errors in dir_horiz for Egap */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) 0;
+ }
+#else
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) NEG_INFINITY_8;
+ }
+#endif
+#else
+ pairscores_col0[0] = (Score8_T) 0+128;
+ /* Initialization just to lband causes errors in dir_horiz for Egap */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) 0+128;
+ }
+#else
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) NEG_INFINITY_8+128;
+ }
+#endif
+#endif
+
+
+ /* Row 0 */
+ r = 0; na1 = 'N';
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+
+ if (revp == false) {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[r-1];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ } else {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[1-r];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ }
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+#endif
+
+ complement_dummy = _mm_set1_epi8(-1);
+
+ FF = (int *) MALLOCA((glength + 1) * sizeof(int));
+
+ gap_open = _mm_set1_epi8((Score8_T) open);
+ gap_extend = _mm_set1_epi8((Score8_T) extend);
+
+#ifndef INFINITE_INITIAL_GAP_PENALTY
+ lband_vector = _mm_set1_epi8(lband);
+ ramp = _mm_setr_epi8(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16);
+ extend_ladder = _mm_setr_epi8(extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*extend,8*extend,
+ 9*extend,10*extend,11*extend,12*extend,13*extend,14*extend,15*extend,16*extend);
+ ramp_chunk = _mm_set1_epi8(SIMD_NCHARS_NONAVX2);
+ extend_chunk = _mm_set1_epi8(SIMD_NCHARS_NONAVX2*extend);
+#endif
+
+ if (jump_late_p) {
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NCHARS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8-open);
+ filter = _mm_cmpgt_epi8(ramp,lband_vector);
+ H_nogap_r = _mm_and_si128(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _mm_adds_epi8(E_r_gap,gap_open);
+
+ ramp = _mm_adds_epi8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi8(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E >= H. To fill in first column of each
+ row block with non-diags, make E == H. */
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8);
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+#else
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ equal to E. */
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
+ filter = _mm_cmpgt_epi8(ramp,lband_vector);
+ H_nogap_r = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),_mm_and_si128(filter,H_nogap_r));
+ E_r_gap = _mm_adds_epi8(H_nogap_r,gap_open);
+ ramp = _mm_adds_epi8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi8(extend_ladder,extend_chunk); /* Prepare for next block */
+#endif
+ } else {
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8);
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ }
+
+ for ( ; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ if (rlo == 0) {
+ X_prev_nogap = _mm_set1_epi8(0);
+ } else {
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+#endif
+
+ } else {
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+ if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+#endif
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+ }
+
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _mm_adds_epi8(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmplt_epi8(E_r_gap,T1); /* E < H */
+ dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
+#else
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+#endif
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+ H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_SSE4_1
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _mm_cmplt_epi8(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+
+
+ /* F loop */
+ if ((rlo_calc = rlo) < c - uband) {
+ rlo_calc = c - uband;
+ }
+ if ((rhigh_calc = rhigh) >= c + lband) {
+ rhigh_calc = c + lband;
+ if (c > 0) {
+ /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
+ pairscore = pairscores[na2][rhigh_calc];
+ if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
+ pairscore = pairscore0;
+ }
+#ifndef HAVE_SSE4_1
+ pairscore -= 128;
+#endif
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_8) {
+ score_column[rhigh_calc] = NEG_INFINITY_8; /* Saturation */
+ } else if (score > POS_INFINITY_8) {
+ /* Should never get here, because we limit size of matrix using 8-bit quantities */
+ score_column[rhigh_calc] = POS_INFINITY_8; /* Saturation */
+ } else {
+ score_column[rhigh_calc] = (Score8_T) score;
+ }
+ (*directions_Egap)[c][rhigh_calc] = DIAG;
+ (*directions_nogap)[c][rhigh_calc] = DIAG;
+ }
+ }
+
+ debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
+ rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
+
+ if (rlo == 0) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else if (c >= rlo + uband) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else {
+ debug3(printf("At c %d, uband %d, reading c_gap %d\n",c,uband,FF[c]));
+ c_gap = FF[c];
+ last_nogap = (int) score_column[rlo_calc-1];
+ }
+
+ if ((r = rlo_calc) == c - uband) {
+ /* Handle top value as a special case to prevent going outside of uband */
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ score = last_nogap + open /* + extend */;
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ r++;
+ }
+
+ /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
+ for ( ; r <= rhigh_calc; r++) {
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
+ c_gap += extend;
+ (*directions_Fgap)[c][r] = VERT;
+ } else {
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ }
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
+ if (c_gap >= last_nogap) { /* Use >= for jump late */
+ last_nogap = c_gap;
+ score_column[r] = (c_gap < NEG_INFINITY_8) ? NEG_INFINITY_8 : (Score8_T) c_gap; /* Saturation */
+ (*directions_nogap)[c][r] = VERT;
+ }
+ }
+
+ FF[c] = c_gap;
+ debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
+ H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+ }
+ }
+
+ } else {
+ /* jump early */
+#if defined(ZERO_INITIAL_GAP_PENALTY) || defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* No need for ones */
+#else
+ ones = _mm_set1_epi8(1);
+#endif
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NCHARS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8-open);
+ filter = _mm_cmpgt_epi8(ramp,lband_vector);
+ H_nogap_r = _mm_and_si128(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _mm_adds_epi8(E_r_gap,gap_open);
+
+ ramp = _mm_adds_epi8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi8(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, make E > H. */
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+#else
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ less than E. */
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open+1); /* To compensate for T1 = H + open */
+ filter = _mm_cmpgt_epi8(ramp,lband_vector);
+ H_nogap_r = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),_mm_and_si128(filter,H_nogap_r));
+ E_r_gap = _mm_adds_epi8(H_nogap_r,gap_open);
+ H_nogap_r = _mm_subs_epi8(H_nogap_r,ones); /* To ensure H < E */
+ ramp = _mm_adds_epi8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi8(extend_ladder,extend_chunk); /* Prepare for next block */
+#endif
+ } else {
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ }
+
+ for ( ; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ if (rlo == 0) {
+ X_prev_nogap = _mm_set1_epi8(0);
+ } else {
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+#endif
+
+ } else {
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+ if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+#endif
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+ }
+
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _mm_adds_epi8(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmpgt_epi8(E_r_gap,T1); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
+#else
+ /* Compare H + open with vert */
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+#endif
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+ H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_SSE4_1
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _mm_cmpgt_epi8(E_r_gap,H_nogap_r); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+
+
+ /* F loop */
+ if ((rlo_calc = rlo) < c - uband) {
+ rlo_calc = c - uband;
+ }
+ if ((rhigh_calc = rhigh) >= c + lband) {
+ rhigh_calc = c + lband;
+ if (c > 0) {
+ /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
+ pairscore = pairscores[na2][rhigh_calc];
+ if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
+ pairscore = pairscore0;
+ }
+#ifndef HAVE_SSE4_1
+ pairscore -= 128;
+#endif
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_8) {
+ score_column[rhigh_calc] = NEG_INFINITY_8; /* Saturation */
+ } else if (score > POS_INFINITY_8) {
+ /* Should never get here, because we limit size of matrix using 8-bit quantities */
+ score_column[rhigh_calc] = POS_INFINITY_8; /* Saturation */
+ } else {
+ score_column[rhigh_calc] = (Score8_T) score;
+ }
+ (*directions_Egap)[c][rhigh_calc] = DIAG;
+ (*directions_nogap)[c][rhigh_calc] = DIAG;
+ }
+ }
+
+ debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
+ rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
+
+ if (rlo == 0) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else if (c >= rlo + uband) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else {
+ c_gap = FF[c];
+ last_nogap = (int) score_column[rlo_calc-1];
+ debug3(printf("LAST_NOGAP gets score_column[%d-1], or %d\n",rlo_calc,last_nogap));
+ }
+
+ if ((r = rlo_calc) == c - uband) {
+ /* Handle top value as a special case to prevent going outside of uband */
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ score = last_nogap + open /* + extend */;
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ r++;
+ }
+
+ /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
+ for ( ; r <= rhigh_calc; r++) {
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
+ c_gap += extend;
+ (*directions_Fgap)[c][r] = VERT;
+ } else {
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ }
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
+ if (c_gap > last_nogap) { /* Use > for jump early */
+ last_nogap = c_gap;
+ score_column[r] = (c_gap < NEG_INFINITY_8) ? NEG_INFINITY_8 : (Score8_T) c_gap; /* Saturation */
+ debug3(printf("Stored at score_column[%d]: %d\n",r,(Score8_T) score_column[r]));
+ (*directions_nogap)[c][r] = VERT;
+ }
+ }
+
+ FF[c] = c_gap;
+ debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
+ H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+ }
+ }
+ }
+
+
+#ifdef CHECK1
+ /* Row 0 and column 0 directions fail anyway due to saturation */
+ /* Handle (0,1) and (1,0) directions, otherwise DIAG */
+ (*directions_Egap)[1][0] = HORIZ;
+ (*directions_Fgap)[0][1] = VERT;
+#endif
+
+#ifdef DEBUG2
+ printf("SIMD: Dynprog_simd_8\n");
+ Matrix8_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+ Directions8_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+#endif
+
+#ifdef CHECK1
+ /* Check for row 0 directions */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ assert((*directions_Egap)[c][0] != DIAG);
+ assert((*directions_nogap)[c][0] != DIAG);
+ }
+ /* Check for column 0 directions */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ assert((*directions_Fgap)[0][r] != DIAG);
+ assert((*directions_nogap)[0][r] != DIAG);
+ }
+#endif
+
+ FREEA(FF);
+ _mm_free(pairscores_col0);
+ _mm_free(pairscores[4]);
+ _mm_free(pairscores[3]);
+ _mm_free(pairscores[2]);
+ _mm_free(pairscores[1]);
+ _mm_free(pairscores[0]);
+
+ return matrix;
+}
+#endif
-#define T Dynprog_T
#if defined(HAVE_SSE2)
/* Modified from Dynprog_simd_8_upper. Operates by columns. */
Score8_T **
-Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
- Direction8_T ***directions_Fgap,
- T this, char *rsequence, char *gsequence, char *gsequence_alt,
- int rlength, int glength,
-#ifdef DEBUG14
- int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
+ Direction8_T ***directions_Fgap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+#endif
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, int uband, bool jump_late_p, bool revp) {
+ int c_gap, last_nogap, score, *FF; /* Need to have the ability to go past NEG_INFINITY */
+ Score8_T **matrix, *score_column;
+#ifdef HAVE_AVX2
+ __m256i pairscores_std, pairscores_alt;
+ __m256i H_nogap_r, X_prev_nogap, E_r_gap, T1;
+ __m256i gap_open, gap_extend, complement_dummy;
+ __m256i dir_horiz;
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ __m256i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter;
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+#else
+ __m256i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter, ones;
+#endif
+
+#else
+ __m128i pairscores_std, pairscores_alt;
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, T1;
+ __m128i gap_open, gap_extend, complement_dummy;
+ __m128i dir_horiz;
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ __m128i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter;
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+#else
+ __m128i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter, ones;
+#endif
+#endif
+#ifndef HAVE_SSE4_1
+ __m128i pairscores_best, all_128;
+#endif
+ int rlength_ceil, lband_ceil, r, c;
+ int rlo, rhigh, rlo_calc, rhigh_calc;
+ int na1, na2, na2_alt;
+ Score8_T *pairscores_col0;
+ Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore, pairscore0;
+ Pairdistance_T **pairdistance_array_type;
+
+#ifdef DEBUG_AVX2
+ Score8_T **matrix_std;
+ Direction8_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
+#elif defined(DEBUG_SIMD)
+ Score32_T **matrix_std;
+ Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
+#endif
+
+
+ debug2(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d, lband %d, uband %d\n",
+ jump_late_p,open,extend,lband,uband));
+
+ rlength_ceil = (int) ((rlength + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+
+#ifdef HAVE_SSE4_1
+ pairdistance_array_type = pairdistance_array[mismatchtype];
+#else
+ /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
+ pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
+ all_128 = _mm_set1_epi8(128);
+#endif
+
+ debug(printf("Dynprog_simd_8: "));
+ debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
+ debug(printf("Query length rounded up to %d\n",rlength_ceil));
+
+ matrix = aligned_score8_alloc(rlength_ceil,glength,
+ this->aligned.one.matrix_ptrs,this->aligned.one.matrix_space);
+ *directions_nogap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned.one.directions_ptrs_0,this->aligned.one.directions_space_0);
+ *directions_Egap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned.one.directions_ptrs_1,this->aligned.one.directions_space_1);
+ /* Need to calloc to save time in F loop */
+ *directions_Fgap = aligned_directions8_calloc(rlength_ceil,glength,
+ this->aligned.one.directions_ptrs_2,this->aligned.one.directions_space_2);
+
+#if 0
+ /* Row 0 initialization */
+ /* penalty = open; */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ /* penalty += extend; */
+ (*directions_Egap)[c][0] = HORIZ;
+ (*directions_nogap)[c][0] = HORIZ;
+ }
+#endif
+#if 0
+ /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ (*directions_Egap)[1][0] = DIAG; /* previously used STOP */
+ (*directions_nogap)[0][0] = DIAG; /* previously used STOP */
+#endif
+
+#if 0
+ /* Column 0 initialization */
+ /* penalty = open; */
+ for (r = 1; r <= SIMD_NCHARS && r <= rlength; r++) {
+ /* penalty += extend; */
+ (*directions_nogap)[0][r] = VERT;
+ }
+#endif
+
+
+ /* Load pairscores. Store match - mismatch */
+ pairscores[0] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[1] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[2] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[3] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[4] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+
+ lband_ceil = (int) ((lband + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+ pairscores_col0 = (Score8_T *) _mm_malloc(lband_ceil * sizeof(Score8_T),ALIGN_SIZE);
+
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score8_T));
+#endif
+
+ /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
+#ifdef HAVE_SSE4_1
+ pairscores_col0[0] = (Score8_T) 0;
+ /* Initialization just to lband causes errors in dir_horiz for Egap */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) 0;
+ }
+#else
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) NEG_INFINITY_8;
+ }
+#endif
+#else
+ pairscores_col0[0] = (Score8_T) 0+128;
+ /* Initialization just to lband causes errors in dir_horiz for Egap */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) 0+128;
+ }
+#else
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score8_T) NEG_INFINITY_8+128;
+ }
+#endif
+#endif
+
+
+ /* Row 0 */
+ r = 0; na1 = 'N';
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+
+ if (revp == false) {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[r-1];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ } else {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[1-r];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ }
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+#endif
+
+ complement_dummy = _MM_SET1_EPI8(-1);
+
+ FF = (int *) MALLOCA((glength + 1) * sizeof(int));
+
+ gap_open = _MM_SET1_EPI8((Score8_T) open);
+ gap_extend = _MM_SET1_EPI8((Score8_T) extend);
+
+
+#ifndef INFINITE_INITIAL_GAP_PENALTY
+#ifdef HAVE_AVX2
+ ramp = _mm256_setr_epi8(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16);
+ extend_ladder = _mm256_setr_epi8(extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*extend,8*extend,
+ 9*extend,10*extend,11*extend,12*extend,13*extend,14*extend,15*extend,16*extend);
+#else
+ ramp = _mm_setr_epi8(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16);
+ extend_ladder = _mm_setr_epi8(extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*extend,8*extend,
+ 9*extend,10*extend,11*extend,12*extend,13*extend,14*extend,15*extend,16*extend);
+#endif
+ lband_vector = _MM_SET1_EPI8(lband);
+ ramp_chunk = _MM_SET1_EPI8(SIMD_NCHARS);
+ extend_chunk = _MM_SET1_EPI8(SIMD_NCHARS*extend);
+#endif
+
+ if (jump_late_p) {
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
+ if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8-open);
+ filter = _MM_CMPGT_EPI8(ramp,lband_vector);
+ H_nogap_r = _MM_AND_SI(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _MM_OR_SI(_mm_andnot_si128(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _MM_ADDS_EPI8(E_r_gap,gap_open);
+
+ ramp = _MM_ADDS_EPI8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI8(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E >= H. To fill in first column of each
+ row block with non-diags, make E == H. */
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8);
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+#else
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ equal to E. */
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
+ filter = _MM_CMPGT_EPI8(ramp,lband_vector);
+ H_nogap_r = _MM_OR_SI(_MM_ANDNOT_SI(filter,extend_ladder),_MM_AND_SI(filter,H_nogap_r));
+ E_r_gap = _MM_ADDS_EPI8(H_nogap_r,gap_open);
+ ramp = _MM_ADDS_EPI8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI8(extend_ladder,extend_chunk); /* Prepare for next block */
+#endif
+ } else {
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8);
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ }
+
+ for ( ; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_setzero_si256();
+ } else {
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+ }
+#else
+ if (rlo == 0) {
+ X_prev_nogap = _mm_setzero_si128();
+ } else {
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+ }
+#endif
+
+ } else {
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_CHAR_INSERT);
+ }
+#else
+ if (rlo == 0) {
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+ }
+#endif
+ }
+
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _MM_ADDS_EPI8(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPLT_EPI8(E_r_gap,T1); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_r_gap = _MM_MAX_EPI8(E_r_gap, T1); /* Compare H + open with vert */
+#else
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+#endif
+ E_r_gap = _MM_ADDS_EPI8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi8(_mm256_setzero_si256(),_mm256_extract_epi8(H_nogap_r,SIMD_NCHARS-1),LAST_CHAR_INSERT);
+ X_prev_nogap = _mm256_insert_epi8(X_prev_nogap,_mm256_extract_epi8(H_nogap_r,MID_CHAR_INSERT-1),MID_CHAR_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_CHAR);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_SHIFT);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm256_adds_epi8(H_nogap_r, _mm256_max_epi8(pairscores_std,pairscores_alt));
+#elif defined(HAVE_SSE4_1)
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _MM_CMPLT_EPI8(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _MM_MAX_EPI8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
+
+ /* F loop */
+ if ((rlo_calc = rlo) < c - uband) {
+ rlo_calc = c - uband;
+ }
+ if ((rhigh_calc = rhigh) >= c + lband) {
+ rhigh_calc = c + lband;
+ if (c > 0) {
+ /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
+ pairscore = pairscores[na2][rhigh_calc];
+ if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
+ pairscore = pairscore0;
+ }
+#ifndef HAVE_SSE4_1
+ pairscore -= 128;
+#endif
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_8) {
+ score_column[rhigh_calc] = NEG_INFINITY_8; /* Saturation */
+ } else if (score > POS_INFINITY_8) {
+ /* Should never get here, because we limit size of matrix using 8-bit quantities */
+ score_column[rhigh_calc] = POS_INFINITY_8; /* Saturation */
+ } else {
+ score_column[rhigh_calc] = (Score8_T) score;
+ }
+ (*directions_Egap)[c][rhigh_calc] = DIAG;
+ (*directions_nogap)[c][rhigh_calc] = DIAG;
+ }
+ }
+
+ debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
+ rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
+
+ if (rlo == 0) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else if (c >= rlo + uband) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else {
+ debug3(printf("At c %d, uband %d, reading c_gap %d\n",c,uband,FF[c]));
+ c_gap = FF[c];
+ last_nogap = (int) score_column[rlo_calc-1];
+ }
+
+ if ((r = rlo_calc) == c - uband) {
+ /* Handle top value as a special case to prevent going outside of uband */
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ score = last_nogap + open /* + extend */;
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ r++;
+ }
+
+ /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
+ for ( ; r <= rhigh_calc; r++) {
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
+ c_gap += extend;
+ (*directions_Fgap)[c][r] = VERT;
+ } else {
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ }
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
+ if (c_gap >= last_nogap) { /* Use >= for jump late */
+ last_nogap = c_gap;
+ score_column[r] = (c_gap < NEG_INFINITY_8) ? NEG_INFINITY_8 : (Score8_T) c_gap; /* Saturation */
+ (*directions_nogap)[c][r] = VERT;
+ }
+ }
+
+ FF[c] = c_gap;
+ debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
+#ifdef HAVE_AVX2
+ H_nogap_r = _mm256_load_si256((__m256i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#else
+ H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#endif
+ }
+ }
+
+ } else {
+ /* jump early */
+#if defined(ZERO_INITIAL_GAP_PENALTY) || defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* No need for ones */
+#else
+ ones = _MM_SET1_EPI8(1);
+#endif
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
+ if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8-open);
+ filter = _MM_CMPGT_EPI8(ramp,lband_vector);
+ H_nogap_r = _MM_AND_SI(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _MM_OR_SI(_MM_ANDNOT_SI(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _MM_ADDS_EPI8(E_r_gap,gap_open);
+
+ ramp = _MM_ADDS_EPI8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI8(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, make E > H. */
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8+1);
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+#else
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ less than E. */
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open+1); /* To compensate for T1 = H + open */
+ filter = _MM_CMPGT_EPI8(ramp,lband_vector);
+ H_nogap_r = _MM_OR_SI(_MM_ANDNOT_SI(filter,extend_ladder),_MM_AND_SI(filter,H_nogap_r));
+ E_r_gap = _MM_ADDS_EPI8(H_nogap_r,gap_open);
+ H_nogap_r = _MM_SUBS_EPI8(H_nogap_r,ones); /* To ensure H < E */
+ ramp = _MM_ADDS_EPI8(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI8(extend_ladder,extend_chunk); /* Prepare for next block */
+#endif
+ } else {
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8+1);
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ }
+
+ for ( ; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_setzero_si256();
+ } else {
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+ }
+#else
+ if (rlo == 0) {
+ X_prev_nogap = _mm_setzero_si128();
+ } else {
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+ }
+#endif
+
+ } else {
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_CHAR_INSERT);
+ }
+#else
+ if (rlo == 0) {
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+ }
+#endif
+
+ }
+
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _MM_ADDS_EPI8(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPGT_EPI8(E_r_gap,T1); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_r_gap = _MM_MAX_EPI8(E_r_gap, T1); /* Compare H + open with vert */
+#else
+ /* Compare H + open with vert */
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+#endif
+ E_r_gap = _MM_ADDS_EPI8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi8(_mm256_setzero_si256(),_mm256_extract_epi8(H_nogap_r,SIMD_NCHARS-1),LAST_CHAR_INSERT);
+ X_prev_nogap = _mm256_insert_epi8(X_prev_nogap,_mm256_extract_epi8(H_nogap_r,MID_CHAR_INSERT-1),MID_CHAR_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_CHAR);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_SHIFT);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm256_adds_epi8(H_nogap_r, _mm256_max_epi8(pairscores_std,pairscores_alt));
+#elif defined(HAVE_SSE4_1)
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _MM_CMPGT_EPI8(E_r_gap,H_nogap_r); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _MM_MAX_EPI8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
+
+
+ /* F loop */
+ if ((rlo_calc = rlo) < c - uband) {
+ rlo_calc = c - uband;
+ }
+ if ((rhigh_calc = rhigh) >= c + lband) {
+ rhigh_calc = c + lband;
+ if (c > 0) {
+ /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
+ pairscore = pairscores[na2][rhigh_calc];
+ if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
+ pairscore = pairscore0;
+ }
+#ifndef HAVE_SSE4_1
+ pairscore -= 128;
+#endif
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_8) {
+ score_column[rhigh_calc] = NEG_INFINITY_8; /* Saturation */
+ } else if (score > POS_INFINITY_8) {
+ /* Should never get here, because we limit size of matrix using 8-bit quantities */
+ score_column[rhigh_calc] = POS_INFINITY_8; /* Saturation */
+ } else {
+ score_column[rhigh_calc] = (Score8_T) score;
+ }
+ (*directions_Egap)[c][rhigh_calc] = DIAG;
+ (*directions_nogap)[c][rhigh_calc] = DIAG;
+ }
+ }
+
+ debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
+ rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
+
+ if (rlo == 0) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else if (c >= rlo + uband) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else {
+ c_gap = FF[c];
+ last_nogap = (int) score_column[rlo_calc-1];
+ debug3(printf("LAST_NOGAP gets score_column[%d-1], or %d\n",rlo_calc,last_nogap));
+ }
+
+ if ((r = rlo_calc) == c - uband) {
+ /* Handle top value as a special case to prevent going outside of uband */
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ score = last_nogap + open /* + extend */;
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ r++;
+ }
+
+ /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
+ for ( ; r <= rhigh_calc; r++) {
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
+ c_gap += extend;
+ (*directions_Fgap)[c][r] = VERT;
+ } else {
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ }
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
+ if (c_gap > last_nogap) { /* Use > for jump early */
+ last_nogap = c_gap;
+ score_column[r] = (c_gap < NEG_INFINITY_8) ? NEG_INFINITY_8 : (Score8_T) c_gap; /* Saturation */
+ debug3(printf("Stored at score_column[%d]: %d\n",r,(Score8_T) score_column[r]));
+ (*directions_nogap)[c][r] = VERT;
+ }
+ }
+
+ FF[c] = c_gap;
+ debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
+#ifdef HAVE_AVX2
+ H_nogap_r = _mm256_load_si256((__m256i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#else
+ H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#endif
+ }
+ }
+ }
+
+
+#ifdef CHECK1
+ /* Row 0 and column 0 directions fail anyway due to saturation */
+ /* Handle (0,1) and (1,0) directions, otherwise DIAG */
+ (*directions_Egap)[1][0] = HORIZ;
+ (*directions_Fgap)[0][1] = VERT;
+#endif
+
+#ifdef DEBUG2
+ printf("SIMD: Dynprog_simd_8\n");
+ Matrix8_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+ Directions8_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+#endif
+
+#ifdef CHECK1
+ /* Check for row 0 directions */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ assert((*directions_Egap)[c][0] != DIAG);
+ assert((*directions_nogap)[c][0] != DIAG);
+ }
+ /* Check for column 0 directions */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ assert((*directions_Fgap)[0][r] != DIAG);
+ assert((*directions_nogap)[0][r] != DIAG);
+ }
+#endif
+
+#ifdef DEBUG_AVX2
+ matrix_std = Dynprog_simd_8_nonavx2(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,gsequence,gsequence_alt,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,uband,jump_late_p,revp);
+#elif defined(DEBUG_SIMD)
+ matrix_std = Dynprog_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_8,
+ /*upperp*/true,/*lowerp*/true);
+#endif
+
+#ifdef DEBUG2
+ printf("Banded %s\n",revp ? "rev" : "fwd");
+ Matrix8_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,revp,lband,uband);
+ Directions8_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,revp,lband,uband);
+#endif
+
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ banded_matrix8_compare(matrix,matrix_std,rlength,glength,lband,uband,
+ rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp);
+
+ banded_directions8_compare_nogap(matrix,*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
+ banded_directions8_compare_Egap(matrix,*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
+ banded_directions8_compare_Fgap(matrix,*directions_Fgap,directions_Fgap_std,rlength,glength,lband,uband);
+#endif
+
+ FREEA(FF);
+ _mm_free(pairscores_col0);
+ _mm_free(pairscores[4]);
+ _mm_free(pairscores[3]);
+ _mm_free(pairscores[2]);
+ _mm_free(pairscores[1]);
+ _mm_free(pairscores[0]);
+
+ return matrix;
+}
+#endif
+
+
+#ifdef DEBUG_AVX2
+/* Designed for computation above the main diagonal, so no F loop or bottom masking needed */
+/* Operates by columns */
+Score8_T **
+Dynprog_simd_8_upper_nonavx2 (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int uband, bool jump_late_p, bool revp) {
+ Score8_T **matrix, *score_column;
+ __m128i pairscores_std, pairscores_alt;
+#ifdef HAVE_SSE4_1
+ __m128i E_infinity;
+#else
+ __m128i E_infinity_plus_128;
+ __m128i pairscores_best, all_128;
+#endif
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, T1;
+ __m128i gap_open, gap_extend, complement_dummy;
+ __m128i dir_horiz;
+ int rlength_ceil, r, c;
+ int rlo, rhigh;
+ int na1, na2, na2_alt;
+ Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore;
+ Pairdistance_T **pairdistance_array_type;
+
+
+ debug2(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+
+ rlength_ceil = (int) ((rlength + SIMD_NCHARS_NONAVX2)/SIMD_NCHARS_NONAVX2) * SIMD_NCHARS_NONAVX2;
+
+#ifdef HAVE_SSE4_1
+ pairdistance_array_type = pairdistance_array[mismatchtype];
+#else
+ /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
+ pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
+ all_128 = _mm_set1_epi8(128);
+#endif
+
+ debug(printf("compute_scores_simd_8_bycols (upper): "));
+ debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
+ debug(printf("Query length rounded up to %d\n",rlength_ceil));
+
+ matrix = aligned_score8_alloc(rlength_ceil,glength,
+ this->aligned_std.two.upper_matrix_ptrs,this->aligned_std.two.upper_matrix_space);
+ *directions_nogap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned_std.two.upper_directions_ptrs_0,this->aligned_std.two.upper_directions_space_0);
+ *directions_Egap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned_std.two.upper_directions_ptrs_1,this->aligned_std.two.upper_directions_space_1);
+
+#if 0
+ /* Row 0 initialization */
+ /* penalty = open; */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ /* penalty += extend; */
+ (*directions_Egap)[c][0] = HORIZ;
+ (*directions_nogap)[c][0] = HORIZ;
+ }
+#endif
+#if 0
+ /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ (*directions_Egap)[1][0] = DIAG; /* previously used STOP */
+ (*directions_nogap)[0][0] = DIAG; /* previously used STOP */
+#endif
+#if 0
+ /* Column 0 initialization */
+ /* penalty = open; */
+ for (r = 1; r <= SIMD_NCHARS_NONAVX2 && r <= rlength; r++) {
+ /* penalty += extend; */
+ (*directions_nogap)[0][r] = VERT;
+ }
+#endif
+
+
+ /* Load pairscores. Store match - mismatch */
+ pairscores[0] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[1] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[2] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[3] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[4] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score8_T));
+#endif
+
+ /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
+ r = 0; na1 = 'N';
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+
+ if (revp == false) {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[r-1];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ } else {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[1-r];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ }
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+#endif
+
+ complement_dummy = _mm_set1_epi8(-1);
+
+ gap_open = _mm_set1_epi8((Score8_T) open);
+ gap_extend = _mm_set1_epi8((Score8_T) extend);
+
+
+#ifdef HAVE_SSE4_1
+ E_infinity = _mm_set1_epi8(POS_INFINITY_8);
+#else
+ E_infinity_plus_128 = _mm_set1_epi8(POS_INFINITY_8+128);
+#endif
+ if (jump_late_p) {
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NCHARS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ /* dir_horiz tests if E >= H . To fill in first column of each
+ row block with non-diags, could make E == H. But irrelevant,
+ because these are below the diagonal. */
+ E_mask = _mm_set1_epi8(1);
+
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8);
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ na2 = na2_alt = 4; /* 'N' */
+ } else {
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
+ }
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+ if (c == 0) {
+ X_prev_nogap = _mm_set1_epi8(0);
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+#endif
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+
+ debug15(print_vector_8(E_mask,rlo,c,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
+#else
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _mm_adds_epi8(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmplt_epi8(E_r_gap,T1); /* E < H */
+ dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
+#elif 1
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_r_gap = _mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_r_gap = _mm_add_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(E_r_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+ H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_SSE4_1
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ debug15(print_vector_8(pairscores_best,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _mm_cmplt_epi8(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+
+
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
+ }
+
+ /* No need for F loop here */
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ }
+ }
+
+ } else {
+ /* jump early */
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NCHARS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, could make E > H. But irrelevant,
+ because these are below the diagonal. */
+ E_mask = _mm_set1_epi8(1);
+
+ E_r_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
+ H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ na2 = na2_alt = 4; /* 'N' */;
+ } else {
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
+ }
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+ if (c == 0) {
+ X_prev_nogap = _mm_set1_epi8(0);
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+#endif
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+
+ debug15(print_vector_8(E_mask,rlo,c,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
+#else
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _mm_adds_epi8(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmpgt_epi8(E_r_gap,T1); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+ /* Compare H + open with vert */
+#ifdef HAVE_SSE4_1
+ E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
+#elif 1
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_r_gap = _mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_r_gap = _mm_add_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(E_r_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+ H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_SSE4_1
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ debug15(print_vector_8(pairscores_best,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _mm_cmpgt_epi8(E_r_gap,H_nogap_r); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
+ }
+
+ /* No need for F loop here */
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ }
+ }
+ }
+
+#ifdef CHECK1
+ /* Row 0 and column 0 directions fail anyway due to saturation */
+ /* Handle (0,1) and (1,0) directions, otherwise DIAG */
+ (*directions_Egap)[1][0] = HORIZ;
+#endif
+
+#ifdef DEBUG2
+ printf("SIMD: Dynprog_simd_8_upper\n");
+ Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+ Directions8_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+#endif
+
+#ifdef CHECK1
+ /* Check for row 0 directions */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ assert((*directions_Egap)[c][0] != DIAG);
+ assert((*directions_nogap)[c][0] != DIAG);
+ }
+#endif
+
+ _mm_free(pairscores[4]);
+ _mm_free(pairscores[3]);
+ _mm_free(pairscores[2]);
+ _mm_free(pairscores[1]);
+ _mm_free(pairscores[0]);
+
+ return matrix;
+}
+#endif
+
+
+/* E_mask works at the wraparound from POS_INFINITY to NEG_INFINITY.
+ It is designed to prevent a horizontal/vertical jump into the empty
+ triangle, by setting horizontal/vertical scores to be as small as
+ possible, e.g., -128. However, it is possible that H is also -128,
+ so we still need to fix the directions along the main diagonal.
+
+ E_mask shifted: 0 0 0 0 1 1 1 1
+ add E_infinity: 127 127 127 127 127 127 127 127
+ resulting mask: 127 127 127 127 -128 -128 -128 -128
+
+ To deal with non-SSE4.1 systems, which lack _mm_min_epi8, we need
+ too add 128 to E and mask, then take _mm_min_epu8, then subtract
+ 128, as follows:
+
+ E_mask shifted: 0 0 0 0 1 1 1 1
+ add E_inf+128: 255 255 255 255 255 255 255 255
+ resulting mask: 255 255 255 255 0 0 0 0
+ (compare w/E+128)
+
+*/
+
+
+#ifdef HAVE_SSE2
+/* Designed for computation above the main diagonal, so no F loop or bottom masking needed */
+/* Operates by columns */
+Score8_T **
+Dynprog_simd_8_upper (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+#endif
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int uband, bool jump_late_p, bool revp) {
+ Score8_T **matrix, *score_column;
+#ifdef HAVE_AVX2
+ __m256i E_infinity;
+#elif defined(HAVE_SSE4_1)
+ __m128i E_infinity;
+#else
+ __m128i E_infinity_plus_128;
+ __m128i pairscores_best, all_128;
+#endif
+#ifdef HAVE_AVX2
+ __m256i pairscores_std, pairscores_alt;
+ __m256i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, T1;
+ __m256i gap_open, gap_extend, complement_dummy;
+ __m256i dir_horiz;
+ Score8_T save;
+#else
+ __m128i pairscores_std, pairscores_alt;
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, T1;
+ __m128i gap_open, gap_extend, complement_dummy;
+ __m128i dir_horiz;
+#endif
+ int rlength_ceil, r, c;
+ int rlo, rhigh;
+ int na1, na2, na2_alt;
+ Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr;
+ Pairdistance_T **pairdistance_array_type;
+
+#ifdef DEBUG_AVX2
+ Score8_T **matrix_std;
+ Direction8_T **directions_nogap_std, **directions_Egap_std;
+ char na2_single;
+#elif defined(DEBUG_SIMD)
+ Score32_T **matrix_std;
+ Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
+ char na2_single;
+#endif
+
+
+ debug2(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+
+ rlength_ceil = (int) ((rlength + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+
+#ifdef HAVE_SSE4_1
+ pairdistance_array_type = pairdistance_array[mismatchtype];
+#else
+ /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
+ pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
+ all_128 = _mm_set1_epi8(128);
+#endif
+
+ debug(printf("compute_scores_simd_8_bycols (upper): "));
+ debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
+ debug(printf("Query length rounded up to %d\n",rlength_ceil));
+
+ matrix = aligned_score8_alloc(rlength_ceil,glength,
+ this->aligned.two.upper_matrix_ptrs,this->aligned.two.upper_matrix_space);
+ *directions_nogap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned.two.upper_directions_ptrs_0,this->aligned.two.upper_directions_space_0);
+ *directions_Egap = aligned_directions8_alloc(rlength_ceil,glength,
+ this->aligned.two.upper_directions_ptrs_1,this->aligned.two.upper_directions_space_1);
+
+#if 0
+ /* Row 0 initialization */
+ /* penalty = open; */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ /* penalty += extend; */
+ (*directions_Egap)[c][0] = HORIZ;
+ (*directions_nogap)[c][0] = HORIZ;
+ }
+#endif
+#if 0
+ /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ (*directions_Egap)[1][0] = DIAG; /* previously used STOP */
+ (*directions_nogap)[0][0] = DIAG; /* previously used STOP */
+#endif
+#if 0
+ /* Column 0 initialization */
+ /* penalty = open; */
+ for (r = 1; r <= SIMD_NCHARS && r <= rlength; r++) {
+ /* penalty += extend; */
+ (*directions_nogap)[0][r] = VERT;
+ }
+#endif
+
+
+ /* Load pairscores. Store match - mismatch */
+ pairscores[0] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[1] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[2] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[3] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[4] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score8_T));
+#endif
+
+ /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
+ r = 0; na1 = 'N';
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+
+ if (revp == false) {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[r-1];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ } else {
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[1-r];
+ pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ }
+ }
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+#endif
+
+ complement_dummy = _MM_SET1_EPI8(-1);
+
+ gap_open = _MM_SET1_EPI8((Score8_T) open);
+ gap_extend = _MM_SET1_EPI8((Score8_T) extend);
+
+#ifdef HAVE_SSE4_1
+ E_infinity = _MM_SET1_EPI8(POS_INFINITY_8);
+#else
+ E_infinity_plus_128 = _mm_set1_epi8(POS_INFINITY_8+128);
+#endif
+ if (jump_late_p) {
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
+ if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ /* dir_horiz tests if E >= H . To fill in first column of each
+ row block with non-diags, could make E == H. But irrelevant,
+ because these are below the diagonal. */
+ E_mask = _MM_SET1_EPI8(1);
+
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8);
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ na2 = na2_alt = 4; /* 'N' */
+ } else {
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ }
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+ if (c == 0) {
+ X_prev_nogap = _MM_SETZERO_SI();
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ } else {
+ /* second or greater block of 8 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ }
+
+ debug15(print_vector_8(E_mask,rlo,c,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_r_gap = _MM_MIN_EPI8(E_r_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#else
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _MM_ADDS_EPI8(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPLT_EPI8(E_r_gap,T1); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_r_gap = _MM_MAX_EPI8(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _MM_ADDS_EPI8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _MM_MIN_EPI8(E_r_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#elif 1
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_r_gap = _mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_r_gap = _mm_add_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(E_r_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi8(_mm256_setzero_si256(),_mm256_extract_epi8(H_nogap_r,SIMD_NCHARS-1),LAST_CHAR_INSERT);
+ X_prev_nogap = _mm256_insert_epi8(X_prev_nogap,_mm256_extract_epi8(H_nogap_r,MID_CHAR_INSERT-1),MID_CHAR_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_CHAR);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_SHIFT);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
+ H_nogap_r = _MM_ADDS_EPI8(H_nogap_r, _MM_MAX_EPI8(pairscores_std,pairscores_alt));
+#elif defined(HAVE_SSE4_1)
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ debug15(print_vector_8(pairscores_best,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _MM_CMPLT_EPI8(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _MM_MAX_EPI8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
+
+
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
+ }
+
+ /* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi8(E_mask,15);
+ E_mask = _mm256_slli_si256(E_mask,ONE_CHAR);
+ E_mask = _mm256_insert_epi8(E_mask,save,16);
+#else
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+#endif
+ }
+ }
+
+ } else {
+ /* jump early */
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
+ if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+ rhigh = rlength;
+ }
+
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, could make E > H. But irrelevant,
+ because these are below the diagonal. */
+ E_mask = _MM_SET1_EPI8(1);
+
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_r_gap = _MM_SET1_EPI8(NEG_INFINITY_8+1);
+ H_nogap_r = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ na2 = na2_alt = 4; /* 'N' */;
+ } else {
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ }
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
+
+ if (c == 0) {
+ X_prev_nogap = _MM_SETZERO_SI();
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ } else {
+ /* second or greater block of 8 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ }
+
+ debug15(print_vector_8(E_mask,rlo,c,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_r_gap = _MM_MIN_EPI8(E_r_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#else
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+
+ /* EGAP */
+ T1 = _MM_ADDS_EPI8(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPGT_EPI8(E_r_gap,T1); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(T1,rlo,c,"T1"));
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+
+ /* Compare H + open with vert */
+#ifdef HAVE_SSE4_1
+ E_r_gap = _MM_MAX_EPI8(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _MM_ADDS_EPI8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _MM_MIN_EPI8(E_r_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#elif 1
+ E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_r_gap = _mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_r_gap = _mm_add_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_sub_epi8(_mm_min_epu8(E_r_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+
+
+ /* NOGAP */
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi8(_mm256_setzero_si256(),_mm256_extract_epi8(H_nogap_r,SIMD_NCHARS-1),LAST_CHAR_INSERT);
+ X_prev_nogap = _mm256_insert_epi8(X_prev_nogap,_mm256_extract_epi8(H_nogap_r,MID_CHAR_INSERT-1),MID_CHAR_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_CHAR);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR_SHIFT);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
+ H_nogap_r = _MM_ADDS_EPI8(H_nogap_r, _MM_MAX_EPI8(pairscores_std,pairscores_alt));
+#elif defined(HAVE_SSE4_1)
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
+ debug15(print_vector_8(pairscores_best,rlo,c,"pairscores_std"));
+ H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+
+ dir_horiz = _MM_CMPGT_EPI8(E_r_gap,H_nogap_r); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_r = _MM_MAX_EPI8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
+
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
+ }
+
+ /* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi8(E_mask,15);
+ E_mask = _mm256_slli_si256(E_mask,ONE_CHAR);
+ E_mask = _mm256_insert_epi8(E_mask,save,16);
+#else
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+#endif
+ }
+ }
+ }
+
+
+#ifdef CHECK1
+ /* Row 0 and column 0 directions fail anyway due to saturation */
+ /* Handle (0,1) and (1,0) directions, otherwise DIAG */
+ (*directions_Egap)[1][0] = HORIZ;
+#endif
+
+#ifdef DEBUG2
+ printf("SIMD: Dynprog_simd_8_upper\n");
+ Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+ Directions8_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+#endif
+
+#ifdef CHECK1
+ /* Check for row 0 directions */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ assert((*directions_Egap)[c][0] != DIAG);
+ assert((*directions_nogap)[c][0] != DIAG);
+ }
+#endif
+
+#ifdef DEBUG_AVX2
+ matrix_std = Dynprog_simd_8_upper_nonavx2(&directions_nogap_std,&directions_Egap_std,
+ this,rsequence,gsequence,gsequence_alt,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,uband,jump_late_p,revp);
+
+#elif defined(DEBUG_SIMD)
+ matrix_std = Dynprog_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,/*lband*/0,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_8,
+ /*upperp*/true,/*lowerp*/false);
+#endif
+
+#ifdef DEBUG2
+ printf("Banded %s\n",revp ? "rev" : "fwd");
+ Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,revp,uband,/*upperp*/true);
+ Directions8_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,revp,uband,/*upperp*/true);
+#endif
+
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ banded_matrix8_compare_upper(matrix,matrix_std,rlength,glength,uband,
+ rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp);
+
+ banded_directions8_compare_nogap_upper(matrix,*directions_nogap,directions_nogap_std,rlength,glength,uband);
+
+ banded_directions8_compare_Egap_upper(matrix,*directions_Egap,directions_Egap_std,rlength,glength,uband);
+#endif
+
+ _mm_free(pairscores[4]);
+ _mm_free(pairscores[3]);
+ _mm_free(pairscores[2]);
+ _mm_free(pairscores[1]);
+ _mm_free(pairscores[0]);
+
+ return matrix;
+}
+#endif
+
+
+#ifdef DEBUG_AVX2
+/* Designed for computation below the main diagonal, so no F loop or bottom masking needed */
+/* Operates by rows */
+Score8_T **
+Dynprog_simd_8_lower_nonavx2 (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, bool jump_late_p, bool revp) {
+ Score8_T **matrix, *score_column;
+ __m128i pairscores_std;
+#ifdef HAVE_SSE4_1
+ __m128i E_infinity;
+#else
+ __m128i pairscores_best, all_128, E_infinity_plus_128;
+#endif
+ __m128i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, T1;
+ __m128i gap_open, gap_extend, complement_dummy;
+ __m128i dir_vert;
+ int glength_ceil, r, c;
+ int clo, chigh;
+ int na1, na2, na2_alt;
+ Score8_T *pairscores[5], *pairscores_ptr, pairscore;
+ Pairdistance_T **pairdistance_array_type, score1, score2;
+
+
+ debug2(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+
+ glength_ceil = (int) ((glength + SIMD_NCHARS_NONAVX2)/SIMD_NCHARS_NONAVX2) * SIMD_NCHARS_NONAVX2;
+
+#ifdef HAVE_SSE4_1
+ pairdistance_array_type = pairdistance_array[mismatchtype];
+#else
+ /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
+ pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
+ all_128 = _mm_set1_epi8(128);
+#endif
+
+ debug(printf("compute_scores_simd_8_byrows (lower): "));
+ debug(printf("Lengths are %d and %d, so band is %d on left\n",rlength,glength,lband));
+ debug(printf("Genome length rounded up to %d\n",glength_ceil));
+
+ matrix = aligned_score8_alloc(glength_ceil,rlength,
+ this->aligned_std.two.lower_matrix_ptrs,this->aligned_std.two.lower_matrix_space);
+ *directions_nogap = aligned_directions8_alloc(glength_ceil,rlength,
+ this->aligned_std.two.lower_directions_ptrs_0,this->aligned_std.two.lower_directions_space_0);
+ *directions_Egap = aligned_directions8_alloc(glength_ceil,rlength,
+ this->aligned_std.two.lower_directions_ptrs_1,this->aligned_std.two.lower_directions_space_1);
+
+#if 0
+ /* Column 0 initialization */
+ /* penalty = open; */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ /* penalty += extend; */
+ (*directions_Egap)[r][0] = VERT;
+ (*directions_nogap)[r][0] = VERT;
+ }
+#endif
+#if 0
+ /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ (*directions_Egap)[1][0] = DIAG; /* previously used STOP */
+ (*directions_nogap)[0][0] = DIAG; /* previously used STOP */
+#endif
+#if 0
+ /* Row 0 initialization */
+ /* penalty = open; */
+ for (c = 1; c <= SIMD_NCHARS_NONAVX2 && c <= glength; c++) {
+ /* penalty += extend; */
+ (*directions_nogap)[0][c] = HORIZ;
+ }
+#endif
+
+
+ /* Load pairscores. Store match - mismatch */
+ pairscores[0] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
+ pairscores[1] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
+ pairscores[2] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
+ pairscores[3] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
+ pairscores[4] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) pairscores[0],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[1],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[2],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[3],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[4],0,glength_ceil*sizeof(Score8_T));
+#endif
+
+ /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
+ c = 0; na2 = na2_alt = 4; /* 'N' */
+#ifdef HAVE_SSE4_1
+ pairscores[0][c] = (Score8_T) pairdistance_array_type[(int) 'A'][na2];
+ pairscores[1][c] = (Score8_T) pairdistance_array_type[(int) 'C'][na2];
+ pairscores[2][c] = (Score8_T) pairdistance_array_type[(int) 'G'][na2];
+ pairscores[3][c] = (Score8_T) pairdistance_array_type[(int) 'T'][na2];
+ pairscores[4][c] = (Score8_T) pairdistance_array_type[(int) 'N'][na2];
+#else
+ pairscores[0][c] = (Score8_T) pairdistance_array_type[(int) 'A'][na2] - 128;
+ pairscores[1][c] = (Score8_T) pairdistance_array_type[(int) 'C'][na2] - 128;
+ pairscores[2][c] = (Score8_T) pairdistance_array_type[(int) 'G'][na2] - 128;
+ pairscores[3][c] = (Score8_T) pairdistance_array_type[(int) 'T'][na2] - 128;
+ pairscores[4][c] = (Score8_T) pairdistance_array_type[(int) 'N'][na2] - 128;
+#endif
+
+ if (revp == false) {
+ for (c = 1; c <= glength; c++) {
+ na2 = gsequence[c-1];
+ na2_alt = gsequence_alt[c-1];
+ /* Take max here */
+ score1 = pairdistance_array_type[(int) 'A'][na2];
+ score2 = pairdistance_array_type[(int) 'A'][na2_alt];
+ pairscores[0][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'C'][na2];
+ score2 = pairdistance_array_type[(int) 'C'][na2_alt];
+ pairscores[1][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'G'][na2];
+ score2 = pairdistance_array_type[(int) 'G'][na2_alt];
+ pairscores[2][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'T'][na2];
+ score2 = pairdistance_array_type[(int) 'T'][na2_alt];
+ pairscores[3][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'N'][na2];
+ score2 = pairdistance_array_type[(int) 'N'][na2_alt];
+ pairscores[4][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+ }
+ } else {
+ for (c = 1; c <= glength; c++) {
+ na2 = gsequence[1-c];
+ na2_alt = gsequence_alt[1-c];
+ /* Take max here */
+ score1 = pairdistance_array_type[(int) 'A'][na2];
+ score2 = pairdistance_array_type[(int) 'A'][na2_alt];
+ pairscores[0][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'C'][na2];
+ score2 = pairdistance_array_type[(int) 'C'][na2_alt];
+ pairscores[1][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'G'][na2];
+ score2 = pairdistance_array_type[(int) 'G'][na2_alt];
+ pairscores[2][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'T'][na2];
+ score2 = pairdistance_array_type[(int) 'T'][na2_alt];
+ pairscores[3][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'N'][na2];
+ score2 = pairdistance_array_type[(int) 'N'][na2_alt];
+ pairscores[4][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+ }
+ }
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) &(pairscores[0][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[1][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[2][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[3][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[4][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+#endif
+
+ complement_dummy = _mm_set1_epi8(-1);
+
+ gap_open = _mm_set1_epi8((Score8_T) open);
+ gap_extend = _mm_set1_epi8((Score8_T) extend);
+
+#ifdef HAVE_SSE4_1
+ E_infinity = _mm_set1_epi8(POS_INFINITY_8);
+#else
+ E_infinity_plus_128 = _mm_set1_epi8(POS_INFINITY_8+128);
+#endif
+ if (jump_late_p) {
+ for (clo = 0; clo <= glength; clo += SIMD_NCHARS_NONAVX2) {
+ if ((chigh = clo + SIMD_NCHARS_NONAVX2 - 1) > glength) {
+ chigh = glength;
+ }
+
+ /* dir_vert tests if E >= H. To fill in first row of each
+ column block with non-diags, make E == H. */
+ E_mask = _mm_set1_epi8(1);
+
+ E_c_gap = _mm_set1_epi8(NEG_INFINITY_8);
+ H_nogap_c = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (r = clo; r <= chigh + lband && r <= rlength; r++) {
+ score_column = matrix[r];
+
+ if (r == 0) {
+ na1 = 4; /* 'N' */
+ } else {
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ }
+ pairscores_ptr = pairscores[na1];
+
+ if (r == 0) {
+ X_prev_nogap = _mm_set1_epi8(0);
+ } else if (clo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the clo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+#endif
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[r-1][clo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+
+ debug15(print_vector_8(E_mask,clo,r,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
+#else
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E_c_gap"));
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c load"));
+
+ /* EGAP */
+ T1 = _mm_adds_epi8(H_nogap_c, gap_open);
+ dir_vert = _mm_cmplt_epi8(E_c_gap,T1); /* E < H */
+ dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+ debug15(print_vector_8(T1,clo,r,"T1"));
+ debug15(print_vector_8(dir_vert,clo,r,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_c_gap = _mm_max_epi8(E_c_gap, T1); /* Compare H + open with horiz */
+ E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
+ E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
+#elif 1
+ E_c_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_c_gap = _mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_c_gap = _mm_add_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(E_c_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E"));
+
+
+ /* NOGAP */
+ T1 = _mm_srli_si128(H_nogap_c,LAST_CHAR_NONAVX2);
+ H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_CHAR);
+ H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores. No alternate chars for query sequence */
+#ifdef HAVE_SSE4_1
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
+ debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_std);
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(pairscores_std, all_128);
+ debug15(print_vector_8(pairscores_best,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_c,clo,r,"H"));
+
+ dir_vert = _mm_cmplt_epi8(E_c_gap,H_nogap_c); /* E < H */
+ dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+ debug15(print_vector_8(dir_vert,clo,r,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_c = _mm_max_epi8(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_c = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_c, all_128), _mm_add_epi8(E_c_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c store"));
+ _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+
+
+ /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
+ if (chigh >= r) {
+ (*directions_Egap)[r][r] = DIAG;
+ (*directions_nogap)[r][r] = DIAG;
+ }
+
+ /* No need for F loop here */
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ }
+ }
+
+ } else {
+ /* jump early */
+ for (clo = 0; clo <= glength; clo += SIMD_NCHARS_NONAVX2) {
+ if ((chigh = clo + SIMD_NCHARS_NONAVX2 - 1) > glength) {
+ chigh = glength;
+ }
+
+ /* dir_vert tests if E > H. To fill in first row of each
+ column block with non-diags, make E > H. */
+ E_mask = _mm_set1_epi8(1);
+
+ E_c_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
+ H_nogap_c = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (r = clo; r <= chigh + lband && r <= rlength; r++) {
+ score_column = matrix[r];
+
+ if (r == 0) {
+ na1 = 4; /* 'N' */
+ } else {
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ }
+ pairscores_ptr = pairscores[na1];
+
+ if (r == 0) {
+ X_prev_nogap = _mm_set1_epi8(0);
+ } else if (clo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi8(0);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the clo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+#endif
+ } else {
+ /* second or greater block of 8 */
+ X_prev_nogap = _mm_set1_epi8(matrix[r-1][clo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_NONAVX2);
+ }
+
+ debug15(print_vector_8(E_mask,clo,r,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
+#else
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E_c_gap"));
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c load"));
+
+ /* EGAP */
+ T1 = _mm_adds_epi8(H_nogap_c, gap_open);
+ dir_vert = _mm_cmpgt_epi8(E_c_gap,T1); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+ debug15(print_vector_8(T1,clo,r,"T1"));
+ debug15(print_vector_8(dir_vert,clo,r,"dir_Egap"));
+
+ /* Compare H + open with vert */
+#ifdef HAVE_SSE4_1
+ E_c_gap = _mm_max_epi8(E_c_gap, T1); /* Compare H + open with vert */
+ E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
+#elif 1
+ E_c_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_c_gap = _mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_c_gap = _mm_add_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(E_c_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E"));
+
+
+ /* NOGAP */
+ T1 = _mm_srli_si128(H_nogap_c,LAST_CHAR_NONAVX2);
+ H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_CHAR);
+ H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores. No alternate chars for query sequence */
+#ifdef HAVE_SSE4_1
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
+ debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_std);
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(pairscores_std, all_128);
+ debug15(print_vector_8(pairscores_best,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_c,clo,r,"H"));
+
+ dir_vert = _mm_cmpgt_epi8(E_c_gap,H_nogap_c); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+ debug15(print_vector_8(dir_vert,clo,r,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_c = _mm_max_epi8(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_c = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_c, all_128), _mm_add_epi8(E_c_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c store"));
+ _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+
+ /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
+ if (chigh >= r) {
+ (*directions_Egap)[r][r] = DIAG;
+ (*directions_nogap)[r][r] = DIAG;
+ }
+
+ /* No need for F loop here */
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ }
+ }
+ }
+
+#ifdef CHECK1
+ /* Row 0 and column 0 directions fail anyway due to saturation */
+ /* Handle (0,1) and (1,0) directions, otherwise DIAG */
+ (*directions_Egap)[1][0] = VERT;
+#endif
+
+#ifdef DEBUG2
+ printf("SIMD: Dynprog_simd_8_lower\n");
+ Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Directions8_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+#endif
+
+#ifdef CHECK1
+ /* Check for column 0 directions */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ assert((*directions_Egap)[r][0] != DIAG);
+ assert((*directions_nogap)[r][0] != DIAG);
+ }
+#endif
+
+ _mm_free(pairscores[4]);
+ _mm_free(pairscores[3]);
+ _mm_free(pairscores[2]);
+ _mm_free(pairscores[1]);
+ _mm_free(pairscores[0]);
+
+ return matrix;
+}
+#endif
+
+
+#ifdef HAVE_SSE2
+/* Designed for computation below the main diagonal, so no F loop or bottom masking needed */
+/* Operates by rows */
+Score8_T **
+Dynprog_simd_8_lower (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+#endif
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, bool jump_late_p, bool revp) {
+ Score8_T **matrix, *score_column;
+#ifdef HAVE_AVX2
+ __m256i E_infinity;
+#elif defined(HAVE_SSE4_1)
+ __m128i E_infinity;
+#else
+ __m128i pairscores_best, all_128, E_infinity_plus_128;
+#endif
+#ifdef HAVE_AVX2
+ __m256i pairscores_std;
+ __m256i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, T1;
+ __m256i gap_open, gap_extend, complement_dummy;
+ __m256i dir_vert;
+ Score8_T save;
+#else
+ __m128i pairscores_std;
+ __m128i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, T1;
+ __m128i gap_open, gap_extend, complement_dummy;
+ __m128i dir_vert;
+#endif
+ int glength_ceil, r, c;
+ int clo, chigh;
+ int na1, na2, na2_alt;
+ Score8_T *pairscores[5], *pairscores_ptr;
+ Pairdistance_T **pairdistance_array_type, score1, score2;
+
+#ifdef DEBUG_AVX2
+ Score8_T **matrix_std;
+ Direction8_T **directions_nogap_std, **directions_Egap_std;
+ char na2_single;
+#elif defined(DEBUG_SIMD)
+ Score32_T **matrix_std;
+ Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
+ char na2_single;
+#endif
+
+
+ debug2(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+
+ glength_ceil = (int) ((glength + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+
+#ifdef HAVE_SSE4_1
+ pairdistance_array_type = pairdistance_array[mismatchtype];
+#else
+ /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
+ pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
+ all_128 = _mm_set1_epi8(128);
+#endif
+
+ debug(printf("compute_scores_simd_8_byrows (lower): "));
+ debug(printf("Lengths are %d and %d, so band is %d on left\n",rlength,glength,lband));
+ debug(printf("Genome length rounded up to %d\n",glength_ceil));
+
+ matrix = aligned_score8_alloc(glength_ceil,rlength,
+ this->aligned.two.lower_matrix_ptrs,this->aligned.two.lower_matrix_space);
+ *directions_nogap = aligned_directions8_alloc(glength_ceil,rlength,
+ this->aligned.two.lower_directions_ptrs_0,this->aligned.two.lower_directions_space_0);
+ *directions_Egap = aligned_directions8_alloc(glength_ceil,rlength,
+ this->aligned.two.lower_directions_ptrs_1,this->aligned.two.lower_directions_space_1);
+
+#if 0
+ /* Column 0 initialization */
+ /* penalty = open; */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ /* penalty += extend; */
+ (*directions_Egap)[r][0] = VERT;
+ (*directions_nogap)[r][0] = VERT;
+ }
+#endif
+#if 0
+ /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ (*directions_Egap)[1][0] = DIAG; /* previously used STOP */
+ (*directions_nogap)[0][0] = DIAG; /* previously used STOP */
+#endif
+#if 0
+ /* Row 0 initialization */
+ /* penalty = open; */
+ for (c = 1; c <= SIMD_NCHARS && c <= glength; c++) {
+ /* penalty += extend; */
+ (*directions_nogap)[0][c] = HORIZ;
+ }
+#endif
+
+
+ /* Load pairscores. Store match - mismatch */
+ pairscores[0] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[1] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[2] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[3] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+ pairscores[4] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),ALIGN_SIZE);
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) pairscores[0],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[1],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[2],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[3],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[4],0,glength_ceil*sizeof(Score8_T));
+#endif
+
+ /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
+ c = 0; na2 = na2_alt = 4; /* 'N' */
+#ifdef HAVE_SSE4_1
+ pairscores[0][c] = (Score8_T) pairdistance_array_type[(int) 'A'][na2];
+ pairscores[1][c] = (Score8_T) pairdistance_array_type[(int) 'C'][na2];
+ pairscores[2][c] = (Score8_T) pairdistance_array_type[(int) 'G'][na2];
+ pairscores[3][c] = (Score8_T) pairdistance_array_type[(int) 'T'][na2];
+ pairscores[4][c] = (Score8_T) pairdistance_array_type[(int) 'N'][na2];
+#else
+ pairscores[0][c] = (Score8_T) pairdistance_array_type[(int) 'A'][na2] - 128;
+ pairscores[1][c] = (Score8_T) pairdistance_array_type[(int) 'C'][na2] - 128;
+ pairscores[2][c] = (Score8_T) pairdistance_array_type[(int) 'G'][na2] - 128;
+ pairscores[3][c] = (Score8_T) pairdistance_array_type[(int) 'T'][na2] - 128;
+ pairscores[4][c] = (Score8_T) pairdistance_array_type[(int) 'N'][na2] - 128;
+#endif
+
+ if (revp == false) {
+ for (c = 1; c <= glength; c++) {
+ na2 = gsequence[c-1];
+ na2_alt = gsequence_alt[c-1];
+ /* Take max here */
+ score1 = pairdistance_array_type[(int) 'A'][na2];
+ score2 = pairdistance_array_type[(int) 'A'][na2_alt];
+ pairscores[0][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'C'][na2];
+ score2 = pairdistance_array_type[(int) 'C'][na2_alt];
+ pairscores[1][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'G'][na2];
+ score2 = pairdistance_array_type[(int) 'G'][na2_alt];
+ pairscores[2][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'T'][na2];
+ score2 = pairdistance_array_type[(int) 'T'][na2_alt];
+ pairscores[3][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'N'][na2];
+ score2 = pairdistance_array_type[(int) 'N'][na2_alt];
+ pairscores[4][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+ }
+ } else {
+ for (c = 1; c <= glength; c++) {
+ na2 = gsequence[1-c];
+ na2_alt = gsequence_alt[1-c];
+ /* Take max here */
+ score1 = pairdistance_array_type[(int) 'A'][na2];
+ score2 = pairdistance_array_type[(int) 'A'][na2_alt];
+ pairscores[0][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'C'][na2];
+ score2 = pairdistance_array_type[(int) 'C'][na2_alt];
+ pairscores[1][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'G'][na2];
+ score2 = pairdistance_array_type[(int) 'G'][na2_alt];
+ pairscores[2][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'T'][na2];
+ score2 = pairdistance_array_type[(int) 'T'][na2_alt];
+ pairscores[3][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'N'][na2];
+ score2 = pairdistance_array_type[(int) 'N'][na2_alt];
+ pairscores[4][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+ }
+ }
+
+#if 0
+ /* Should not be necessary */
+ memset((void *) &(pairscores[0][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[1][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[2][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[3][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+ memset((void *) &(pairscores[4][c]),0,(glength_ceil-c)*sizeof(Score8_T));
+#endif
+
+ complement_dummy = _MM_SET1_EPI8(-1);
+
+ gap_open = _MM_SET1_EPI8((Score8_T) open);
+ gap_extend = _MM_SET1_EPI8((Score8_T) extend);
+
+#ifdef HAVE_SSE4_1
+ E_infinity = _MM_SET1_EPI8(POS_INFINITY_8);
+#else
+ E_infinity_plus_128 = _mm_set1_epi8(POS_INFINITY_8+128);
+#endif
+ if (jump_late_p) {
+ for (clo = 0; clo <= glength; clo += SIMD_NCHARS) {
+ if ((chigh = clo + SIMD_NCHARS - 1) > glength) {
+ chigh = glength;
+ }
+
+ /* dir_vert tests if E >= H. To fill in first row of each
+ column block with non-diags, make E == H. */
+ E_mask = _MM_SET1_EPI8(1);
+
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_c_gap = _MM_SET1_EPI8(NEG_INFINITY_8);
+ H_nogap_c = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (r = clo; r <= chigh + lband && r <= rlength; r++) {
+ score_column = matrix[r];
+
+ if (r == 0) {
+ na1 = 4; /* 'N' */
+ } else {
+ na1 = revp ? nt_to_int_array[(int) rsequence[1-r]] : nt_to_int_array[(int) rsequence[r-1]];
+ }
+ pairscores_ptr = pairscores[na1];
+
+ if (r == 0) {
+ X_prev_nogap = _MM_SETZERO_SI();
+ } else if (clo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the clo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ } else {
+ /* second or greater block of 8 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),matrix[r-1][clo-1],LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(matrix[r-1][clo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ }
+
+ debug15(print_vector_8(E_mask,clo,r,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_c_gap = _MM_MIN_EPI8(E_c_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#else
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E_c_gap"));
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c load"));
+
+ /* EGAP */
+ T1 = _MM_ADDS_EPI8(H_nogap_c, gap_open);
+ dir_vert = _MM_CMPLT_EPI8(E_c_gap,T1); /* E < H */
+ dir_vert = _MM_ANDNOT_SI(dir_vert,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[r][clo]),dir_vert);
+#else
+ _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+#endif
+ debug15(print_vector_8(T1,clo,r,"T1"));
+ debug15(print_vector_8(dir_vert,clo,r,"dir_Egap"));
+
+#ifdef HAVE_SSE4_1
+ E_c_gap = _MM_MAX_EPI8(E_c_gap, T1); /* Compare H + open with horiz */
+ E_c_gap = _MM_ADDS_EPI8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
+ E_c_gap = _MM_MIN_EPI8(E_c_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#elif 1
+ E_c_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_c_gap = _mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_c_gap = _mm_add_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(E_c_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E"));
+
+
+ /* NOGAP */
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi8(_mm256_setzero_si256(),_mm256_extract_epi8(H_nogap_c,SIMD_NCHARS-1),LAST_CHAR_INSERT);
+ X_prev_nogap = _mm256_insert_epi8(X_prev_nogap,_mm256_extract_epi8(H_nogap_c,MID_CHAR_INSERT-1),MID_CHAR_INSERT);
+ H_nogap_c = _mm256_slli_si256(H_nogap_c,ONE_CHAR);
+#else
+ T1 = _mm_srli_si128(H_nogap_c,LAST_CHAR_SHIFT);
+ H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_CHAR);
+#endif
+ H_nogap_c = _MM_OR_SI(H_nogap_c, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores. No alternate chars for query sequence */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_ptr[clo]));
+ debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
+ H_nogap_c = _MM_ADDS_EPI8(H_nogap_c, pairscores_std);
+#elif defined(HAVE_SSE4_1)
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
+ debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_std);
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(pairscores_std, all_128);
+ debug15(print_vector_8(pairscores_best,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_c,clo,r,"H"));
+
+ dir_vert = _MM_CMPLT_EPI8(E_c_gap,H_nogap_c); /* E < H */
+ dir_vert = _MM_ANDNOT_SI(dir_vert,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[r][clo]),dir_vert);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+#endif
+ debug15(print_vector_8(dir_vert,clo,r,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_c = _MM_MAX_EPI8(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_c = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_c, all_128), _mm_add_epi8(E_c_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[clo]), H_nogap_c);
+#else
+ _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+#endif
+
+
+ /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
+ if (chigh >= r) {
+ (*directions_Egap)[r][r] = DIAG;
+ (*directions_nogap)[r][r] = DIAG;
+ }
+
+ /* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi8(E_mask,15);
+ E_mask = _mm256_slli_si256(E_mask,ONE_CHAR);
+ E_mask = _mm256_insert_epi8(E_mask,save,16);
+#else
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+#endif
+ }
+ }
+
+ } else {
+ /* jump early */
+ for (clo = 0; clo <= glength; clo += SIMD_NCHARS) {
+ if ((chigh = clo + SIMD_NCHARS - 1) > glength) {
+ chigh = glength;
+ }
+
+ /* dir_vert tests if E > H. To fill in first row of each
+ column block with non-diags, make E > H. */
+ E_mask = _MM_SET1_EPI8(1);
+
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_c_gap = _MM_SET1_EPI8(NEG_INFINITY_8+1);
+ H_nogap_c = _MM_SET1_EPI8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+
+ for (r = clo; r <= chigh + lband && r <= rlength; r++) {
+ score_column = matrix[r];
+
+ if (r == 0) {
+ na1 = 4; /* 'N' */
+ } else {
+ na1 = revp ? nt_to_int_array[(int) rsequence[1-r]] : nt_to_int_array[(int) rsequence[r-1]];
+ }
+ pairscores_ptr = pairscores[na1];
+
+ if (r == 0) {
+ X_prev_nogap = _MM_SETZERO_SI();
+ } else if (clo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),NEG_INFINITY_8,LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the clo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ } else {
+ /* second or greater block of 8 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi8(_mm256_setzero_si256(),matrix[r-1][clo-1],LAST_CHAR_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi8(matrix[r-1][clo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR_SHIFT);
+#endif
+ }
+
+ debug15(print_vector_8(E_mask,clo,r,"E_mask"));
+#ifdef HAVE_SSE4_1
+ E_c_gap = _MM_MIN_EPI8(E_c_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#else
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E_c_gap"));
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c load"));
+
+ /* EGAP */
+ T1 = _MM_ADDS_EPI8(H_nogap_c, gap_open);
+ dir_vert = _MM_CMPGT_EPI8(E_c_gap,T1); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[r][clo]),dir_vert);
+#else
+ _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+#endif
+ debug15(print_vector_8(T1,clo,r,"T1"));
+ debug15(print_vector_8(dir_vert,clo,r,"dir_Egap"));
+
+ /* Compare H + open with vert */
+#ifdef HAVE_SSE4_1
+ E_c_gap = _MM_MAX_EPI8(E_c_gap, T1); /* Compare H + open with vert */
+ E_c_gap = _MM_ADDS_EPI8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _MM_MIN_EPI8(E_c_gap,_MM_ADD_EPI8(E_mask,E_infinity));
+#elif 1
+ E_c_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
+ E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#else
+ /* Try to avoid unnecessary shifts by 128, but overflows */
+ E_c_gap = _mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128));
+ E_c_gap = _mm_add_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_sub_epi8(_mm_min_epu8(E_c_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+#endif
+ debug15(print_vector_8(E_c_gap,clo,r,"E"));
+
+
+ /* NOGAP */
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi8(_mm256_setzero_si256(),_mm256_extract_epi8(H_nogap_c,SIMD_NCHARS-1),LAST_CHAR_INSERT);
+ X_prev_nogap = _mm256_insert_epi8(X_prev_nogap,_mm256_extract_epi8(H_nogap_c,MID_CHAR_INSERT-1),MID_CHAR_INSERT);
+ H_nogap_c = _mm256_slli_si256(H_nogap_c,ONE_CHAR);
+#else
+ T1 = _mm_srli_si128(H_nogap_c,LAST_CHAR_SHIFT);
+ H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_CHAR);
+#endif
+ H_nogap_c = _MM_OR_SI(H_nogap_c, X_prev_nogap);
+ X_prev_nogap = T1;
+
+ /* Add pairscores. No alternate chars for query sequence */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_ptr[clo]));
+ debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
+ H_nogap_c = _MM_ADDS_EPI8(H_nogap_c, pairscores_std);
+#elif defined(HAVE_SSE4_1)
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
+ debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_std);
+#else
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo])); /* Has 128 added already */
+ pairscores_best = _mm_sub_epi8(pairscores_std, all_128);
+ debug15(print_vector_8(pairscores_best,clo,r,"pairscores_std"));
+ H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_best);
+#endif
+ _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_8(H_nogap_c,clo,r,"H"));
+
+ dir_vert = _MM_CMPGT_EPI8(E_c_gap,H_nogap_c); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[r][clo]),dir_vert);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+#endif
+ debug15(print_vector_8(dir_vert,clo,r,"dir_nogap"));
+
+
+#ifdef HAVE_SSE4_1
+ H_nogap_c = _MM_MAX_EPI8(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+#else
+ /* Compare H + pairscores with horiz + extend */
+ H_nogap_c = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_c, all_128), _mm_add_epi8(E_c_gap, all_128)), all_128);
+#endif
+ debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[clo]), H_nogap_c);
+#else
+ _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+#endif
+
+ /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
+ if (chigh >= r) {
+ (*directions_Egap)[r][r] = DIAG;
+ (*directions_nogap)[r][r] = DIAG;
+ }
+
+ /* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi8(E_mask,15);
+ E_mask = _mm256_slli_si256(E_mask,ONE_CHAR);
+ E_mask = _mm256_insert_epi8(E_mask,save,16);
+#else
+ E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+#endif
+ }
+ }
+ }
+
+#ifdef CHECK1
+ /* Row 0 and column 0 directions fail anyway due to saturation */
+ /* Handle (0,1) and (1,0) directions, otherwise DIAG */
+ (*directions_Egap)[1][0] = VERT;
#endif
- Mismatchtype_T mismatchtype, int open, int extend,
- int lband, int uband, bool jump_late_p, bool revp) {
- int c_gap, last_nogap, score, *FF; /* Need to have the ability to go past NEG_INFINITY */
- Score8_T **matrix, *score_column;
- __m128i pairscores_std, pairscores_alt;
-#ifndef HAVE_SSE4_1
- __m128i pairscores_best, all_128;
+
+#ifdef DEBUG2
+ printf("SIMD: Dynprog_simd_8_lower\n");
+ Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Directions8_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+#endif
+
+#ifdef CHECK1
+ /* Check for column 0 directions */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ assert((*directions_Egap)[r][0] != DIAG);
+ assert((*directions_nogap)[r][0] != DIAG);
+ }
+#endif
+
+#ifdef DEBUG_AVX2
+ matrix_std = Dynprog_simd_8_lower_nonavx2(&directions_nogap_std,&directions_Egap_std,
+ this,rsequence,gsequence,gsequence_alt,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,jump_late_p,revp);
+#elif defined(DEBUG_SIMD)
+ matrix_std = Dynprog_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,/*uband*/0,jump_late_p,revp,/*saturation*/NEG_INFINITY_8,
+ /*upperp*/false,/*lowerp*/true);
+#endif
+
+#ifdef DEBUG2
+ printf("Banded %s\n",revp ? "rev" : "fwd");
+ Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Directions8_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+#endif
+
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ banded_matrix8_compare_lower(matrix,matrix_std,rlength,glength,lband,
+ rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp);
+
+ banded_directions8_compare_nogap_lower(matrix,*directions_nogap,directions_nogap_std,rlength,glength,lband);
+
+ banded_directions8_compare_Egap_lower(matrix,*directions_Egap,directions_Egap_std,rlength,glength,lband);
+#endif
+
+ _mm_free(pairscores[4]);
+ _mm_free(pairscores[3]);
+ _mm_free(pairscores[2]);
+ _mm_free(pairscores[1]);
+ _mm_free(pairscores[0]);
+
+ return matrix;
+}
#endif
+
+
+#ifdef DEBUG_AVX2
+Score16_T **
+Dynprog_simd_16_nonavx2 (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
+ Direction16_T ***directions_Fgap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, int uband, bool jump_late_p, bool revp) {
+ int c_gap, last_nogap, score, *FF; /* Need to have the ability to go past NEG_INFINITY */
+ Score16_T **matrix, *score_column;
+ __m128i pairscores_std, pairscores_alt;
__m128i H_nogap_r, X_prev_nogap, E_r_gap, T1;
- __m128i gap_open, gap_extend, complement_dummy;
+ __m128i gap_open, gap_extend, extend_ladder, extend_chunk, complement_dummy;
__m128i dir_horiz;
+ __m128i ramp, ramp_chunk, lband_vector, filter, ones;
int rlength_ceil, lband_ceil, r, c;
int rlo, rhigh, rlo_calc, rhigh_calc;
int na1, na2, na2_alt;
- Score8_T *pairscores_col0;
- Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore, pairscore0;
+ Score16_T *pairscores_col0;
+ Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore, pairscore0;
Pairdistance_T **pairdistance_array_type;
-#ifdef DEBUG14
- Score32_T **matrix_std;
- Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
-#endif
-
-
- debug2(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- debug15(printf("Dynprog_simd_8. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- rlength_ceil = (int) ((rlength + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+ debug2(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d, lband %d, uband %d\n",
+ jump_late_p,open,extend,lband,uband));
-#ifdef HAVE_SSE4_1
+ rlength_ceil = (int) ((rlength + SIMD_NSHORTS_NONAVX2)/SIMD_NSHORTS_NONAVX2) * SIMD_NSHORTS_NONAVX2;
pairdistance_array_type = pairdistance_array[mismatchtype];
-#else
- /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
- pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
- all_128 = _mm_set1_epi8(128);
-#endif
- debug(printf("Dynprog_simd_8: "));
+ debug(printf("compute_scores_simd_16_bycols (upper): "));
debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
debug(printf("Query length rounded up to %d\n",rlength_ceil));
- matrix = aligned_score8_alloc(rlength_ceil,glength,
- this->aligned.one.matrix_ptrs,this->aligned.one.matrix_space);
- *directions_nogap = aligned_directions8_alloc(rlength_ceil,glength,
- this->aligned.one.directions_ptrs_0,this->aligned.one.directions_space_0);
- *directions_Egap = aligned_directions8_alloc(rlength_ceil,glength,
- this->aligned.one.directions_ptrs_1,this->aligned.one.directions_space_1);
+ matrix = aligned_score16_alloc(rlength_ceil,glength,
+ this->aligned_std.one.matrix_ptrs,this->aligned_std.one.matrix_space);
+ *directions_nogap = aligned_directions16_alloc(rlength_ceil,glength,
+ this->aligned_std.one.directions_ptrs_0,this->aligned_std.one.directions_space_0);
+ *directions_Egap = aligned_directions16_alloc(rlength_ceil,glength,
+ this->aligned_std.one.directions_ptrs_1,this->aligned_std.one.directions_space_1);
/* Need to calloc to save time in F loop */
- *directions_Fgap = aligned_directions8_calloc(rlength_ceil,glength,
- this->aligned.one.directions_ptrs_2,this->aligned.one.directions_space_2);
+ *directions_Fgap = aligned_directions16_calloc(rlength_ceil,glength,
+ this->aligned_std.one.directions_ptrs_2,this->aligned_std.one.directions_space_2);
#if 0
/* Row 0 initialization */
@@ -1469,15 +5827,14 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
}
#endif
#if 0
- /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ /* Already initialized to DIAG. Actually, no longer initializing directions_Egap */
(*directions_Egap)[1][0] = DIAG; /* previously used STOP */
(*directions_nogap)[0][0] = DIAG; /* previously used STOP */
#endif
-
#if 0
/* Column 0 initialization */
/* penalty = open; */
- for (r = 1; r <= SIMD_NCHARS && r <= rlength; r++) {
+ for (r = 1; r <= SIMD_NSHORTS_NONAVX2 && r <= rlength; r++) {
/* penalty += extend; */
(*directions_nogap)[0][r] = VERT;
}
@@ -1485,127 +5842,147 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
/* Load pairscores. Store match - mismatch */
- pairscores[0] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[1] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[2] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[3] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[4] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
-
- lband_ceil = (int) ((lband + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
- pairscores_col0 = (Score8_T *) _mm_malloc(lband_ceil * sizeof(Score8_T),16);
+ pairscores[0] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[1] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[2] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[3] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[4] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ lband_ceil = (int) ((lband + SIMD_NSHORTS_NONAVX2)/SIMD_NSHORTS_NONAVX2) * SIMD_NSHORTS_NONAVX2;
+ pairscores_col0 = (Score16_T *) _mm_malloc(lband_ceil * sizeof(Score16_T),16);
#if 0
/* Should not be necessary */
- memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score16_T));
#endif
- /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
-#ifdef HAVE_SSE4_1
- pairscores_col0[0] = (Score8_T) 0;
- /* Initialization just to lband causes errors in dir_horiz for Egap */
-#ifdef NO_INITIAL_GAP_PENALTY
- for (r = 1; r < lband_ceil; r++) {
- pairscores_col0[r] = (Score8_T) 0;
- }
-#else
- for (r = 1; r < lband_ceil; r++) {
- pairscores_col0[r] = (Score8_T) NEG_INFINITY_8;
- }
-#endif
-#else
- pairscores_col0[0] = (Score8_T) 0+128;
+
+ pairscores_col0[0] = (Score16_T) 0;
/* Initialization just to lband causes errors in dir_horiz for Egap */
-#ifdef NO_INITIAL_GAP_PENALTY
+#ifdef ZERO_INITIAL_GAP_PENALTY
for (r = 1; r < lband_ceil; r++) {
- pairscores_col0[r] = (Score8_T) 0+128;
+ pairscores_col0[r] = (Score16_T) 0;
}
#else
for (r = 1; r < lband_ceil; r++) {
- pairscores_col0[r] = (Score8_T) NEG_INFINITY_8+128;
+ pairscores_col0[r] = (Score16_T) NEG_INFINITY_16;
}
#endif
-#endif
-
- /* Row 0 */
r = 0; na1 = 'N';
- pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
if (revp == false) {
for (r = 1; r <= rlength; r++) {
na1 = (int) rsequence[r-1];
- pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
}
} else {
for (r = 1; r <= rlength; r++) {
na1 = (int) rsequence[1-r];
- pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
}
}
#if 0
/* Should not be necessary */
- memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
#endif
- complement_dummy = _mm_set1_epi8(-1);
-
+ complement_dummy = _mm_set1_epi16(-1);
+
FF = (int *) MALLOCA((glength + 1) * sizeof(int));
- gap_open = _mm_set1_epi8((Score8_T) open);
- gap_extend = _mm_set1_epi8((Score8_T) extend);
+ gap_open = _mm_set1_epi16((Score16_T) open);
+ gap_extend = _mm_set1_epi16((Score16_T) extend);
+
+
+#ifndef INFINITE_INITIAL_GAP_PENALTY
+ lband_vector = _mm_set1_epi16(lband);
+ ramp = _mm_setr_epi16(1,2,3,4,5,6,7,8);
+ extend_ladder = _mm_setr_epi16(extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*extend,8*extend);
+ ramp_chunk = _mm_set1_epi16(SIMD_NSHORTS_NONAVX2);
+ extend_chunk = _mm_set1_epi16(SIMD_NSHORTS_NONAVX2*extend);
+#endif
if (jump_late_p) {
- for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
- if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NSHORTS_NONAVX2 - 1) > rlength) {
rhigh = rlength;
}
- /* dir_horiz tests if E >= H. To fill in first column of each
- row block with non-diags, make E == H. */
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi8(-extend);
- H_nogap_r = _mm_set1_epi8(-open-extend);
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16-open);
+ filter = _mm_cmpgt_epi16(ramp,lband_vector);
+ H_nogap_r = _mm_and_si128(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _mm_adds_epi16(E_r_gap,gap_open);
+
+ ramp = _mm_adds_epi16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi16(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E >= H. To fill in first column of each
+ row block with non-diags, make E == H. */
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16);
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
#else
- E_r_gap = _mm_set1_epi8(NEG_INFINITY_8);
- H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ equal to E. */
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
+ filter = _mm_cmpgt_epi16(ramp,lband_vector);
+ H_nogap_r = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),_mm_and_si128(filter,H_nogap_r));
+ E_r_gap = _mm_adds_epi16(H_nogap_r,gap_open);
+ ramp = _mm_adds_epi16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi16(extend_ladder,extend_chunk); /* Prepare for next block */
#endif
- if ((c = rlo - lband) < 0) {
- c = 0;
+ } else {
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16);
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
}
+
for ( ; c <= rhigh + uband && c <= glength; c++) {
score_column = matrix[c];
if (c == 0) {
pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi16(0);
+#else
if (rlo == 0) {
- X_prev_nogap = _mm_set1_epi8(0);
+ X_prev_nogap = _mm_set1_epi16(0);
} else {
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
+#endif
+
} else {
na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
@@ -1613,77 +5990,60 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
pairscores_alt_ptr = pairscores[na2_alt];
if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi8(0);
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi16(0);
#else
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
} else {
- /* second or greater block of 8 */
- X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
}
- debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
/* EGAP */
- T1 = _mm_adds_epi8(H_nogap_r, gap_open);
- dir_horiz = _mm_cmplt_epi8(E_r_gap,T1); /* E < H */
+ T1 = _mm_adds_epi16(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmplt_epi16(E_r_gap,T1); /* E < H */
dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
_mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(T1,rlo,c,"T1"));
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+ debug15(print_vector_16(T1,rlo,c,"T1"));
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
-#ifdef HAVE_SSE4_1
- E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
-#else
- E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
-#endif
- E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+ E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR);
- H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
-
- /* Add pairscores, allowing for alternate genomic nt */
-#ifdef HAVE_SSE4_1
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
-#else
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
- pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
- H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
-#endif
+
+ /* Add pairscores, allowing for alternate genomic nt */
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
_mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
- dir_horiz = _mm_cmplt_epi8(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _mm_cmplt_epi16(E_r_gap,H_nogap_r); /* E < H */
dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
_mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
-
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
-#ifdef HAVE_SSE4_1
- H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
-#else
- /* Compare H + pairscores with horiz + extend */
- H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
-#endif
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+ H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
_mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
/* F loop */
- if ((rlo_calc = rlo) < c - uband) {
+ if ((rlo_calc = rlo) <= c - uband) {
rlo_calc = c - uband;
}
if ((rhigh_calc = rhigh) >= c + lband) {
@@ -1694,16 +6054,13 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
pairscore = pairscore0;
}
-#ifndef HAVE_SSE4_1
- pairscore -= 128;
-#endif
- if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_8) {
- score_column[rhigh_calc] = NEG_INFINITY_8; /* Saturation */
- } else if (score > POS_INFINITY_8) {
- /* Should never get here, because we limit size of matrix using 8-bit quantities */
- score_column[rhigh_calc] = POS_INFINITY_8; /* Saturation */
+ /* No need to fix for non-SSE4.1: pairscore -= 128; */
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_16) {
+ score_column[rhigh_calc] = NEG_INFINITY_16; /* Saturation */
+ } else if (score > POS_INFINITY_16) {
+ score_column[rhigh_calc] = POS_INFINITY_16; /* Saturation */
} else {
- score_column[rhigh_calc] = (Score8_T) score;
+ score_column[rhigh_calc] = (Score16_T) score;
}
(*directions_Egap)[c][rhigh_calc] = DIAG;
(*directions_nogap)[c][rhigh_calc] = DIAG;
@@ -1757,7 +6114,7 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
if (c_gap >= last_nogap) { /* Use >= for jump late */
last_nogap = c_gap;
- score_column[r] = (c_gap < NEG_INFINITY_8) ? NEG_INFINITY_8 : (Score8_T) c_gap; /* Saturation */
+ score_column[r] = (c_gap < NEG_INFINITY_16) ? NEG_INFINITY_16 : (Score16_T) c_gap; /* Saturation */
(*directions_nogap)[c][r] = VERT;
}
}
@@ -1770,35 +6127,69 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
} else {
/* jump early */
- for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
- if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
- rhigh = rlength;
- }
-
- /* dir_horiz tests if E > H. To fill in first column of each
- row block with non-diags, make E > H. */
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi8(-extend);
- H_nogap_r = _mm_set1_epi8(-open-extend-1);
+#if defined(ZERO_INITIAL_GAP_PENALTY) || defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* No need for ones */
#else
- E_r_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
- H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ ones = _mm_set1_epi16(1);
#endif
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NSHORTS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
+ }
if ((c = rlo - lband) < 0) {
c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16-open);
+ filter = _mm_cmpgt_epi16(ramp,lband_vector);
+ H_nogap_r = _mm_and_si128(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _mm_adds_epi16(E_r_gap,gap_open);
+
+ ramp = _mm_adds_epi16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi16(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, make E > H. */
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
+#else
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ less than E. */
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open+1); /* To compensate for T1 = H + open */
+ filter = _mm_cmpgt_epi16(ramp,lband_vector);
+ H_nogap_r = _mm_or_si128(_mm_andnot_si128(filter,extend_ladder),_mm_and_si128(filter,H_nogap_r));
+ E_r_gap = _mm_adds_epi16(H_nogap_r,gap_open);
+ H_nogap_r = _mm_subs_epi16(H_nogap_r,ones); /* To ensure H < E */
+ ramp = _mm_adds_epi16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _mm_adds_epi16(extend_ladder,extend_chunk); /* Prepare for next block */
+#endif
+
+ } else {
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
}
+
for ( ; c <= rhigh + uband && c <= glength; c++) {
score_column = matrix[c];
if (c == 0) {
pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi16(0);
+#else
if (rlo == 0) {
- X_prev_nogap = _mm_set1_epi8(0);
+ X_prev_nogap = _mm_set1_epi16(0);
} else {
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
+#endif
+
} else {
na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
@@ -1806,71 +6197,53 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
pairscores_alt_ptr = pairscores[na2_alt];
if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi8(0);
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi16(0);
#else
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8);
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
} else {
- /* second or greater block of 8 */
- X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
}
- debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
/* EGAP */
- T1 = _mm_adds_epi8(H_nogap_r, gap_open);
- dir_horiz = _mm_cmpgt_epi8(E_r_gap,T1); /* E > H, for jump early */
+ T1 = _mm_adds_epi16(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmpgt_epi16(E_r_gap,T1); /* E > H, for jump early */
_mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(T1,rlo,c,"T1"));
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+ debug15(print_vector_16(T1,rlo,c,"T1"));
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
-#ifdef HAVE_SSE4_1
- E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
-#else
- /* Compare H + open with vert */
- E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
-#endif
- E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+ E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR);
- H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores, allowing for alternate genomic nt */
-#ifdef HAVE_SSE4_1
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
-#else
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
- pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
- H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
-#endif
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
_mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
- dir_horiz = _mm_cmpgt_epi8(E_r_gap,H_nogap_r); /* E > H, for jump early */
+ dir_horiz = _mm_cmpgt_epi16(E_r_gap,H_nogap_r); /* E > H, for jump early */
_mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
-
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
-#ifdef HAVE_SSE4_1
- H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
-#else
- /* Compare H + pairscores with horiz + extend */
- H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
-#endif
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
+ H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
_mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
@@ -1886,16 +6259,13 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
pairscore = pairscore0;
}
-#ifndef HAVE_SSE4_1
- pairscore -= 128;
-#endif
- if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_8) {
- score_column[rhigh_calc] = NEG_INFINITY_8; /* Saturation */
- } else if (score > POS_INFINITY_8) {
- /* Should never get here, because we limit size of matrix using 8-bit quantities */
- score_column[rhigh_calc] = POS_INFINITY_8; /* Saturation */
+ /* No need to fix for non-SSE4.1: pairscore -= 128; */
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_16) {
+ score_column[rhigh_calc] = NEG_INFINITY_16; /* Saturation */
+ } else if (score > POS_INFINITY_16) {
+ score_column[rhigh_calc] = POS_INFINITY_16; /* Saturation */
} else {
- score_column[rhigh_calc] = (Score8_T) score;
+ score_column[rhigh_calc] = (Score16_T) score;
}
(*directions_Egap)[c][rhigh_calc] = DIAG;
(*directions_nogap)[c][rhigh_calc] = DIAG;
@@ -1914,7 +6284,6 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
} else {
c_gap = FF[c];
last_nogap = (int) score_column[rlo_calc-1];
- debug3(printf("LAST_NOGAP gets score_column[%d-1], or %d\n",rlo_calc,last_nogap));
}
if ((r = rlo_calc) == c - uband) {
@@ -1925,7 +6294,7 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
score = last_nogap + open /* + extend */;
c_gap = score + extend;
/* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
-
+
/* NOGAP */
last_nogap = (int) score_column[r];
r++;
@@ -1949,8 +6318,7 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
if (c_gap > last_nogap) { /* Use > for jump early */
last_nogap = c_gap;
- score_column[r] = (c_gap < NEG_INFINITY_8) ? NEG_INFINITY_8 : (Score8_T) c_gap; /* Saturation */
- debug3(printf("Stored at score_column[%d]: %d\n",r,(Score8_T) score_column[r]));
+ score_column[r] = (c_gap < NEG_INFINITY_16) ? NEG_INFINITY_16 : (Score16_T) c_gap; /* Saturation */
(*directions_nogap)[c][r] = VERT;
}
}
@@ -1968,17 +6336,17 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
/* Handle (0,1) and (1,0) directions, otherwise DIAG */
(*directions_Egap)[1][0] = HORIZ;
(*directions_Fgap)[0][1] = VERT;
-#endif
+#endif
+
#ifdef DEBUG2
- printf("SIMD: Dynprog_simd_8\n");
- Matrix8_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
- Directions8_print(*directions_nogap,*directions_Egap,*directions_Fgap,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
+ printf("SIMD: Dynprog_simd_16\n");
+ Matrix16_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+ Directions16_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,revp,lband,uband);
#endif
-
+
#ifdef CHECK1
/* Check for row 0 directions */
for (c = 1; c <= uband && c <= glength; c++) {
@@ -1992,30 +6360,6 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
}
#endif
-#ifdef DEBUG14
- matrix_std = compute_scores_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
- this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
- rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
- open,extend,lband,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_8);
-
-#ifdef DEBUG2
- printf("Banded %s\n",revp ? "rev" : "fwd");
- Dynprog_Matrix32_print(matrix_std,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
- Dynprog_Directions32_print(directions_nogap_std,directions_Egap_std,directions_Fgap_std,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
-#endif
-
- banded_matrix8_compare(matrix,matrix_std,rlength,glength,lband,uband,
- rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp);
-
- banded_directions8_compare_nogap(matrix,*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
- banded_directions8_compare_Egap(matrix,*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
- banded_directions8_compare_Fgap(matrix,*directions_Fgap,directions_Fgap_std,rlength,glength,lband,uband);
-#endif
-
FREEA(FF);
_mm_free(pairscores_col0);
_mm_free(pairscores[4]);
@@ -2025,92 +6369,88 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
_mm_free(pairscores[0]);
return matrix;
-}
+ }
#endif
-/* E_mask works at the wraparound from POS_INFINITY to NEG_INFINITY.
- It is designed to prevent a horizontal/vertical jump into the empty
- triangle, by setting horizontal/vertical scores to be as small as
- possible, e.g., -128. However, it is possible that H is also -128,
- so we still need to fix the directions along the main diagonal.
-
- E_mask shifted: 0 0 0 0 1 1 1 1
- add E_infinity: 127 127 127 127 127 127 127 127
- resulting mask: 127 127 127 127 -128 -128 -128 -128
-
- To deal with non-SSE4.1 systems, which lack _mm_min_epi8, we need
- too add 128 to E and mask, then take _mm_min_epu8, then subtract
- 128, as follows:
-
- E_mask shifted: 0 0 0 0 1 1 1 1
- add E_inf+128: 255 255 255 255 255 255 255 255
- resulting mask: 255 255 255 255 0 0 0 0
- (compare w/E+128)
-
-*/
-
-#ifdef HAVE_SSE2
-/* Designed for computation above the main diagonal, so no F loop or bottom masking needed */
-/* Operates by columns */
-Score8_T **
-Dynprog_simd_8_upper (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
- T this, char *rsequence, char *gsequence, char *gsequence_alt,
- int rlength, int glength,
-#ifdef DEBUG14
- int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+#if defined(HAVE_SSE2)
+/* Modified from Dynprog_simd_16_upper. Operates by columns. */
+Score16_T **
+Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
+ Direction16_T ***directions_Fgap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
- Mismatchtype_T mismatchtype, int open, int extend,
- int uband, bool jump_late_p, bool revp) {
- Score8_T **matrix, *score_column;
- __m128i pairscores_std, pairscores_alt;
-#ifdef HAVE_SSE4_1
- __m128i E_infinity;
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, int uband, bool jump_late_p, bool revp) {
+ int c_gap, last_nogap, score, *FF; /* Need to have the ability to go past NEG_INFINITY */
+ Score16_T **matrix, *score_column;
+#ifdef HAVE_AVX2
+ __m256i pairscores_std, pairscores_alt;
+ __m256i H_nogap_r, X_prev_nogap, E_r_gap, T1;
+ __m256i gap_open, gap_extend, complement_dummy;
+ __m256i dir_horiz;
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ __m256i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter;
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
#else
- __m128i E_infinity_plus_128;
- __m128i pairscores_best, all_128;
+ __m256i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter, ones;
#endif
- __m128i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, T1;
+
+#else
+ __m128i pairscores_std, pairscores_alt;
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, T1;
__m128i gap_open, gap_extend, complement_dummy;
__m128i dir_horiz;
- int rlength_ceil, r, c;
- int rlo, rhigh;
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ __m128i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter;
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+#else
+ __m128i ramp, ramp_chunk, extend_ladder, extend_chunk, lband_vector, filter, ones;
+#endif
+
+#endif
+
+ int rlength_ceil, lband_ceil, r, c;
+ int rlo, rhigh, rlo_calc, rhigh_calc;
int na1, na2, na2_alt;
- Score8_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore;
+ Score16_T *pairscores_col0;
+ Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore, pairscore0;
Pairdistance_T **pairdistance_array_type;
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2)
+ Score16_T **matrix_std;
+ Direction16_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
+#elif defined(DEBUG_SIMD)
Score32_T **matrix_std;
- Direction32_T **directions_nogap_std, **directions_Egap_std;
- char na2_single;
+ Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
#endif
- debug2(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- debug15(printf("Dynprog_simd_8_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
-
- rlength_ceil = (int) ((rlength + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+ debug2(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d, lband %d, uband %d\n",
+ jump_late_p,open,extend,lband,uband));
-#ifdef HAVE_SSE4_1
+ rlength_ceil = (int) ((rlength + SIMD_NSHORTS)/SIMD_NSHORTS) * SIMD_NSHORTS;
pairdistance_array_type = pairdistance_array[mismatchtype];
-#else
- /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
- pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
- all_128 = _mm_set1_epi8(128);
-#endif
- debug(printf("compute_scores_simd_8_bycols (upper): "));
+ debug(printf("compute_scores_simd_16_bycols (upper): "));
debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
debug(printf("Query length rounded up to %d\n",rlength_ceil));
- matrix = aligned_score8_alloc(rlength_ceil,glength,
- this->aligned.two.upper_matrix_ptrs,this->aligned.two.upper_matrix_space);
- *directions_nogap = aligned_directions8_alloc(rlength_ceil,glength,
- this->aligned.two.upper_directions_ptrs_0,this->aligned.two.upper_directions_space_0);
- *directions_Egap = aligned_directions8_alloc(rlength_ceil,glength,
- this->aligned.two.upper_directions_ptrs_1,this->aligned.two.upper_directions_space_1);
+ matrix = aligned_score16_alloc(rlength_ceil,glength,
+ this->aligned.one.matrix_ptrs,this->aligned.one.matrix_space);
+ *directions_nogap = aligned_directions16_alloc(rlength_ceil,glength,
+ this->aligned.one.directions_ptrs_0,this->aligned.one.directions_space_0);
+ *directions_Egap = aligned_directions16_alloc(rlength_ceil,glength,
+ this->aligned.one.directions_ptrs_1,this->aligned.one.directions_space_1);
+ /* Need to calloc to save time in F loop */
+ *directions_Fgap = aligned_directions16_calloc(rlength_ceil,glength,
+ this->aligned.one.directions_ptrs_2,this->aligned.one.directions_space_2);
#if 0
/* Row 0 initialization */
@@ -2122,14 +6462,14 @@ Dynprog_simd_8_upper (Direction8_T ***directions_nogap, Direction8_T ***directio
}
#endif
#if 0
- /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ /* Already initialized to DIAG. Actually, no longer initializing directions_Egap */
(*directions_Egap)[1][0] = DIAG; /* previously used STOP */
(*directions_nogap)[0][0] = DIAG; /* previously used STOP */
#endif
#if 0
/* Column 0 initialization */
/* penalty = open; */
- for (r = 1; r <= SIMD_NCHARS && r <= rlength; r++) {
+ for (r = 1; r <= SIMD_NSHORTS && r <= rlength; r++) {
/* penalty += extend; */
(*directions_nogap)[0][r] = VERT;
}
@@ -2137,371 +6477,645 @@ Dynprog_simd_8_upper (Direction8_T ***directions_nogap, Direction8_T ***directio
/* Load pairscores. Store match - mismatch */
- pairscores[0] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[1] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[2] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[3] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
- pairscores[4] = (Score8_T *) _mm_malloc(rlength_ceil * sizeof(Score8_T),16);
+ pairscores[0] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[1] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[2] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[3] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[4] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+
+ lband_ceil = (int) ((lband + SIMD_NSHORTS)/SIMD_NSHORTS) * SIMD_NSHORTS;
+ pairscores_col0 = (Score16_T *) _mm_malloc(lband_ceil * sizeof(Score16_T),ALIGN_SIZE);
#if 0
/* Should not be necessary */
- memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score16_T));
+#endif
+
+
+ pairscores_col0[0] = (Score16_T) 0;
+ /* Initialization just to lband causes errors in dir_horiz for Egap */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score16_T) 0;
+ }
+#else
+ for (r = 1; r < lband_ceil; r++) {
+ pairscores_col0[r] = (Score16_T) NEG_INFINITY_16;
+ }
#endif
- /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
r = 0; na1 = 'N';
- pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
if (revp == false) {
for (r = 1; r <= rlength; r++) {
na1 = (int) rsequence[r-1];
- pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
}
} else {
for (r = 1; r <= rlength; r++) {
na1 = (int) rsequence[1-r];
- pairscores[0][r] = (Score8_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score8_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score8_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score8_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score8_T) pairdistance_array_type[na1][(int) 'N'];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
}
}
#if 0
/* Should not be necessary */
- memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
- memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score8_T));
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
#endif
- complement_dummy = _mm_set1_epi8(-1);
+ complement_dummy = _MM_SET1_EPI16(-1);
+
+ FF = (int *) MALLOCA((glength + 1) * sizeof(int));
- gap_open = _mm_set1_epi8((Score8_T) open);
- gap_extend = _mm_set1_epi8((Score8_T) extend);
+ gap_open = _MM_SET1_EPI16((Score16_T) open);
+ gap_extend = _MM_SET1_EPI16((Score16_T) extend);
-#ifdef HAVE_SSE4_1
- E_infinity = _mm_set1_epi8(POS_INFINITY_8);
+#ifndef INFINITE_INITIAL_GAP_PENALTY
+#ifdef HAVE_AVX2
+ ramp = _mm256_setr_epi16(1,2,3,4,5,6,7,8);
+ extend_ladder = _mm256_setr_epi16(extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*extend,8*extend);
#else
- E_infinity_plus_128 = _mm_set1_epi8(POS_INFINITY_8+128);
+ ramp = _mm_setr_epi16(1,2,3,4,5,6,7,8);
+ extend_ladder = _mm_setr_epi16(extend,2*extend,3*extend,4*extend,5*extend,6*extend,7*extend,8*extend);
+#endif
+ lband_vector = _MM_SET1_EPI16(lband);
+ ramp_chunk = _MM_SET1_EPI16(SIMD_NSHORTS);
+ extend_chunk = _MM_SET1_EPI16(SIMD_NSHORTS*extend);
#endif
+
if (jump_late_p) {
- for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
- if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS) {
+ if ((rhigh = rlo + SIMD_NSHORTS - 1) > rlength) {
rhigh = rlength;
}
- /* dir_horiz tests if E >= H . To fill in first column of each
- row block with non-diags, could make E == H. But irrelevant,
- because these are below the diagonal. */
- E_mask = _mm_set1_epi8(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi8(-extend);
- H_nogap_r = _mm_set1_epi8(-open-extend);
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16-open);
+ filter = _MM_CMPGT_EPI16(ramp,lband_vector);
+ H_nogap_r = _MM_AND_SI(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _MM_OR_SI(_mm_andnot_si128(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _MM_ADDS_EPI16(E_r_gap,gap_open);
+
+ ramp = _MM_ADDS_EPI16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI16(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E >= H. To fill in first column of each
+ row block with non-diags, make E == H. */
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16);
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
#else
- E_r_gap = _mm_set1_epi8(NEG_INFINITY_8);
- H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ equal to E. */
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_8-open); /* To compensate for T1 = H + open */
+ filter = _MM_CMPGT_EPI16(ramp,lband_vector);
+ H_nogap_r = _MM_OR_SI(_mm_andnot_si128(filter,extend_ladder),_mm_and_si128(filter,H_nogap_r));
+ E_r_gap = _MM_ADDS_EPI16(H_nogap_r,gap_open);
+ ramp = _MM_ADDS_EPI16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI16(extend_ladder,extend_chunk); /* Prepare for next block */
#endif
- for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ } else {
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16);
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
+ }
+
+ for ( ; c <= rhigh + uband && c <= glength; c++) {
score_column = matrix[c];
if (c == 0) {
- na2 = na2_alt = 4; /* 'N' */
- } else {
- na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
- na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
- }
- pairscores_std_ptr = pairscores[na2];
- pairscores_alt_ptr = pairscores[na2_alt];
-
- if (c == 0) {
- X_prev_nogap = _mm_set1_epi8(0);
- } else if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi8(0);
+ pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_setzero_si256();
+ } else {
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
+ }
#else
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the rlo bounds */
+ if (rlo == 0) {
+ X_prev_nogap = _mm_setzero_si128();
+ } else {
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+ }
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+
} else {
- /* second or greater block of 8 */
- X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
- }
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
- debug15(print_vector_8(E_mask,rlo,c,"E_mask"));
-#ifdef HAVE_SSE4_1
- E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
+ } else {
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_SHORT_INSERT);
+ }
#else
- E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+ if (rlo == 0) {
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+ } else {
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+ }
#endif
- debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+ }
- /* EGAP */
- T1 = _mm_adds_epi8(H_nogap_r, gap_open);
- dir_horiz = _mm_cmplt_epi8(E_r_gap,T1); /* E < H */
- dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
- _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(T1,rlo,c,"T1"));
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
-#ifdef HAVE_SSE4_1
- E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
- E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
-#elif 1
- E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
- E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+ /* EGAP */
+ T1 = _MM_ADDS_EPI16(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPLT_EPI16(E_r_gap,T1); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
#else
- /* Try to avoid unnecessary shifts by 128, but overflows */
- E_r_gap = _mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128));
- E_r_gap = _mm_add_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_sub_epi8(_mm_min_epu8(E_r_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
#endif
- debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+ debug15(print_vector_16(T1,rlo,c,"T1"));
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
+
+ E_r_gap = _MM_MAX_EPI16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _MM_ADDS_EPI16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR);
- H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
- H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi16(_mm256_setzero_si256(),_mm256_extract_epi16(H_nogap_r,SIMD_NSHORTS-1),LAST_SHORT_INSERT);
+ X_prev_nogap = _mm256_insert_epi16(X_prev_nogap,_mm256_extract_epi16(H_nogap_r,MID_SHORT_INSERT-1),MID_SHORT_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_SHORT);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_SHIFT);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores, allowing for alternate genomic nt */
-#ifdef HAVE_SSE4_1
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm256_adds_epi16(H_nogap_r, _mm256_max_epi16(pairscores_std,pairscores_alt));
+#else
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
- H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
-#else
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
- pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
- debug15(print_vector_8(pairscores_best,rlo,c,"pairscores_std"));
- H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
#endif
_mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
- dir_horiz = _mm_cmplt_epi8(E_r_gap,H_nogap_r); /* E < H */
- dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ dir_horiz = _MM_CMPLT_EPI16(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
_mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
+#endif
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
+
+ H_nogap_r = _MM_MAX_EPI16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
+
+
+ /* F loop */
+ if ((rlo_calc = rlo) <= c - uband) {
+ rlo_calc = c - uband;
+ }
+ if ((rhigh_calc = rhigh) >= c + lband) {
+ rhigh_calc = c + lband;
+ if (c > 0) {
+ /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
+ pairscore = pairscores[na2][rhigh_calc];
+ if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
+ pairscore = pairscore0;
+ }
+ /* No need to fix for non-SSE4.1: pairscore -= 128; */
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_16) {
+ score_column[rhigh_calc] = NEG_INFINITY_16; /* Saturation */
+ } else if (score > POS_INFINITY_16) {
+ score_column[rhigh_calc] = POS_INFINITY_16; /* Saturation */
+ } else {
+ score_column[rhigh_calc] = (Score16_T) score;
+ }
+ (*directions_Egap)[c][rhigh_calc] = DIAG;
+ (*directions_nogap)[c][rhigh_calc] = DIAG;
+ }
+ }
+
+ debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
+ rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
+
+ if (rlo == 0) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else if (c >= rlo + uband) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else {
+ debug3(printf("At c %d, uband %d, reading c_gap %d\n",c,uband,FF[c]));
+ c_gap = FF[c];
+ last_nogap = (int) score_column[rlo_calc-1];
+ }
-#ifdef HAVE_SSE4_1
- H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
-#else
- /* Compare H + pairscores with horiz + extend */
- H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
-#endif
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
- _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+ if ((r = rlo_calc) == c - uband) {
+ /* Handle top value as a special case to prevent going outside of uband */
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ score = last_nogap + open /* + extend */;
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ r++;
+ }
- /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
- if (rhigh >= c) {
- (*directions_Egap)[c][c] = DIAG;
- (*directions_nogap)[c][c] = DIAG;
+ /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
+ for ( ; r <= rhigh_calc; r++) {
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
+ c_gap += extend;
+ (*directions_Fgap)[c][r] = VERT;
+ } else {
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ }
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
+ if (c_gap >= last_nogap) { /* Use >= for jump late */
+ last_nogap = c_gap;
+ score_column[r] = (c_gap < NEG_INFINITY_16) ? NEG_INFINITY_16 : (Score16_T) c_gap; /* Saturation */
+ (*directions_nogap)[c][r] = VERT;
+ }
}
- /* No need for F loop here */
- E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ FF[c] = c_gap;
+ debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
+#ifdef HAVE_AVX2
+ H_nogap_r = _mm256_load_si256((__m256i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#else
+ H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#endif
}
}
} else {
/* jump early */
- for (rlo = 0; rlo <= rlength; rlo += SIMD_NCHARS) {
- if ((rhigh = rlo + SIMD_NCHARS - 1) > rlength) {
+#if defined(ZERO_INITIAL_GAP_PENALTY) || defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* No need for ones */
+#else
+ ones = _MM_SET1_EPI16(1);
+#endif
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS) {
+ if ((rhigh = rlo + SIMD_NSHORTS - 1) > rlength) {
rhigh = rlength;
}
- /* dir_horiz tests if E > H. To fill in first column of each
- row block with non-diags, could make E > H. But irrelevant,
- because these are below the diagonal. */
- E_mask = _mm_set1_epi8(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi8(-extend);
- H_nogap_r = _mm_set1_epi8(-open-extend-1);
+ if ((c = rlo - lband) < 0) {
+ c = 0;
+
+#if defined(ZERO_INITIAL_GAP_PENALTY)
+ /* Initial H in column 0 determined by zeroed out H. E needs to equal gap_open for column 1. */
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16-open);
+ filter = _MM_CMPGT_EPI16(ramp,lband_vector);
+ H_nogap_r = _MM_AND_SI(filter,E_r_gap); /* Use zeros for score */
+
+ E_r_gap = _MM_OR_SI(_MM_ANDNOT_SI(filter,extend_ladder),H_nogap_r);
+ E_r_gap = _MM_ADDS_EPI16(E_r_gap,gap_open);
+
+ ramp = _MM_ADDS_EPI16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI16(extend_ladder,extend_chunk); /* Prepare for next block */
+#elif defined(INFINITE_INITIAL_GAP_PENALTY)
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, make E > H. */
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16+1);
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
#else
- E_r_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
- H_nogap_r = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
+ /* Initial H in column 0 determined by E, which needs to equal
+ gap_open + extend_ladder for column 1. H is free to be set
+ less than E. */
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open+1); /* To compensate for T1 = H + open */
+ filter = _MM_CMPGT_EPI16(ramp,lband_vector);
+ H_nogap_r = _MM_OR_SI(_MM_ANDNOT_SI(filter,extend_ladder),_MM_AND_SI(filter,H_nogap_r));
+ E_r_gap = _MM_ADDS_EPI16(H_nogap_r,gap_open);
+ H_nogap_r = _MM_SUBS_EPI16(H_nogap_r,ones); /* To ensure H < E */
+ ramp = _MM_ADDS_EPI16(ramp,ramp_chunk); /* Prepare for next block */
+ extend_ladder = _MM_ADDS_EPI16(extend_ladder,extend_chunk); /* Prepare for next block */
#endif
+
+ } else {
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16+1);
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
+ }
- for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ for ( ; c <= rhigh + uband && c <= glength; c++) {
score_column = matrix[c];
if (c == 0) {
- na2 = na2_alt = 4; /* 'N' */;
- } else {
- na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
- na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
- }
- pairscores_std_ptr = pairscores[na2];
- pairscores_alt_ptr = pairscores[na2_alt];
-
- if (c == 0) {
- X_prev_nogap = _mm_set1_epi8(0);
- } else if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi8(0);
+ pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_setzero_si256();
+ } else {
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
+ }
#else
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the rlo bounds */
+ if (rlo == 0) {
+ X_prev_nogap = _mm_setzero_si128();
+ } else {
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+ }
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+
} else {
- /* second or greater block of 8 */
- X_prev_nogap = _mm_set1_epi8(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
- }
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
- debug15(print_vector_8(E_mask,rlo,c,"E_mask"));
-#ifdef HAVE_SSE4_1
- E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ if (rlo == 0) {
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
+ } else {
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_SHORT_INSERT);
+ }
#else
- E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+ if (rlo == 0) {
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+ } else {
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+ }
#endif
- debug15(print_vector_8(E_r_gap,rlo,c,"E_r_gap"));
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r load"));
+ }
- /* EGAP */
- T1 = _mm_adds_epi8(H_nogap_r, gap_open);
- dir_horiz = _mm_cmpgt_epi8(E_r_gap,T1); /* E > H, for jump early */
- _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(T1,rlo,c,"T1"));
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_Egap"));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
- /* Compare H + open with vert */
-#ifdef HAVE_SSE4_1
- E_r_gap = _mm_max_epi8(E_r_gap, T1); /* Compare H + open with vert */
- E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_min_epi8(E_r_gap,_mm_add_epi8(E_mask,E_infinity));
-#elif 1
- E_r_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
- E_r_gap = _mm_adds_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_r_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+ /* EGAP */
+ T1 = _MM_ADDS_EPI16(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPGT_EPI16(E_r_gap,T1); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
#else
- /* Try to avoid unnecessary shifts by 128, but overflows */
- E_r_gap = _mm_max_epu8(_mm_add_epi8(E_r_gap, all_128), _mm_add_epi8(T1, all_128));
- E_r_gap = _mm_add_epi8(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_sub_epi8(_mm_min_epu8(E_r_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
#endif
- debug15(print_vector_8(E_r_gap,rlo,c,"E"));
+ debug15(print_vector_16(T1,rlo,c,"T1"));
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
+
+ E_r_gap = _MM_MAX_EPI16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _MM_ADDS_EPI16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_CHAR);
- H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_CHAR);
- H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi16(_mm256_setzero_si256(),_mm256_extract_epi16(H_nogap_r,SIMD_NSHORTS-1),LAST_SHORT_INSERT);
+ X_prev_nogap = _mm256_insert_epi16(X_prev_nogap,_mm256_extract_epi16(H_nogap_r,MID_SHORT_INSERT-1),MID_SHORT_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_SHORT);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_SHIFT);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores, allowing for alternate genomic nt */
-#ifdef HAVE_SSE4_1
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm256_adds_epi16(H_nogap_r, _mm256_max_epi16(pairscores_std,pairscores_alt));
+#else
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- debug15(print_vector_8(pairscores_std,rlo,c,"pairscores_std"));
- H_nogap_r = _mm_adds_epi8(H_nogap_r, _mm_max_epi8(pairscores_std,pairscores_alt));
-#else
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo])); /* Has 128 added already */
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo])); /* Has 128 added already */
- pairscores_best = _mm_sub_epi8(_mm_max_epu8(pairscores_std, pairscores_alt), all_128);
- debug15(print_vector_8(pairscores_best,rlo,c,"pairscores_std"));
- H_nogap_r = _mm_adds_epi8(H_nogap_r, pairscores_best);
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
#endif
_mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_8(H_nogap_r,rlo,c,"H"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
- dir_horiz = _mm_cmpgt_epi8(E_r_gap,H_nogap_r); /* E > H, for jump early */
+ dir_horiz = _MM_CMPGT_EPI16(E_r_gap,H_nogap_r); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
_mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_8(dir_horiz,rlo,c,"dir_nogap"));
-
+#endif
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
-#ifdef HAVE_SSE4_1
- H_nogap_r = _mm_max_epi8(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _MM_MAX_EPI16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
#else
- /* Compare H + pairscores with horiz + extend */
- H_nogap_r = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_r, all_128), _mm_add_epi8(E_r_gap, all_128)), all_128);
-#endif
- debug15(print_vector_8(H_nogap_r,rlo,c,"H_nogap_r store"));
_mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
- /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
- if (rhigh >= c) {
- (*directions_Egap)[c][c] = DIAG;
- (*directions_nogap)[c][c] = DIAG;
+ /* F loop */
+ if ((rlo_calc = rlo) < c - uband) {
+ rlo_calc = c - uband;
+ }
+ if ((rhigh_calc = rhigh) >= c + lband) {
+ rhigh_calc = c + lband;
+ if (c > 0) {
+ /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
+ pairscore = pairscores[na2][rhigh_calc];
+ if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
+ pairscore = pairscore0;
+ }
+ /* No need to fix for non-SSE4.1: pairscore -= 128; */
+ if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_16) {
+ score_column[rhigh_calc] = NEG_INFINITY_16; /* Saturation */
+ } else if (score > POS_INFINITY_16) {
+ score_column[rhigh_calc] = POS_INFINITY_16; /* Saturation */
+ } else {
+ score_column[rhigh_calc] = (Score16_T) score;
+ }
+ (*directions_Egap)[c][rhigh_calc] = DIAG;
+ (*directions_nogap)[c][rhigh_calc] = DIAG;
+ }
+ }
+
+ debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
+ rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
+
+ if (rlo == 0) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else if (c >= rlo + uband) {
+ c_gap = NEG_INFINITY_INT;
+ last_nogap = NEG_INFINITY_INT;
+ } else {
+ c_gap = FF[c];
+ last_nogap = (int) score_column[rlo_calc-1];
+ }
+
+ if ((r = rlo_calc) == c - uband) {
+ /* Handle top value as a special case to prevent going outside of uband */
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ score = last_nogap + open /* + extend */;
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ r++;
+ }
+
+ /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
+ for ( ; r <= rhigh_calc; r++) {
+ /* FGAP */
+ debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
+ r,c,c_gap + extend,last_nogap + open + extend));
+ if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
+ c_gap += extend;
+ (*directions_Fgap)[c][r] = VERT;
+ } else {
+ c_gap = score + extend;
+ /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ }
+
+ /* NOGAP */
+ last_nogap = (int) score_column[r];
+ debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
+ if (c_gap > last_nogap) { /* Use > for jump early */
+ last_nogap = c_gap;
+ score_column[r] = (c_gap < NEG_INFINITY_16) ? NEG_INFINITY_16 : (Score16_T) c_gap; /* Saturation */
+ (*directions_nogap)[c][r] = VERT;
+ }
}
- /* No need for F loop here */
- E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ FF[c] = c_gap;
+ debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
+#ifdef HAVE_AVX2
+ H_nogap_r = _mm256_load_si256((__m256i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#else
+ H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+#endif
}
}
}
+
#ifdef CHECK1
/* Row 0 and column 0 directions fail anyway due to saturation */
/* Handle (0,1) and (1,0) directions, otherwise DIAG */
(*directions_Egap)[1][0] = HORIZ;
+ (*directions_Fgap)[0][1] = VERT;
#endif
+
#ifdef DEBUG2
- printf("SIMD: Dynprog_simd_8_upper\n");
- Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,uband,/*upperp*/true);
- Directions8_print_ud(*directions_nogap,*directions_Egap,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,uband,/*upperp*/true);
+ printf("SIMD: Dynprog_simd_16\n");
+ Matrix16_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+ Directions16_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
#endif
-
+
#ifdef CHECK1
/* Check for row 0 directions */
for (c = 1; c <= uband && c <= glength; c++) {
assert((*directions_Egap)[c][0] != DIAG);
assert((*directions_nogap)[c][0] != DIAG);
}
+ /* Check for column 0 directions */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ assert((*directions_Fgap)[0][r] != DIAG);
+ assert((*directions_nogap)[0][r] != DIAG);
+ }
#endif
-#ifdef DEBUG14
- matrix_std = compute_scores_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
- this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+#ifdef DEBUG_AVX2
+ matrix_std = Dynprog_simd_16_nonavx2(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,gsequence,gsequence_alt,
rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
open,extend,lband,uband,jump_late_p,revp);
+#elif defined(DEBUG_SIMD)
+ matrix_std = Dynprog_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_16,
+ /*upperp*/true,/*lowerp*/true);
+#endif
#ifdef DEBUG2
- printf("Banded %s\n",revp ? "rev" : "fwd");
- Matrix32_print(matrix_std,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
- Directions32_print(directions_nogap_std,directions_Egap_std,directions_Fgap_std,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
+ printf("Banded\n");
+ Matrix16_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,uband);
+ Directions16_print(*directions_nogap,*directions_Egap,*directions_Fgap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,revp,lband,uband);
#endif
- banded_matrix8_compare(matrix,matrix_std,rlength,glength,lband,uband,
- rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp);
-
- banded_directions8_compare_nogap(matrix,*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ banded_matrix16_compare(matrix,matrix_std,rlength,glength,lband,uband,
+ rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp);
- banded_directions8_compare_Egap(matrix,*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
+ banded_directions16_compare_nogap(*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
+ banded_directions16_compare_Egap(*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
+ banded_directions16_compare_Fgap(*directions_Fgap,directions_Fgap_std,rlength,glength,lband,uband);
#endif
+ FREEA(FF);
+ _mm_free(pairscores_col0);
_mm_free(pairscores[4]);
_mm_free(pairscores[3]);
_mm_free(pairscores[2]);
@@ -2509,438 +7123,315 @@ Dynprog_simd_8_upper (Direction8_T ***directions_nogap, Direction8_T ***directio
_mm_free(pairscores[0]);
return matrix;
-}
+ }
#endif
-#ifdef HAVE_SSE2
-/* Designed for computation below the main diagonal, so no F loop or bottom masking needed */
-/* Operates by rows */
-Score8_T **
-Dynprog_simd_8_lower (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
- T this, char *rsequence, char *gsequence, char *gsequence_alt,
- int rlength, int glength,
-#ifdef DEBUG14
- int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
-#endif
- Mismatchtype_T mismatchtype, int open, int extend,
- int lband, bool jump_late_p, bool revp) {
- Score8_T **matrix, *score_column;
- __m128i pairscores_std;
-#ifdef HAVE_SSE4_1
- __m128i E_infinity;
-#else
- __m128i pairscores_best, all_128, E_infinity_plus_128;
-#endif
- __m128i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, T1;
+#ifdef DEBUG_AVX2
+/* Designed for computation above the diagonal, so no F loop or bottom masking needed */
+/* Operates by columns */
+Score16_T **
+Dynprog_simd_16_upper_nonavx2 (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int uband, bool jump_late_p, bool revp) {
+ Score16_T **matrix, *score_column;
+ __m128i pairscores_std, pairscores_alt;
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, E_infinity, T1;
__m128i gap_open, gap_extend, complement_dummy;
- __m128i dir_vert;
- int glength_ceil, r, c;
- int clo, chigh;
+ __m128i dir_horiz;
+ int rlength_ceil, r, c;
+ int rlo, rhigh;
int na1, na2, na2_alt;
- Score8_T *pairscores[5], *pairscores_ptr, pairscore;
- Pairdistance_T **pairdistance_array_type, score1, score2;
-
-#ifdef DEBUG14
- Score32_T **matrix_std;
- Direction32_T **directions_nogap_std, **directions_Egap_std;
- char na2_single;
-#endif
-
+ Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore;
+ Pairdistance_T **pairdistance_array_type;
- debug2(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- debug15(printf("Dynprog_simd_8_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- glength_ceil = (int) ((glength + SIMD_NCHARS)/SIMD_NCHARS) * SIMD_NCHARS;
+ debug2(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
-#ifdef HAVE_SSE4_1
+ rlength_ceil = (int) ((rlength + SIMD_NSHORTS_NONAVX2)/SIMD_NSHORTS_NONAVX2) * SIMD_NSHORTS_NONAVX2;
pairdistance_array_type = pairdistance_array[mismatchtype];
-#else
- /* Needed to use _mm_max_epu8 and _mm_min_epu8, instead of signed versions */
- pairdistance_array_type = pairdistance_array_plus_128[mismatchtype];
- all_128 = _mm_set1_epi8(128);
-#endif
- debug(printf("compute_scores_simd_8_byrows (lower): "));
- debug(printf("Lengths are %d and %d, so band is %d on left\n",rlength,glength,lband));
- debug(printf("Genome length rounded up to %d\n",glength_ceil));
+ debug(printf("compute_scores_simd_16_bycols (upper): "));
+ debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
+ debug(printf("Query length rounded up to %d\n",rlength_ceil));
- matrix = aligned_score8_alloc(glength_ceil,rlength,
- this->aligned.two.lower_matrix_ptrs,this->aligned.two.lower_matrix_space);
- *directions_nogap = aligned_directions8_alloc(glength_ceil,rlength,
- this->aligned.two.lower_directions_ptrs_0,this->aligned.two.lower_directions_space_0);
- *directions_Egap = aligned_directions8_alloc(glength_ceil,rlength,
- this->aligned.two.lower_directions_ptrs_1,this->aligned.two.lower_directions_space_1);
+ matrix = aligned_score16_alloc(rlength_ceil,glength,
+ this->aligned_std.two.upper_matrix_ptrs,this->aligned_std.two.upper_matrix_space);
+ *directions_nogap = aligned_directions16_alloc(rlength_ceil,glength,
+ this->aligned_std.two.upper_directions_ptrs_0,this->aligned_std.two.upper_directions_space_0);
+ *directions_Egap = aligned_directions16_alloc(rlength_ceil,glength,
+ this->aligned_std.two.upper_directions_ptrs_1,this->aligned_std.two.upper_directions_space_1);
#if 0
- /* Column 0 initialization */
+ /* Row 0 initialization */
/* penalty = open; */
- for (r = 1; r <= lband && r <= rlength; r++) {
+ for (c = 1; c <= uband && c <= glength; c++) {
/* penalty += extend; */
- (*directions_Egap)[r][0] = VERT;
- (*directions_nogap)[r][0] = VERT;
+ (*directions_Egap)[c][0] = HORIZ;
+ (*directions_nogap)[c][0] = HORIZ;
}
#endif
#if 0
- /* Already initialized to DIAG. Actually no longer initializing directions_Egap */
+ /* Already initialized to DIAG. Actually, no longer initializing directions_Egap */
(*directions_Egap)[1][0] = DIAG; /* previously used STOP */
(*directions_nogap)[0][0] = DIAG; /* previously used STOP */
#endif
#if 0
- /* Row 0 initialization */
+ /* Column 0 initialization */
/* penalty = open; */
- for (c = 1; c <= SIMD_NCHARS && c <= glength; c++) {
+ for (r = 1; r <= SIMD_NSHORTS_NONAVX2 && r <= rlength; r++) {
/* penalty += extend; */
- (*directions_nogap)[0][c] = HORIZ;
+ (*directions_nogap)[0][r] = VERT;
}
#endif
/* Load pairscores. Store match - mismatch */
- pairscores[0] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
- pairscores[1] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
- pairscores[2] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
- pairscores[3] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
- pairscores[4] = (Score8_T *) _mm_malloc(glength_ceil * sizeof(Score8_T),16);
+ pairscores[0] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[1] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[2] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[3] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[4] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
#if 0
/* Should not be necessary */
- memset((void *) pairscores[0],0,glength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[1],0,glength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[2],0,glength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[3],0,glength_ceil*sizeof(Score8_T));
- memset((void *) pairscores[4],0,glength_ceil*sizeof(Score8_T));
+ memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score16_T));
#endif
- /* For non-SSE4.1, addition of 128 taken care of by using pairdistance_array_plus_128 above */
- c = 0; na2 = na2_alt = 4; /* 'N' */
-#ifdef HAVE_SSE4_1
- pairscores[0][c] = (Score8_T) pairdistance_array_type[(int) 'A'][na2];
- pairscores[1][c] = (Score8_T) pairdistance_array_type[(int) 'C'][na2];
- pairscores[2][c] = (Score8_T) pairdistance_array_type[(int) 'G'][na2];
- pairscores[3][c] = (Score8_T) pairdistance_array_type[(int) 'T'][na2];
- pairscores[4][c] = (Score8_T) pairdistance_array_type[(int) 'N'][na2];
-#else
- pairscores[0][c] = (Score8_T) pairdistance_array_type[(int) 'A'][na2] - 128;
- pairscores[1][c] = (Score8_T) pairdistance_array_type[(int) 'C'][na2] - 128;
- pairscores[2][c] = (Score8_T) pairdistance_array_type[(int) 'G'][na2] - 128;
- pairscores[3][c] = (Score8_T) pairdistance_array_type[(int) 'T'][na2] - 128;
- pairscores[4][c] = (Score8_T) pairdistance_array_type[(int) 'N'][na2] - 128;
-#endif
+ r = 0; na1 = 'N';
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
if (revp == false) {
- for (c = 1; c <= glength; c++) {
- na2 = gsequence[c-1];
- na2_alt = gsequence_alt[c-1];
- /* Take max here */
- score1 = pairdistance_array_type[(int) 'A'][na2];
- score2 = pairdistance_array_type[(int) 'A'][na2_alt];
- pairscores[0][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'C'][na2];
- score2 = pairdistance_array_type[(int) 'C'][na2_alt];
- pairscores[1][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'G'][na2];
- score2 = pairdistance_array_type[(int) 'G'][na2_alt];
- pairscores[2][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'T'][na2];
- score2 = pairdistance_array_type[(int) 'T'][na2_alt];
- pairscores[3][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'N'][na2];
- score2 = pairdistance_array_type[(int) 'N'][na2_alt];
- pairscores[4][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[r-1];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
}
} else {
- for (c = 1; c <= glength; c++) {
- na2 = gsequence[1-c];
- na2_alt = gsequence_alt[1-c];
- /* Take max here */
- score1 = pairdistance_array_type[(int) 'A'][na2];
- score2 = pairdistance_array_type[(int) 'A'][na2_alt];
- pairscores[0][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'C'][na2];
- score2 = pairdistance_array_type[(int) 'C'][na2_alt];
- pairscores[1][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'G'][na2];
- score2 = pairdistance_array_type[(int) 'G'][na2_alt];
- pairscores[2][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'T'][na2];
- score2 = pairdistance_array_type[(int) 'T'][na2_alt];
- pairscores[3][c] = (Score8_T) (score1 > score2) ? score1 : score2;
-
- score1 = pairdistance_array_type[(int) 'N'][na2];
- score2 = pairdistance_array_type[(int) 'N'][na2_alt];
- pairscores[4][c] = (Score8_T) (score1 > score2) ? score1 : score2;
+ for (r = 1; r <= rlength; r++) {
+ na1 = (int) rsequence[1-r];
+ pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
+ pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
+ pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
+ pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
+ pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
}
}
#if 0
/* Should not be necessary */
- memset((void *) &(pairscores[0][c]),0,(glength_ceil-c)*sizeof(Score8_T));
- memset((void *) &(pairscores[1][c]),0,(glength_ceil-c)*sizeof(Score8_T));
- memset((void *) &(pairscores[2][c]),0,(glength_ceil-c)*sizeof(Score8_T));
- memset((void *) &(pairscores[3][c]),0,(glength_ceil-c)*sizeof(Score8_T));
- memset((void *) &(pairscores[4][c]),0,(glength_ceil-c)*sizeof(Score8_T));
-#endif
-
- complement_dummy = _mm_set1_epi8(-1);
-
- gap_open = _mm_set1_epi8((Score8_T) open);
- gap_extend = _mm_set1_epi8((Score8_T) extend);
-
-#ifdef HAVE_SSE4_1
- E_infinity = _mm_set1_epi8(POS_INFINITY_8);
-#else
- E_infinity_plus_128 = _mm_set1_epi8(POS_INFINITY_8+128);
+ memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
#endif
+
+ complement_dummy = _mm_set1_epi16(-1);
+
+ gap_open = _mm_set1_epi16((Score16_T) open);
+ gap_extend = _mm_set1_epi16((Score16_T) extend);
+
+ E_infinity = _mm_set1_epi16(POS_INFINITY_16);
if (jump_late_p) {
- for (clo = 0; clo <= glength; clo += SIMD_NCHARS) {
- if ((chigh = clo + SIMD_NCHARS - 1) > glength) {
- chigh = glength;
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NSHORTS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
}
- /* dir_vert tests if E >= H. To fill in first row of each
- column block with non-diags, make E == H. */
- E_mask = _mm_set1_epi8(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_c_gap = _mm_set1_epi8(-extend);
- H_nogap_c = _mm_set1_epi8(-open-extend);
-#else
- E_c_gap = _mm_set1_epi8(NEG_INFINITY_8);
- H_nogap_c = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
-#endif
+ /* dir_horiz tests if E >= H. To fill in first column of each
+ row block with non-diags, could make E == H. But irrelevant,
+ because these are above the diagonal. */
+ E_mask = _mm_set1_epi16(1);
- for (r = clo; r <= chigh + lband && r <= rlength; r++) {
- score_column = matrix[r];
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16);
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
- if (r == 0) {
- na1 = 4; /* 'N' */
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ na2 = na2_alt = 4; /* 'N' */
} else {
- na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
}
- pairscores_ptr = pairscores[na1];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
- if (r == 0) {
- X_prev_nogap = _mm_set1_epi8(0);
- } else if (clo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi8(0);
+ if (c == 0) {
+ X_prev_nogap = _mm_set1_epi16(0);
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi16(0);
#else
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the clo bounds */
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
} else {
- /* second or greater block of 8 */
- X_prev_nogap = _mm_set1_epi8(matrix[r-1][clo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
- debug15(print_vector_8(E_mask,clo,r,"E_mask"));
-#ifdef HAVE_SSE4_1
- E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
-#else
- E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
-#endif
- debug15(print_vector_8(E_c_gap,clo,r,"E_c_gap"));
- debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c load"));
+ debug15(print_vector_16(E_mask,rlo,c,"E_mask"));
+ E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
/* EGAP */
- T1 = _mm_adds_epi8(H_nogap_c, gap_open);
- dir_vert = _mm_cmplt_epi8(E_c_gap,T1); /* E < H */
- dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
- _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
- debug15(print_vector_8(T1,clo,r,"T1"));
- debug15(print_vector_8(dir_vert,clo,r,"dir_Egap"));
+ T1 = _mm_adds_epi16(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmplt_epi16(E_r_gap,T1); /* E < H */
+ dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+ debug15(print_vector_16(T1,rlo,c,"T1"));
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
-#ifdef HAVE_SSE4_1
- E_c_gap = _mm_max_epi8(E_c_gap, T1); /* Compare H + open with horiz */
- E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
- E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
-#elif 1
- E_c_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
- E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
- E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
-#else
- /* Try to avoid unnecessary shifts by 128, but overflows */
- E_c_gap = _mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128));
- E_c_gap = _mm_add_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (horiz + open) */
- E_c_gap = _mm_sub_epi8(_mm_min_epu8(E_c_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
-#endif
- debug15(print_vector_8(E_c_gap,clo,r,"E"));
+ E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_c,LAST_CHAR);
- H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_CHAR);
- H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
+ H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
- /* Add pairscores. No alternate chars for query sequence */
-#ifdef HAVE_SSE4_1
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
- debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
- H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_std);
-#else
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo])); /* Has 128 added already */
- pairscores_best = _mm_sub_epi8(pairscores_std, all_128);
- debug15(print_vector_8(pairscores_best,clo,r,"pairscores_std"));
- H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_best);
-#endif
- _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_8(H_nogap_c,clo,r,"H"));
-
- dir_vert = _mm_cmplt_epi8(E_c_gap,H_nogap_c); /* E < H */
- dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
- _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
- debug15(print_vector_8(dir_vert,clo,r,"dir_nogap"));
+ /* Add pairscores, allowing for alternate genomic nt */
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
+ dir_horiz = _mm_cmplt_epi16(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
-#ifdef HAVE_SSE4_1
- H_nogap_c = _mm_max_epi8(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
-#else
- /* Compare H + pairscores with horiz + extend */
- H_nogap_c = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_c, all_128), _mm_add_epi8(E_c_gap, all_128)), all_128);
-#endif
- debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c store"));
- _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+ H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
- /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
- if (chigh >= r) {
- (*directions_Egap)[r][r] = DIAG;
- (*directions_nogap)[r][r] = DIAG;
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
}
/* No need for F loop here */
- E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ E_mask = _mm_slli_si128(E_mask,ONE_SHORT);
}
}
} else {
/* jump early */
- for (clo = 0; clo <= glength; clo += SIMD_NCHARS) {
- if ((chigh = clo + SIMD_NCHARS - 1) > glength) {
- chigh = glength;
+ for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS_NONAVX2) {
+ if ((rhigh = rlo + SIMD_NSHORTS_NONAVX2 - 1) > rlength) {
+ rhigh = rlength;
}
- /* dir_vert tests if E > H. To fill in first row of each
- column block with non-diags, make E > H. */
- E_mask = _mm_set1_epi8(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_c_gap = _mm_set1_epi8(-extend);
- H_nogap_c = _mm_set1_epi8(-open-extend-1);
-#else
- E_c_gap = _mm_set1_epi8(NEG_INFINITY_8+1);
- H_nogap_c = _mm_set1_epi8(NEG_INFINITY_8-open); /* Compensate for T1 = H + open */
-#endif
+ /* dir_horiz tests if E > H. To fill in first column of each
+ row block with non-diags, could make E > H. But irrelevant,
+ because these are above the diagonal. */
+ E_mask = _mm_set1_epi16(1);
- for (r = clo; r <= chigh + lband && r <= rlength; r++) {
- score_column = matrix[r];
+ E_r_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
+ H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
- if (r == 0) {
- na1 = 4; /* 'N' */
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
+ score_column = matrix[c];
+
+ if (c == 0) {
+ na2 = na2_alt = 4; /* 'N' */
} else {
- na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
}
- pairscores_ptr = pairscores[na1];
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
- if (r == 0) {
- X_prev_nogap = _mm_set1_epi8(0);
- } else if (clo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi8(0);
+ if (c == 0) {
+ X_prev_nogap = _mm_set1_epi16(0);
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _mm_set1_epi16(0);
#else
- X_prev_nogap = _mm_set1_epi8(NEG_INFINITY_8); /* works if we start outside the clo bounds */
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
} else {
- /* second or greater block of 8 */
- X_prev_nogap = _mm_set1_epi8(matrix[r-1][clo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_CHAR);
+ /* second or greater block of 16 */
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
- debug15(print_vector_8(E_mask,clo,r,"E_mask"));
-#ifdef HAVE_SSE4_1
- E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
-#else
- E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
-#endif
- debug15(print_vector_8(E_c_gap,clo,r,"E_c_gap"));
- debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c load"));
+ debug15(print_vector_16(E_mask,rlo,c,"E_mask"));
+ E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
/* EGAP */
- T1 = _mm_adds_epi8(H_nogap_c, gap_open);
- dir_vert = _mm_cmpgt_epi8(E_c_gap,T1); /* E > H, for jump early */
- _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
- debug15(print_vector_8(T1,clo,r,"T1"));
- debug15(print_vector_8(dir_vert,clo,r,"dir_Egap"));
+ T1 = _mm_adds_epi16(H_nogap_r, gap_open);
+ dir_horiz = _mm_cmpgt_epi16(E_r_gap,T1); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+ debug15(print_vector_16(T1,rlo,c,"T1"));
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
- /* Compare H + open with vert */
-#ifdef HAVE_SSE4_1
- E_c_gap = _mm_max_epi8(E_c_gap, T1); /* Compare H + open with vert */
- E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_c_gap = _mm_min_epi8(E_c_gap,_mm_add_epi8(E_mask,E_infinity));
-#elif 1
- E_c_gap = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128)), all_128);
- E_c_gap = _mm_adds_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_c_gap = _mm_sub_epi8(_mm_min_epu8(_mm_add_epi8(E_c_gap, all_128),_mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
-#else
- /* Try to avoid unnecessary shifts by 128, but overflows */
- E_c_gap = _mm_max_epu8(_mm_add_epi8(E_c_gap, all_128), _mm_add_epi8(T1, all_128));
- E_c_gap = _mm_add_epi8(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_c_gap = _mm_sub_epi8(_mm_min_epu8(E_c_gap, _mm_add_epi8(E_mask,E_infinity_plus_128)), all_128);
-#endif
- debug15(print_vector_8(E_c_gap,clo,r,"E"));
+ E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_c,LAST_CHAR);
- H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_CHAR);
- H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
- X_prev_nogap = T1;
-
- /* Add pairscores. No alternate chars for query sequence */
-#ifdef HAVE_SSE4_1
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
- debug15(print_vector_8(pairscores_std,clo,r,"pairscores_std"));
- H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_std);
-#else
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo])); /* Has 128 added already */
- pairscores_best = _mm_sub_epi8(pairscores_std, all_128);
- debug15(print_vector_8(pairscores_best,clo,r,"pairscores_std"));
- H_nogap_c = _mm_adds_epi8(H_nogap_c, pairscores_best);
-#endif
- _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_8(H_nogap_c,clo,r,"H"));
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_NONAVX2);
+ H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
+ H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ X_prev_nogap = T1;
- dir_vert = _mm_cmpgt_epi8(E_c_gap,H_nogap_c); /* E > H, for jump early */
- _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
- debug15(print_vector_8(dir_vert,clo,r,"dir_nogap"));
+ /* Add pairscores, allowing for alternate genomic nt */
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
+ dir_horiz = _mm_cmpgt_epi16(E_r_gap,H_nogap_r); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
-#ifdef HAVE_SSE4_1
- H_nogap_c = _mm_max_epi8(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
-#else
- /* Compare H + pairscores with horiz + extend */
- H_nogap_c = _mm_sub_epi8(_mm_max_epu8(_mm_add_epi8(H_nogap_c, all_128), _mm_add_epi8(E_c_gap, all_128)), all_128);
-#endif
- debug15(print_vector_8(H_nogap_c,clo,r,"H_nogap_c store"));
- _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+ H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
- /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
- if (chigh >= r) {
- (*directions_Egap)[r][r] = DIAG;
- (*directions_nogap)[r][r] = DIAG;
+
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
}
/* No need for F loop here */
- E_mask = _mm_slli_si128(E_mask,ONE_CHAR);
+ E_mask = _mm_slli_si128(E_mask,ONE_SHORT);
}
}
}
@@ -2948,50 +7439,26 @@ Dynprog_simd_8_lower (Direction8_T ***directions_nogap, Direction8_T ***directio
#ifdef CHECK1
/* Row 0 and column 0 directions fail anyway due to saturation */
/* Handle (0,1) and (1,0) directions, otherwise DIAG */
- (*directions_Egap)[1][0] = VERT;
+ (*directions_Egap)[1][0] = HORIZ;
#endif
#ifdef DEBUG2
- printf("SIMD: Dynprog_simd_8_lower\n");
- Matrix8_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,/*upperp*/false);
- Directions8_print_ud(*directions_nogap,*directions_Egap,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,/*upperp*/false);
+ printf("SIMD: Dynprog_simd_16_upper\n");
+ Matrix16_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+ Directions16_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
#endif
-
+
#ifdef CHECK1
- /* Check for column 0 directions */
- for (r = 1; r <= lband && r <= rlength; r++) {
- assert((*directions_Egap)[r][0] != DIAG);
- assert((*directions_nogap)[r][0] != DIAG);
+ /* Check for row 0 directions */
+ for (c = 1; c <= uband && c <= glength; c++) {
+ assert((*directions_Egap)[c][0] != DIAG);
+ assert((*directions_nogap)[c][0] != DIAG);
}
#endif
-#ifdef DEBUG14
- matrix_std = compute_scores_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
- this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
- rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
- open,extend,lband,uband,jump_late_p,revp);
-
-#ifdef DEBUG2
- printf("Banded %s\n",revp ? "rev" : "fwd");
- Matrix32_print(matrix_std,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
- Directions32_print(directions_nogap_std,directions_Egap_std,directions_Fgap_std,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
-#endif
-
- banded_matrix8_compare(matrix,matrix_std,rlength,glength,lband,uband,
- rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp);
-
- banded_directions8_compare_nogap(matrix,*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
-
- banded_directions8_compare_Egap(matrix,*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
-#endif
-
_mm_free(pairscores[4]);
_mm_free(pairscores[3]);
_mm_free(pairscores[2]);
@@ -3004,38 +7471,49 @@ Dynprog_simd_8_lower (Direction8_T ***directions_nogap, Direction8_T ***directio
#ifdef HAVE_SSE2
-/* Modified from Dynprog_simd_16_upper. Operates by columns. */
+/* Designed for computation above the diagonal, so no F loop or bottom masking needed */
+/* Operates by columns */
Score16_T **
-Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
- Direction16_T ***directions_Fgap,
- T this, char *rsequence, char *gsequence, char *gsequence_alt,
- int rlength, int glength,
-#ifdef DEBUG14
- int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
- Mismatchtype_T mismatchtype, int open, int extend,
- int lband, int uband, bool jump_late_p, bool revp) {
- int c_gap, last_nogap, score, *FF; /* Need to have the ability to go past NEG_INFINITY */
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int uband, bool jump_late_p, bool revp) {
Score16_T **matrix, *score_column;
+#ifdef HAVE_AVX2
+ __m256i pairscores_std, pairscores_alt;
+ __m256i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, E_infinity, T1;
+ __m256i gap_open, gap_extend, complement_dummy;
+ __m256i dir_horiz;
+ Score16_T save;
+#else
__m128i pairscores_std, pairscores_alt;
- __m128i H_nogap_r, X_prev_nogap, E_r_gap, T1;
+ __m128i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, E_infinity, T1;
__m128i gap_open, gap_extend, complement_dummy;
__m128i dir_horiz;
- int rlength_ceil, lband_ceil, r, c;
- int rlo, rhigh, rlo_calc, rhigh_calc;
+#endif
+ int rlength_ceil, r, c;
+ int rlo, rhigh;
int na1, na2, na2_alt;
- Score16_T *pairscores_col0;
- Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore, pairscore0;
+ Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr;
Pairdistance_T **pairdistance_array_type;
-#ifdef DEBUG14
+#ifdef DEBUG_AVX2
+ Score16_T **matrix_std;
+ Direction16_T **directions_nogap_std, **directions_Egap_std;
+ char na2_single;
+#elif defined(DEBUG_SIMD)
Score32_T **matrix_std;
Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
+ char na2_single;
#endif
- debug2(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- debug15(printf("Dynprog_simd_16. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug2(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
rlength_ceil = (int) ((rlength + SIMD_NSHORTS)/SIMD_NSHORTS) * SIMD_NSHORTS;
pairdistance_array_type = pairdistance_array[mismatchtype];
@@ -3045,14 +7523,11 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
debug(printf("Query length rounded up to %d\n",rlength_ceil));
matrix = aligned_score16_alloc(rlength_ceil,glength,
- this->aligned.one.matrix_ptrs,this->aligned.one.matrix_space);
+ this->aligned.two.upper_matrix_ptrs,this->aligned.two.upper_matrix_space);
*directions_nogap = aligned_directions16_alloc(rlength_ceil,glength,
- this->aligned.one.directions_ptrs_0,this->aligned.one.directions_space_0);
+ this->aligned.two.upper_directions_ptrs_0,this->aligned.two.upper_directions_space_0);
*directions_Egap = aligned_directions16_alloc(rlength_ceil,glength,
- this->aligned.one.directions_ptrs_1,this->aligned.one.directions_space_1);
- /* Need to calloc to save time in F loop */
- *directions_Fgap = aligned_directions16_calloc(rlength_ceil,glength,
- this->aligned.one.directions_ptrs_2,this->aligned.one.directions_space_2);
+ this->aligned.two.upper_directions_ptrs_1,this->aligned.two.upper_directions_space_1);
#if 0
/* Row 0 initialization */
@@ -3079,14 +7554,11 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
/* Load pairscores. Store match - mismatch */
- pairscores[0] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[1] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[2] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[3] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[4] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
-
- lband_ceil = (int) ((lband + SIMD_NSHORTS)/SIMD_NSHORTS) * SIMD_NSHORTS;
- pairscores_col0 = (Score16_T *) _mm_malloc(lband_ceil * sizeof(Score16_T),16);
+ pairscores[0] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[1] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[2] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[3] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[4] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),ALIGN_SIZE);
#if 0
/* Should not be necessary */
@@ -3097,19 +7569,6 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score16_T));
#endif
-
- pairscores_col0[0] = (Score16_T) 0;
- /* Initialization just to lband causes errors in dir_horiz for Egap */
-#ifdef NO_INITIAL_GAP_PENALTY
- for (r = 1; r < lband_ceil; r++) {
- pairscores_col0[r] = (Score16_T) 0;
- }
-#else
- for (r = 1; r < lband_ceil; r++) {
- pairscores_col0[r] = (Score16_T) NEG_INFINITY_16;
- }
-#endif
-
r = 0; na1 = 'N';
pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
@@ -3146,13 +7605,12 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
#endif
- complement_dummy = _mm_set1_epi16(-1);
+ complement_dummy = _MM_SET1_EPI16(-1);
- FF = (int *) MALLOCA((glength + 1) * sizeof(int));
-
- gap_open = _mm_set1_epi16((Score16_T) open);
- gap_extend = _mm_set1_epi16((Score16_T) extend);
+ gap_open = _MM_SET1_EPI16((Score16_T) open);
+ gap_extend = _MM_SET1_EPI16((Score16_T) extend);
+ E_infinity = _MM_SET1_EPI16(POS_INFINITY_16);
if (jump_late_p) {
for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS) {
if ((rhigh = rlo + SIMD_NSHORTS - 1) > rlength) {
@@ -3160,168 +7618,128 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
}
/* dir_horiz tests if E >= H. To fill in first column of each
- row block with non-diags, make E == H. */
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi16(-extend);
- H_nogap_r = _mm_set1_epi16(-open-extend);
-#else
- E_r_gap = _mm_set1_epi16(NEG_INFINITY_16);
- H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
-#endif
+ row block with non-diags, could make E == H. But irrelevant,
+ because these are above the diagonal. */
+ E_mask = _MM_SET1_EPI16(1);
- if ((c = rlo - lband) < 0) {
- c = 0;
- }
- for ( ; c <= rhigh + uband && c <= glength; c++) {
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16);
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
+
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
score_column = matrix[c];
if (c == 0) {
- pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
- if (rlo == 0) {
- X_prev_nogap = _mm_set1_epi16(0);
- } else {
- X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
- }
+ na2 = na2_alt = 4; /* 'N' */
} else {
- na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
- na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
- pairscores_std_ptr = pairscores[na2];
- pairscores_alt_ptr = pairscores[na2_alt];
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ }
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
- if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi16(0);
+ if (c == 0) {
+ X_prev_nogap = _MM_SETZERO_SI();
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
#else
- X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+#endif
+ } else {
+ /* second or greater block of 16 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_SHORT_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
- } else {
- /* second or greater block of 16 */
- X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
- }
}
+ debug15(print_vector_16(E_mask,rlo,c,"E_mask"));
+ E_r_gap = _MM_MIN_EPI16(E_r_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
/* EGAP */
- T1 = _mm_adds_epi16(H_nogap_r, gap_open);
- dir_horiz = _mm_cmplt_epi16(E_r_gap,T1); /* E < H */
- dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
+ T1 = _MM_ADDS_EPI16(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPLT_EPI16(E_r_gap,T1); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#else
_mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#endif
debug15(print_vector_16(T1,rlo,c,"T1"));
debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
- E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
- E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _MM_MAX_EPI16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _MM_ADDS_EPI16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _MM_MIN_EPI16(E_r_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT);
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi16(_mm256_setzero_si256(),_mm256_extract_epi16(H_nogap_r,SIMD_NSHORTS-1),LAST_SHORT_INSERT);
+ X_prev_nogap = _mm256_insert_epi16(X_prev_nogap,_mm256_extract_epi16(H_nogap_r,MID_SHORT_INSERT-1),MID_SHORT_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_SHORT);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_SHIFT);
H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
- H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm256_adds_epi16(H_nogap_r, _mm256_max_epi16(pairscores_std,pairscores_alt));
+#else
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
- _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
-
- dir_horiz = _mm_cmplt_epi16(E_r_gap,H_nogap_r); /* E < H */
- dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
- _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
-
- H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
- debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
- _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
-
-
- /* F loop */
- if ((rlo_calc = rlo) <= c - uband) {
- rlo_calc = c - uband;
- }
- if ((rhigh_calc = rhigh) >= c + lband) {
- rhigh_calc = c + lband;
- if (c > 0) {
- /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
- pairscore = pairscores[na2][rhigh_calc];
- if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
- pairscore = pairscore0;
- }
- /* No need to fix for non-SSE4.1: pairscore -= 128; */
- if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_16) {
- score_column[rhigh_calc] = NEG_INFINITY_16; /* Saturation */
- } else if (score > POS_INFINITY_16) {
- score_column[rhigh_calc] = POS_INFINITY_16; /* Saturation */
- } else {
- score_column[rhigh_calc] = (Score16_T) score;
- }
- (*directions_Egap)[c][rhigh_calc] = DIAG;
- (*directions_nogap)[c][rhigh_calc] = DIAG;
- }
- }
-
- debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
- rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
-
- if (rlo == 0) {
- c_gap = NEG_INFINITY_INT;
- last_nogap = NEG_INFINITY_INT;
- } else if (c >= rlo + uband) {
- c_gap = NEG_INFINITY_INT;
- last_nogap = NEG_INFINITY_INT;
- } else {
- debug3(printf("At c %d, uband %d, reading c_gap %d\n",c,uband,FF[c]));
- c_gap = FF[c];
- last_nogap = (int) score_column[rlo_calc-1];
- }
-
- if ((r = rlo_calc) == c - uband) {
- /* Handle top value as a special case to prevent going outside of uband */
- /* FGAP */
- debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
- r,c,c_gap + extend,last_nogap + open + extend));
- score = last_nogap + open /* + extend */;
- c_gap = score + extend;
- /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
+ H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
+#endif
+ _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
- /* NOGAP */
- last_nogap = (int) score_column[r];
- r++;
- }
+ dir_horiz = _MM_CMPLT_EPI16(E_r_gap,H_nogap_r); /* E < H */
+ dir_horiz = _MM_ANDNOT_SI(dir_horiz,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
+ _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#endif
+ debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
- /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
- for ( ; r <= rhigh_calc; r++) {
- /* FGAP */
- debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
- r,c,c_gap + extend,last_nogap + open + extend));
- if (c_gap /* + extend */ >= (score = last_nogap + open /* + extend */)) { /* Use >= for jump late */
- c_gap += extend;
- (*directions_Fgap)[c][r] = VERT;
- } else {
- c_gap = score + extend;
- /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
- }
-
- /* NOGAP */
- last_nogap = (int) score_column[r];
- debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
- if (c_gap >= last_nogap) { /* Use >= for jump late */
- last_nogap = c_gap;
- score_column[r] = (c_gap < NEG_INFINITY_16) ? NEG_INFINITY_16 : (Score16_T) c_gap; /* Saturation */
- (*directions_nogap)[c][r] = VERT;
- }
+ H_nogap_r = _MM_MAX_EPI16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
+ _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
+
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
}
- FF[c] = c_gap;
- debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
- H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+ /* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi16(E_mask,7);
+ E_mask = _mm256_slli_si256(E_mask,ONE_SHORT);
+ E_mask = _mm256_insert_epi16(E_mask,save,8);
+#else
+ E_mask = _mm_slli_si128(E_mask,ONE_SHORT);
+#endif
}
}
@@ -3333,185 +7751,141 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
}
/* dir_horiz tests if E > H. To fill in first column of each
- row block with non-diags, make E > H. */
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi16(-extend);
- H_nogap_r = _mm_set1_epi16(-open-extend-1);
-#else
- E_r_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
- H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
-#endif
+ row block with non-diags, could make E > H. But irrelevant,
+ because these are above the diagonal. */
+ E_mask = _MM_SET1_EPI16(1);
- if ((c = rlo - lband) < 0) {
- c = 0;
- }
- for ( ; c <= rhigh + uband && c <= glength; c++) {
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_r_gap = _MM_SET1_EPI16(NEG_INFINITY_16+1);
+ H_nogap_r = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
+
+ for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
score_column = matrix[c];
if (c == 0) {
- pairscores_std_ptr = pairscores_alt_ptr = pairscores_col0;
- if (rlo == 0) {
- X_prev_nogap = _mm_set1_epi16(0);
- } else {
- X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
- }
+ na2 = na2_alt = 4; /* 'N' */
} else {
- na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
- na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
- pairscores_std_ptr = pairscores[na2];
- pairscores_alt_ptr = pairscores[na2_alt];
+ na2 = revp ? nt_to_int_array[(int) gsequence[1-c]] : nt_to_int_array[(int) gsequence[c-1]];
+ na2_alt = revp ? nt_to_int_array[(int) gsequence_alt[1-c]] : nt_to_int_array[(int) gsequence_alt[c-1]];
+ }
+ pairscores_std_ptr = pairscores[na2];
+ pairscores_alt_ptr = pairscores[na2_alt];
- if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi16(0);
+ if (c == 0) {
+ X_prev_nogap = _MM_SETZERO_SI();
+ } else if (rlo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
#else
- X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16);
+ X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+#endif
+ } else {
+ /* second or greater block of 16 */
+#ifdef HAVE_AVX2
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),matrix[c-1][rlo-1],LAST_SHORT_INSERT);
+#else
+ X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
- } else {
- /* second or greater block of 16 */
- X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
- }
}
+ debug15(print_vector_16(E_mask,rlo,c,"E_mask"));
+ E_r_gap = _MM_MIN_EPI16(E_r_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
/* EGAP */
- T1 = _mm_adds_epi16(H_nogap_r, gap_open);
- dir_horiz = _mm_cmpgt_epi16(E_r_gap,T1); /* E > H, for jump early */
+ T1 = _MM_ADDS_EPI16(H_nogap_r, gap_open);
+ dir_horiz = _MM_CMPGT_EPI16(E_r_gap,T1); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#else
_mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
+#endif
debug15(print_vector_16(T1,rlo,c,"T1"));
debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
- E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
- E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _MM_MAX_EPI16(E_r_gap, T1); /* Compare H + open with vert */
+ E_r_gap = _MM_ADDS_EPI16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_r_gap = _MM_MIN_EPI16(E_r_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_r_gap,rlo,c,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT);
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi16(_mm256_setzero_si256(),_mm256_extract_epi16(H_nogap_r,SIMD_NSHORTS-1),LAST_SHORT_INSERT);
+ X_prev_nogap = _mm256_insert_epi16(X_prev_nogap,_mm256_extract_epi16(H_nogap_r,MID_SHORT_INSERT-1),MID_SHORT_INSERT);
+ H_nogap_r = _mm256_slli_si256(H_nogap_r,ONE_SHORT);
+#else
+ T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT_SHIFT);
H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
- H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+#endif
+ H_nogap_r = _MM_OR_SI(H_nogap_r, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores, allowing for alternate genomic nt */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_std_ptr[rlo]));
+ pairscores_alt = _mm256_load_si256((__m256i *) &(pairscores_alt_ptr[rlo]));
+ H_nogap_r = _mm256_adds_epi16(H_nogap_r, _mm256_max_epi16(pairscores_std,pairscores_alt));
+#else
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
+#endif
_mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
- dir_horiz = _mm_cmpgt_epi16(E_r_gap,H_nogap_r); /* E > H, for jump early */
+ dir_horiz = _MM_CMPGT_EPI16(E_r_gap,H_nogap_r); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#else
_mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
+#endif
debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
- H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
+ H_nogap_r = _MM_MAX_EPI16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[rlo]), H_nogap_r);
+#else
_mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+#endif
-
- /* F loop */
- if ((rlo_calc = rlo) < c - uband) {
- rlo_calc = c - uband;
- }
- if ((rhigh_calc = rhigh) >= c + lband) {
- rhigh_calc = c + lband;
- if (c > 0) {
- /* Set bottom values to DIAG (not HORIZ) to prevent going outside of lband */
- pairscore = pairscores[na2][rhigh_calc];
- if ((pairscore0 = pairscores[(int) na2_alt][rhigh_calc]) > pairscore) {
- pairscore = pairscore0;
- }
- /* No need to fix for non-SSE4.1: pairscore -= 128; */
- if ((score = (int) matrix[c-1][rhigh_calc-1] + (int) pairscore) < NEG_INFINITY_16) {
- score_column[rhigh_calc] = NEG_INFINITY_16; /* Saturation */
- } else if (score > POS_INFINITY_16) {
- score_column[rhigh_calc] = POS_INFINITY_16; /* Saturation */
- } else {
- score_column[rhigh_calc] = (Score16_T) score;
- }
- (*directions_Egap)[c][rhigh_calc] = DIAG;
- (*directions_nogap)[c][rhigh_calc] = DIAG;
- }
- }
-
- debug3(printf("F loop: rlo %d, rhigh %d, c %d, lband %d, uband %d => rlo_calc %d, rhigh_calc %d\n",
- rlo,rhigh,rlo_calc,c,lband,uband,rhigh_calc));
-
- if (rlo == 0) {
- c_gap = NEG_INFINITY_INT;
- last_nogap = NEG_INFINITY_INT;
- } else if (c >= rlo + uband) {
- c_gap = NEG_INFINITY_INT;
- last_nogap = NEG_INFINITY_INT;
- } else {
- c_gap = FF[c];
- last_nogap = (int) score_column[rlo_calc-1];
- }
-
- if ((r = rlo_calc) == c - uband) {
- /* Handle top value as a special case to prevent going outside of uband */
- /* FGAP */
- debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
- r,c,c_gap + extend,last_nogap + open + extend));
- score = last_nogap + open /* + extend */;
- c_gap = score + extend;
- /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
-
- /* NOGAP */
- last_nogap = (int) score_column[r];
- r++;
- }
-
- /* score_ptr = &(score_column[rlo_calc]); -- Also possible, but less transparent */
- for ( ; r <= rhigh_calc; r++) {
- /* FGAP */
- debug3(printf("Fgap at r %d, c %d: c_gap + extend %d vs last_nogap + open + extend %d\n",
- r,c,c_gap + extend,last_nogap + open + extend));
- if (c_gap /* + extend */ > (score = last_nogap + open /* + extend */)) { /* Use > for jump early */
- c_gap += extend;
- (*directions_Fgap)[c][r] = VERT;
- } else {
- c_gap = score + extend;
- /* (*directions_Fgap)[c][r] = DIAG: -- Already initialized to DIAG */
- }
-
- /* NOGAP */
- last_nogap = (int) score_column[r];
- debug3(printf("assign nogap at r %d, c %d: H/E %d vs vert + extend %d\n",r,c,last_nogap,c_gap));
- if (c_gap > last_nogap) { /* Use > for jump early */
- last_nogap = c_gap;
- score_column[r] = (c_gap < NEG_INFINITY_16) ? NEG_INFINITY_16 : (Score16_T) c_gap; /* Saturation */
- (*directions_nogap)[c][r] = VERT;
- }
+ /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
+ if (rhigh >= c) {
+ (*directions_Egap)[c][c] = DIAG;
+ (*directions_nogap)[c][c] = DIAG;
}
- FF[c] = c_gap;
- debug3(printf("At c %d, storing c_gap %d\n",c,FF[c]));
- H_nogap_r = _mm_load_si128((__m128i *) &(score_column[rlo])); /* Need to reload because of changes by F loop */
+ /* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi16(E_mask,7);
+ E_mask = _mm256_slli_si256(E_mask,ONE_SHORT);
+ E_mask = _mm256_insert_epi16(E_mask,save,8);
+#else
+ E_mask = _mm_slli_si128(E_mask,ONE_SHORT);
+#endif
}
}
}
-
#ifdef CHECK1
/* Row 0 and column 0 directions fail anyway due to saturation */
/* Handle (0,1) and (1,0) directions, otherwise DIAG */
(*directions_Egap)[1][0] = HORIZ;
- (*directions_Fgap)[0][1] = VERT;
#endif
-
#ifdef DEBUG2
- printf("SIMD: Dynprog_simd_16\n");
- Matrix16_print(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
- Directions16_print(*directions_nogap,*directions_Egap,*directions_Fgap,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
+ printf("SIMD: Dynprog_simd_16_upper\n");
+ Matrix16_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+ Directions16_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
#endif
#ifdef CHECK1
@@ -3520,105 +7894,96 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
assert((*directions_Egap)[c][0] != DIAG);
assert((*directions_nogap)[c][0] != DIAG);
}
- /* Check for column 0 directions */
- for (r = 1; r <= lband && r <= rlength; r++) {
- assert((*directions_Fgap)[0][r] != DIAG);
- assert((*directions_nogap)[0][r] != DIAG);
- }
#endif
-#ifdef DEBUG14
- matrix_std = compute_scores_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
- this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
- rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
- open,extend,lband,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_16);
+#ifdef DEBUG_AVX2
+ matrix_std = Dynprog_simd_16_upper_nonavx2(&directions_nogap_std,&directions_Egap_std,
+ this,rsequence,gsequence,gsequence_alt,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,uband,jump_late_p,revp);
+#elif defined(DEBUG_SIMD)
+ matrix_std = Dynprog_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+ rlength,glength,
+ goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,/*lband*/0,uband,jump_late_p,revp,/*saturation*/NEG_INFINITY_16,
+ /*upperp*/true,/*lowerp*/false);
+#endif
#ifdef DEBUG2
printf("Banded\n");
- Dynprog_Matrix32_print(matrix_std,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
- Dynprog_Directions32_print(directions_nogap_std,directions_Egap_std,directions_Fgap_std,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,lband,uband);
+ Matrix16_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,uband,/*upperp*/true);
+ Directions16_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,revp,uband,/*upperp*/true);
#endif
- banded_matrix16_compare(matrix,matrix_std,rlength,glength,lband,uband,
- rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp);
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ banded_matrix16_compare_upper(matrix,matrix_std,rlength,glength,uband,
+ rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp);
- banded_directions16_compare_nogap(*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
- banded_directions16_compare_Egap(*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
- banded_directions16_compare_Fgap(*directions_Fgap,directions_Fgap_std,rlength,glength,lband,uband);
+ banded_directions16_compare_nogap_upper(*directions_nogap,directions_nogap_std,rlength,glength,uband);
+
+ banded_directions16_compare_Egap_upper(*directions_Egap,directions_Egap_std,rlength,glength,uband);
#endif
- FREEA(FF);
- _mm_free(pairscores_col0);
_mm_free(pairscores[4]);
_mm_free(pairscores[3]);
_mm_free(pairscores[2]);
_mm_free(pairscores[1]);
_mm_free(pairscores[0]);
- return matrix;
- }
-#endif
-
-
-
-#ifdef HAVE_SSE2
-/* Designed for computation above the diagonal, so no F loop or bottom masking needed */
-/* Operates by columns */
-Score16_T **
-Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
- T this, char *rsequence, char *gsequence, char *gsequence_alt,
- int rlength, int glength,
-#ifdef DEBUG14
- int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
-#endif
- Mismatchtype_T mismatchtype, int open, int extend,
- int uband, bool jump_late_p, bool revp) {
- Score16_T **matrix, *score_column;
- __m128i pairscores_std, pairscores_alt;
- __m128i H_nogap_r, X_prev_nogap, E_r_gap, E_mask, E_infinity, T1;
- __m128i gap_open, gap_extend, complement_dummy;
- __m128i dir_horiz;
- int rlength_ceil, r, c;
- int rlo, rhigh;
- int na1, na2, na2_alt;
- Score16_T *pairscores[5], *pairscores_std_ptr, *pairscores_alt_ptr, pairscore;
- Pairdistance_T **pairdistance_array_type;
-
-#ifdef DEBUG14
- Score32_T **matrix_std;
- Direction32_T **directions_nogap_std, **directions_Egap_std;
- char na2_single;
+ return matrix;
+}
#endif
- debug2(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
- debug15(printf("Dynprog_simd_16_upper. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+#ifdef DEBUG_AVX2
+/* Designed for computation below the diagonal, so no F loop or bottom masking needed */
+/* Operates by rows */
+Score16_T **
+Dynprog_simd_16_lower_nonavx2 (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
+ T this, char *rsequence, char *gsequence, char *gsequence_alt,
+ int rlength, int glength,
+ int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
+ Mismatchtype_T mismatchtype, int open, int extend,
+ int lband, bool jump_late_p, bool revp) {
+ Score16_T **matrix, *score_column;
+ __m128i pairscores_std;
+ __m128i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, E_infinity, T1;
+ __m128i gap_open, gap_extend, complement_dummy;
+ __m128i dir_vert;
+ int glength_ceil, r, c;
+ int clo, chigh;
+ int na1, na2, na2_alt;
+ Score16_T *pairscores[5], *pairscores_ptr, pairscore;
+ Pairdistance_T **pairdistance_array_type, score1, score2;
- rlength_ceil = (int) ((rlength + SIMD_NSHORTS)/SIMD_NSHORTS) * SIMD_NSHORTS;
+ debug2(printf("Dynprog_simd_16_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+ debug15(printf("Dynprog_simd_16_lower. jump_late_p %d, open %d, extend %d\n",jump_late_p,open,extend));
+
+ glength_ceil = (int) ((glength + SIMD_NSHORTS_NONAVX2)/SIMD_NSHORTS_NONAVX2) * SIMD_NSHORTS_NONAVX2;
pairdistance_array_type = pairdistance_array[mismatchtype];
- debug(printf("compute_scores_simd_16_bycols (upper): "));
- debug(printf("Lengths are %d and %d, so band is %d on right\n",rlength,glength,uband));
- debug(printf("Query length rounded up to %d\n",rlength_ceil));
+ debug(printf("compute_scores_simd_16_byrows (lower): "));
+ debug(printf("Lengths are %d and %d, so band is %d on left\n",rlength,glength,lband));
+ debug(printf("Genome length rounded up to %d\n",glength_ceil));
- matrix = aligned_score16_alloc(rlength_ceil,glength,
- this->aligned.two.upper_matrix_ptrs,this->aligned.two.upper_matrix_space);
- *directions_nogap = aligned_directions16_alloc(rlength_ceil,glength,
- this->aligned.two.upper_directions_ptrs_0,this->aligned.two.upper_directions_space_0);
- *directions_Egap = aligned_directions16_alloc(rlength_ceil,glength,
- this->aligned.two.upper_directions_ptrs_1,this->aligned.two.upper_directions_space_1);
+ matrix = aligned_score16_alloc(glength_ceil,rlength,
+ this->aligned_std.two.lower_matrix_ptrs,this->aligned_std.two.lower_matrix_space);
+ *directions_nogap = aligned_directions16_alloc(glength_ceil,rlength,
+ this->aligned_std.two.lower_directions_ptrs_0,this->aligned_std.two.lower_directions_space_0);
+ *directions_Egap = aligned_directions16_alloc(glength_ceil,rlength,
+ this->aligned_std.two.lower_directions_ptrs_1,this->aligned_std.two.lower_directions_space_1);
#if 0
- /* Row 0 initialization */
+ /* Column 0 initialization */
/* penalty = open; */
- for (c = 1; c <= uband && c <= glength; c++) {
+ for (r = 1; r <= lband && r <= rlength; r++) {
/* penalty += extend; */
- (*directions_Egap)[c][0] = HORIZ;
- (*directions_nogap)[c][0] = HORIZ;
+ (*directions_Egap)[r][0] = VERT;
+ (*directions_nogap)[r][0] = VERT;
}
#endif
#if 0
@@ -3627,164 +7992,188 @@ Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***direc
(*directions_nogap)[0][0] = DIAG; /* previously used STOP */
#endif
#if 0
- /* Column 0 initialization */
+ /* Row 0 initialization */
/* penalty = open; */
- for (r = 1; r <= SIMD_NSHORTS && r <= rlength; r++) {
+ for (c = 1; c <= SIMD_NSHORTS_NONAVX2 && c <= glength; c++) {
/* penalty += extend; */
- (*directions_nogap)[0][r] = VERT;
+ (*directions_nogap)[0][c] = HORIZ;
}
#endif
/* Load pairscores. Store match - mismatch */
- pairscores[0] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[1] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[2] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[3] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
- pairscores[4] = (Score16_T *) _mm_malloc(rlength_ceil * sizeof(Score16_T),16);
+ pairscores[0] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
+ pairscores[1] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
+ pairscores[2] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
+ pairscores[3] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
+ pairscores[4] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
#if 0
/* Should not be necessary */
- memset((void *) pairscores[0],0,rlength_ceil*sizeof(Score16_T));
- memset((void *) pairscores[1],0,rlength_ceil*sizeof(Score16_T));
- memset((void *) pairscores[2],0,rlength_ceil*sizeof(Score16_T));
- memset((void *) pairscores[3],0,rlength_ceil*sizeof(Score16_T));
- memset((void *) pairscores[4],0,rlength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[0],0,glength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[1],0,glength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[2],0,glength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[3],0,glength_ceil*sizeof(Score16_T));
+ memset((void *) pairscores[4],0,glength_ceil*sizeof(Score16_T));
#endif
- r = 0; na1 = 'N';
- pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
+ c = 0; na2 = na2_alt = 'N';
+ pairscores[0][c] = (Score16_T) pairdistance_array_type[(int) 'A'][na2];
+ pairscores[1][c] = (Score16_T) pairdistance_array_type[(int) 'C'][na2];
+ pairscores[2][c] = (Score16_T) pairdistance_array_type[(int) 'G'][na2];
+ pairscores[3][c] = (Score16_T) pairdistance_array_type[(int) 'T'][na2];
+ pairscores[4][c] = (Score16_T) pairdistance_array_type[(int) 'N'][na2];
if (revp == false) {
- for (r = 1; r <= rlength; r++) {
- na1 = (int) rsequence[r-1];
- pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
+ for (c = 1; c <= glength; c++) {
+ na2 = gsequence[c-1];
+ na2_alt = gsequence_alt[c-1];
+ /* Take max here */
+ score1 = pairdistance_array_type[(int) 'A'][na2];
+ score2 = pairdistance_array_type[(int) 'A'][na2_alt];
+ pairscores[0][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'C'][na2];
+ score2 = pairdistance_array_type[(int) 'C'][na2_alt];
+ pairscores[1][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'G'][na2];
+ score2 = pairdistance_array_type[(int) 'G'][na2_alt];
+ pairscores[2][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'T'][na2];
+ score2 = pairdistance_array_type[(int) 'T'][na2_alt];
+ pairscores[3][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'N'][na2];
+ score2 = pairdistance_array_type[(int) 'N'][na2_alt];
+ pairscores[4][c] = (Score16_T) (score1 > score2) ? score1 : score2;
}
} else {
- for (r = 1; r <= rlength; r++) {
- na1 = (int) rsequence[1-r];
- pairscores[0][r] = (Score16_T) pairdistance_array_type[na1][(int) 'A'];
- pairscores[1][r] = (Score16_T) pairdistance_array_type[na1][(int) 'C'];
- pairscores[2][r] = (Score16_T) pairdistance_array_type[na1][(int) 'G'];
- pairscores[3][r] = (Score16_T) pairdistance_array_type[na1][(int) 'T'];
- pairscores[4][r] = (Score16_T) pairdistance_array_type[na1][(int) 'N'];
+ for (c = 1; c <= glength; c++) {
+ na2 = gsequence[1-c];
+ na2_alt = gsequence_alt[1-c];
+ /* Take max here */
+ score1 = pairdistance_array_type[(int) 'A'][na2];
+ score2 = pairdistance_array_type[(int) 'A'][na2_alt];
+ pairscores[0][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'C'][na2];
+ score2 = pairdistance_array_type[(int) 'C'][na2_alt];
+ pairscores[1][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'G'][na2];
+ score2 = pairdistance_array_type[(int) 'G'][na2_alt];
+ pairscores[2][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'T'][na2];
+ score2 = pairdistance_array_type[(int) 'T'][na2_alt];
+ pairscores[3][c] = (Score16_T) (score1 > score2) ? score1 : score2;
+
+ score1 = pairdistance_array_type[(int) 'N'][na2];
+ score2 = pairdistance_array_type[(int) 'N'][na2_alt];
+ pairscores[4][c] = (Score16_T) (score1 > score2) ? score1 : score2;
}
}
#if 0
/* Should not be necessary */
- memset((void *) &(pairscores[0][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
- memset((void *) &(pairscores[1][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
- memset((void *) &(pairscores[2][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
- memset((void *) &(pairscores[3][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
- memset((void *) &(pairscores[4][r]),0,(rlength_ceil-r)*sizeof(Score16_T));
+ memset((void *) &(pairscores[0][c]),0,(glength_ceil-c)*sizeof(Score16_T));
+ memset((void *) &(pairscores[1][c]),0,(glength_ceil-c)*sizeof(Score16_T));
+ memset((void *) &(pairscores[2][c]),0,(glength_ceil-c)*sizeof(Score16_T));
+ memset((void *) &(pairscores[3][c]),0,(glength_ceil-c)*sizeof(Score16_T));
+ memset((void *) &(pairscores[4][c]),0,(glength_ceil-c)*sizeof(Score16_T));
#endif
complement_dummy = _mm_set1_epi16(-1);
-
+
gap_open = _mm_set1_epi16((Score16_T) open);
gap_extend = _mm_set1_epi16((Score16_T) extend);
E_infinity = _mm_set1_epi16(POS_INFINITY_16);
if (jump_late_p) {
- for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS) {
- if ((rhigh = rlo + SIMD_NSHORTS - 1) > rlength) {
- rhigh = rlength;
+ for (clo = 0; clo <= glength; clo += SIMD_NSHORTS_NONAVX2) {
+ if ((chigh = clo + SIMD_NSHORTS_NONAVX2 - 1) > glength) {
+ chigh = glength;
}
- /* dir_horiz tests if E >= H. To fill in first column of each
- row block with non-diags, could make E == H. But irrelevant,
- because these are above the diagonal. */
+ /* dir_vert tests if E >= H. To fill in first row of each
+ column block with non-diags, make E == H. */
E_mask = _mm_set1_epi16(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi16(-extend);
- H_nogap_r = _mm_set1_epi16(-open-extend);
-#else
- E_r_gap = _mm_set1_epi16(NEG_INFINITY_16);
- H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
-#endif
- for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
- score_column = matrix[c];
+ E_c_gap = _mm_set1_epi16(NEG_INFINITY_16);
+ H_nogap_c = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
- if (c == 0) {
- na2 = na2_alt = 4; /* 'N' */
+ for (r = clo; r <= chigh + lband && r <= rlength; r++) {
+ score_column = matrix[r];
+
+ if (r == 0) {
+ na1 = 4; /* 'N' */
} else {
- na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
- na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
}
- pairscores_std_ptr = pairscores[na2];
- pairscores_alt_ptr = pairscores[na2_alt];
+ pairscores_ptr = pairscores[na1];
- if (c == 0) {
+ if (r == 0) {
X_prev_nogap = _mm_set1_epi16(0);
- } else if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
+ } else if (clo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
X_prev_nogap = _mm_set1_epi16(0);
#else
X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
} else {
/* second or greater block of 16 */
- X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
+ X_prev_nogap = _mm_set1_epi16(matrix[r-1][clo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
- debug15(print_vector_16(E_mask,rlo,c,"E_mask"));
- E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
- debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
- debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
+ debug15(print_vector_16(E_mask,clo,r,"E_mask"));
+ E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_c_gap,clo,r,"E_c_gap"));
+ debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c load"));
/* EGAP */
- T1 = _mm_adds_epi16(H_nogap_r, gap_open);
- dir_horiz = _mm_cmplt_epi16(E_r_gap,T1); /* E < H */
- dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
- _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
- debug15(print_vector_16(T1,rlo,c,"T1"));
- debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
+ T1 = _mm_adds_epi16(H_nogap_c, gap_open);
+ dir_vert = _mm_cmplt_epi16(E_c_gap,T1); /* E < H */
+ dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+ debug15(print_vector_16(T1,clo,r,"T1"));
+ debug15(print_vector_16(dir_vert,clo,r,"dir_Egap"));
- E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
- E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
- debug15(print_vector_16(E_r_gap,rlo,c,"E"));
+ E_c_gap = _mm_max_epi16(E_c_gap, T1); /* Compare H + open with vert */
+ E_c_gap = _mm_adds_epi16(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_c_gap,clo,r,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT);
- H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
- H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ T1 = _mm_srli_si128(H_nogap_c,LAST_SHORT_NONAVX2);
+ H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_SHORT);
+ H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
X_prev_nogap = T1;
- /* Add pairscores, allowing for alternate genomic nt */
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
- _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
+ /* Add pairscores. No alternate chars for query sequence. */
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
+ H_nogap_c = _mm_adds_epi16(H_nogap_c, pairscores_std);
+ _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_16(H_nogap_c,clo,r,"H"));
- dir_horiz = _mm_cmplt_epi16(E_r_gap,H_nogap_r); /* E < H */
- dir_horiz = _mm_andnot_si128(dir_horiz,complement_dummy); /* E >= H, for jump late */
- _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
+ dir_vert = _mm_cmplt_epi16(E_c_gap,H_nogap_c); /* E < H */
+ dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+ debug15(print_vector_16(dir_vert,clo,r,"dir_nogap"));
- H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
- debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
- _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+ H_nogap_c = _mm_max_epi16(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c store"));
+ _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
- /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
- if (rhigh >= c) {
- (*directions_Egap)[c][c] = DIAG;
- (*directions_nogap)[c][c] = DIAG;
+ /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
+ if (chigh >= r) {
+ (*directions_Egap)[r][r] = DIAG;
+ (*directions_nogap)[r][r] = DIAG;
}
/* No need for F loop here */
@@ -3794,94 +8183,86 @@ Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***direc
} else {
/* jump early */
- for (rlo = 0; rlo <= rlength; rlo += SIMD_NSHORTS) {
- if ((rhigh = rlo + SIMD_NSHORTS - 1) > rlength) {
- rhigh = rlength;
+ for (clo = 0; clo <= glength; clo += SIMD_NSHORTS_NONAVX2) {
+ if ((chigh = clo + SIMD_NSHORTS_NONAVX2 - 1) > glength) {
+ chigh = glength;
}
- /* dir_horiz tests if E > H. To fill in first column of each
- row block with non-diags, could make E > H. But irrelevant,
- because these are above the diagonal. */
+ /* dir_vert tests if E > H. To fill in first row of each
+ column block with non-diags, make E > H. */
E_mask = _mm_set1_epi16(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_r_gap = _mm_set1_epi16(-extend);
- H_nogap_r = _mm_set1_epi16(-open-extend-1);
-#else
- E_r_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
- H_nogap_r = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
-#endif
- for (c = rlo; c <= rhigh + uband && c <= glength; c++) {
- score_column = matrix[c];
+ E_c_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
+ H_nogap_c = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
- if (c == 0) {
- na2 = na2_alt = 4; /* 'N' */
+ for (r = clo; r <= chigh + lband && r <= rlength; r++) {
+ score_column = matrix[r];
+
+ if (r == 0) {
+ na1 = 4; /* 'N' */
} else {
- na2 = revp ? nt_to_int_array[gsequence[1-c]] : nt_to_int_array[gsequence[c-1]];
- na2_alt = revp ? nt_to_int_array[gsequence_alt[1-c]] : nt_to_int_array[gsequence_alt[c-1]];
+ na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
}
- pairscores_std_ptr = pairscores[na2];
- pairscores_alt_ptr = pairscores[na2_alt];
+ pairscores_ptr = pairscores[na1];
- if (c == 0) {
+ if (r == 0) {
X_prev_nogap = _mm_set1_epi16(0);
- } else if (rlo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
+ } else if (clo == 0) {
+#ifdef ZERO_INITIAL_GAP_PENALTY
X_prev_nogap = _mm_set1_epi16(0);
#else
X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
} else {
/* second or greater block of 16 */
- X_prev_nogap = _mm_set1_epi16(matrix[c-1][rlo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
+ X_prev_nogap = _mm_set1_epi16(matrix[r-1][clo-1]); /* get H from previous block and previous column */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_NONAVX2);
}
- debug15(print_vector_16(E_mask,rlo,c,"E_mask"));
- E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
- debug15(print_vector_16(E_r_gap,rlo,c,"E_r_gap"));
- debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r load"));
+ debug15(print_vector_16(E_mask,clo,r,"E_mask"));
+ E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_c_gap,clo,r,"E_c_gap"));
+ debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c load"));
/* EGAP */
- T1 = _mm_adds_epi16(H_nogap_r, gap_open);
- dir_horiz = _mm_cmpgt_epi16(E_r_gap,T1); /* E > H, for jump early */
- _mm_store_si128((__m128i *) &((*directions_Egap)[c][rlo]),dir_horiz);
- debug15(print_vector_16(T1,rlo,c,"T1"));
- debug15(print_vector_16(dir_horiz,rlo,c,"dir_Egap"));
+ T1 = _mm_adds_epi16(H_nogap_c, gap_open);
+ dir_vert = _mm_cmpgt_epi16(E_c_gap,T1); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+ debug15(print_vector_16(T1,clo,r,"T1"));
+ debug15(print_vector_16(dir_vert,clo,r,"dir_Egap"));
- E_r_gap = _mm_max_epi16(E_r_gap, T1); /* Compare H + open with vert */
- E_r_gap = _mm_adds_epi16(E_r_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_r_gap = _mm_min_epi16(E_r_gap,_mm_add_epi16(E_mask,E_infinity));
- debug15(print_vector_16(E_r_gap,rlo,c,"E"));
+ E_c_gap = _mm_max_epi16(E_c_gap, T1); /* Compare H + open with vert */
+ E_c_gap = _mm_adds_epi16(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ debug15(print_vector_16(E_c_gap,clo,r,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_r,LAST_SHORT);
- H_nogap_r = _mm_slli_si128(H_nogap_r,ONE_SHORT);
- H_nogap_r = _mm_or_si128(H_nogap_r, X_prev_nogap);
+ T1 = _mm_srli_si128(H_nogap_c,LAST_SHORT_NONAVX2);
+ H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_SHORT);
+ H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
X_prev_nogap = T1;
- /* Add pairscores, allowing for alternate genomic nt */
- pairscores_std = _mm_load_si128((__m128i *) &(pairscores_std_ptr[rlo]));
- pairscores_alt = _mm_load_si128((__m128i *) &(pairscores_alt_ptr[rlo]));
- H_nogap_r = _mm_adds_epi16(H_nogap_r, _mm_max_epi16(pairscores_std,pairscores_alt));
- _mm_clflush(&H_nogap_r); /* Needed for opencc -O3 on AMD */
- debug15(print_vector_16(H_nogap_r,rlo,c,"H"));
+ /* Add pairscores. No alternate chars for query sequence */
+ pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
+ H_nogap_c = _mm_adds_epi16(H_nogap_c, pairscores_std);
+ _mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
+ debug15(print_vector_16(H_nogap_c,clo,r,"H"));
- dir_horiz = _mm_cmpgt_epi16(E_r_gap,H_nogap_r); /* E > H, for jump early */
- _mm_store_si128((__m128i *) &((*directions_nogap)[c][rlo]),dir_horiz);
- debug15(print_vector_16(dir_horiz,rlo,c,"dir_nogap"));
+ dir_vert = _mm_cmpgt_epi16(E_c_gap,H_nogap_c); /* E > H, for jump early */
+ _mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+ debug15(print_vector_16(dir_vert,clo,r,"dir_nogap"));
- H_nogap_r = _mm_max_epi16(H_nogap_r, E_r_gap); /* Compare H + pairscores with horiz + extend */
- debug15(print_vector_16(H_nogap_r,rlo,c,"H_nogap_r store"));
- _mm_store_si128((__m128i *) &(score_column[rlo]), H_nogap_r);
+ H_nogap_c = _mm_max_epi16(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+ debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c store"));
+ _mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
- /* Fix gaps along diagonal to prevent going into lower triangle, which can happen with ties between E and H */
- if (rhigh >= c) {
- (*directions_Egap)[c][c] = DIAG;
- (*directions_nogap)[c][c] = DIAG;
+ /* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
+ if (chigh >= r) {
+ (*directions_Egap)[r][r] = DIAG;
+ (*directions_nogap)[r][r] = DIAG;
}
/* No need for F loop here */
@@ -3890,54 +8271,30 @@ Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***direc
}
}
+
#ifdef CHECK1
/* Row 0 and column 0 directions fail anyway due to saturation */
/* Handle (0,1) and (1,0) directions, otherwise DIAG */
- (*directions_Egap)[1][0] = HORIZ;
+ (*directions_Egap)[1][0] = VERT;
#endif
#ifdef DEBUG2
- printf("SIMD: Dynprog_simd_16_upper\n");
+ printf("SIMD: Dynprog_simd_16_lower\n");
Matrix16_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,uband,/*upperp*/true);
+ revp,lband,/*upperp*/false);
Directions16_print_ud(*directions_nogap,*directions_Egap,
rlength,glength,rsequence,gsequence,gsequence_alt,
- revp,uband,/*upperp*/true);
+ revp,lband,/*upperp*/false);
#endif
#ifdef CHECK1
- /* Check for row 0 directions */
- for (c = 1; c <= uband && c <= glength; c++) {
- assert((*directions_Egap)[c][0] != DIAG);
- assert((*directions_nogap)[c][0] != DIAG);
+ /* Check for column 0 directions */
+ for (r = 1; r <= lband && r <= rlength; r++) {
+ assert((*directions_Egap)[r][0] != DIAG);
+ assert((*directions_nogap)[r][0] != DIAG);
}
#endif
-#ifdef DEBUG14
- matrix_std = compute_scores_standard(&directions_nogap_std,&directions_Egap_std,
- this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
- rlength,glength,
- goffset,chroffset,chrhigh,watsonp,mismatchtype,
- open,extend,lband,uband,jump_late_p,revp);
-
-#ifdef DEBUG2
- printf("Banded\n");
- Matrix32_print(matrix_std,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
- Directions32_print(directions_nogap_std,directions_Egap_std,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
-#endif
-
- banded_matrix16_compare(matrix,matrix_std,rlength,glength,lband,uband,
- rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp);
-
- banded_directions16_compare_nogap(*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
-
- banded_directions16_compare_Egap(*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
-#endif
-
_mm_free(pairscores[4]);
_mm_free(pairscores[3]);
_mm_free(pairscores[2]);
@@ -3949,8 +8306,6 @@ Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***direc
#endif
-
-
#ifdef HAVE_SSE2
/* Designed for computation below the diagonal, so no F loop or bottom masking needed */
/* Operates by rows */
@@ -3958,25 +8313,37 @@ Score16_T **
Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
int lband, bool jump_late_p, bool revp) {
Score16_T **matrix, *score_column;
+#ifdef HAVE_AVX2
+ __m256i pairscores_std;
+ __m256i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, E_infinity, T1;
+ __m256i gap_open, gap_extend, complement_dummy;
+ __m256i dir_vert;
+ Score16_T save;
+#else
__m128i pairscores_std;
__m128i H_nogap_c, X_prev_nogap, E_c_gap, E_mask, E_infinity, T1;
__m128i gap_open, gap_extend, complement_dummy;
__m128i dir_vert;
+#endif
int glength_ceil, r, c;
int clo, chigh;
int na1, na2, na2_alt;
- Score16_T *pairscores[5], *pairscores_ptr, pairscore;
+ Score16_T *pairscores[5], *pairscores_ptr;
Pairdistance_T **pairdistance_array_type, score1, score2;
-#ifdef DEBUG14
+#ifdef DEBUG_AVX2
+ Score16_T **matrix_std;
+ Direction16_T **directions_nogap_std, **directions_Egap_std;
+ char na2_single;
+#elif defined(DEBUG_SIMD)
Score32_T **matrix_std;
- Direction32_T **directions_nogap_std, **directions_Egap_std;
+ Direction32_T **directions_nogap_std, **directions_Egap_std, **directions_Fgap_std;
char na2_single;
#endif
@@ -4023,11 +8390,11 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
/* Load pairscores. Store match - mismatch */
- pairscores[0] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
- pairscores[1] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
- pairscores[2] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
- pairscores[3] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
- pairscores[4] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),16);
+ pairscores[0] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[1] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[2] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[3] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),ALIGN_SIZE);
+ pairscores[4] = (Score16_T *) _mm_malloc(glength_ceil * sizeof(Score16_T),ALIGN_SIZE);
#if 0
/* Should not be necessary */
@@ -4106,12 +8473,12 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
memset((void *) &(pairscores[4][c]),0,(glength_ceil-c)*sizeof(Score16_T));
#endif
- complement_dummy = _mm_set1_epi16(-1);
+ complement_dummy = _MM_SET1_EPI16(-1);
- gap_open = _mm_set1_epi16((Score16_T) open);
- gap_extend = _mm_set1_epi16((Score16_T) extend);
+ gap_open = _MM_SET1_EPI16((Score16_T) open);
+ gap_extend = _MM_SET1_EPI16((Score16_T) extend);
- E_infinity = _mm_set1_epi16(POS_INFINITY_16);
+ E_infinity = _MM_SET1_EPI16(POS_INFINITY_16);
if (jump_late_p) {
for (clo = 0; clo <= glength; clo += SIMD_NSHORTS) {
if ((chigh = clo + SIMD_NSHORTS - 1) > glength) {
@@ -4120,14 +8487,11 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
/* dir_vert tests if E >= H. To fill in first row of each
column block with non-diags, make E == H. */
- E_mask = _mm_set1_epi16(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_c_gap = _mm_set1_epi16(-extend);
- H_nogap_c = _mm_set1_epi16(-open-extend);
-#else
- E_c_gap = _mm_set1_epi16(NEG_INFINITY_16);
- H_nogap_c = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
-#endif
+ E_mask = _MM_SET1_EPI16(1);
+
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_c_gap = _MM_SET1_EPI16(NEG_INFINITY_16);
+ H_nogap_c = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
for (r = clo; r <= chigh + lband && r <= rlength; r++) {
score_column = matrix[r];
@@ -4135,64 +8499,95 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
if (r == 0) {
na1 = 4; /* 'N' */
} else {
- na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ na1 = revp ? nt_to_int_array[(int) rsequence[1-r]] : nt_to_int_array[(int) rsequence[r-1]];
}
pairscores_ptr = pairscores[na1];
if (r == 0) {
- X_prev_nogap = _mm_set1_epi16(0);
+ X_prev_nogap = _MM_SETZERO_SI();
} else if (clo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi16(0);
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
#else
X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
} else {
/* second or greater block of 16 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),matrix[r-1][clo-1],LAST_SHORT_INSERT);
+#else
X_prev_nogap = _mm_set1_epi16(matrix[r-1][clo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+#endif
}
debug15(print_vector_16(E_mask,clo,r,"E_mask"));
- E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ E_c_gap = _MM_MIN_EPI16(E_c_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_c_gap,clo,r,"E_c_gap"));
debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c load"));
/* EGAP */
- T1 = _mm_adds_epi16(H_nogap_c, gap_open);
- dir_vert = _mm_cmplt_epi16(E_c_gap,T1); /* E < H */
- dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
+ T1 = _MM_ADDS_EPI16(H_nogap_c, gap_open);
+ dir_vert = _MM_CMPLT_EPI16(E_c_gap,T1); /* E < H */
+ dir_vert = _MM_ANDNOT_SI(dir_vert,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[r][clo]),dir_vert);
+#else
_mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+#endif
debug15(print_vector_16(T1,clo,r,"T1"));
debug15(print_vector_16(dir_vert,clo,r,"dir_Egap"));
- E_c_gap = _mm_max_epi16(E_c_gap, T1); /* Compare H + open with vert */
- E_c_gap = _mm_adds_epi16(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ E_c_gap = _MM_MAX_EPI16(E_c_gap, T1); /* Compare H + open with vert */
+ E_c_gap = _MM_ADDS_EPI16(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _MM_MIN_EPI16(E_c_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_c_gap,clo,r,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_c,LAST_SHORT);
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi16(_mm256_setzero_si256(),_mm256_extract_epi16(H_nogap_c,SIMD_NSHORTS-1),LAST_SHORT_INSERT);
+ X_prev_nogap = _mm256_insert_epi16(X_prev_nogap,_mm256_extract_epi16(H_nogap_c,MID_SHORT_INSERT-1),MID_SHORT_INSERT);
+ H_nogap_c = _mm256_slli_si256(H_nogap_c,ONE_SHORT);
+#else
+ T1 = _mm_srli_si128(H_nogap_c,LAST_SHORT_SHIFT);
H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_SHORT);
- H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
+#endif
+ H_nogap_c = _MM_OR_SI(H_nogap_c, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores. No alternate chars for query sequence. */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_ptr[clo]));
+ H_nogap_c = _mm256_adds_epi16(H_nogap_c, pairscores_std);
+#else
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
H_nogap_c = _mm_adds_epi16(H_nogap_c, pairscores_std);
+#endif
_mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
debug15(print_vector_16(H_nogap_c,clo,r,"H"));
- dir_vert = _mm_cmplt_epi16(E_c_gap,H_nogap_c); /* E < H */
- dir_vert = _mm_andnot_si128(dir_vert,complement_dummy); /* E >= H, for jump late */
+ dir_vert = _MM_CMPLT_EPI16(E_c_gap,H_nogap_c); /* E < H */
+ dir_vert = _MM_ANDNOT_SI(dir_vert,complement_dummy); /* E >= H, for jump late */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[r][clo]),dir_vert);
+#else
_mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+#endif
debug15(print_vector_16(dir_vert,clo,r,"dir_nogap"));
- H_nogap_c = _mm_max_epi16(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+ H_nogap_c = _MM_MAX_EPI16(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[clo]), H_nogap_c);
+#else
_mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+#endif
/* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
@@ -4202,7 +8597,13 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
}
/* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi16(E_mask,7);
+ E_mask = _mm256_slli_si256(E_mask,ONE_SHORT);
+ E_mask = _mm256_insert_epi16(E_mask,save,8);
+#else
E_mask = _mm_slli_si128(E_mask,ONE_SHORT);
+#endif
}
}
@@ -4215,14 +8616,11 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
/* dir_vert tests if E > H. To fill in first row of each
column block with non-diags, make E > H. */
- E_mask = _mm_set1_epi16(1);
-#ifdef NO_INITIAL_GAP_PENALTY
- E_c_gap = _mm_set1_epi16(-extend);
- H_nogap_c = _mm_set1_epi16(-open-extend-1);
-#else
- E_c_gap = _mm_set1_epi16(NEG_INFINITY_16+1);
- H_nogap_c = _mm_set1_epi16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
-#endif
+ E_mask = _MM_SET1_EPI16(1);
+
+ /* Holds for all INITIAL_GAP_PENALTY */
+ E_c_gap = _MM_SET1_EPI16(NEG_INFINITY_16+1);
+ H_nogap_c = _MM_SET1_EPI16(NEG_INFINITY_16-open); /* Compensate for T1 = H + open */
for (r = clo; r <= chigh + lband && r <= rlength; r++) {
score_column = matrix[r];
@@ -4230,62 +8628,93 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
if (r == 0) {
na1 = 4; /* 'N' */
} else {
- na1 = revp ? nt_to_int_array[rsequence[1-r]] : nt_to_int_array[rsequence[r-1]];
+ na1 = revp ? nt_to_int_array[(int) rsequence[1-r]] : nt_to_int_array[(int) rsequence[r-1]];
}
pairscores_ptr = pairscores[na1];
if (r == 0) {
- X_prev_nogap = _mm_set1_epi16(0);
+ X_prev_nogap = _MM_SETZERO_SI();
} else if (clo == 0) {
-#ifdef NO_INITIAL_GAP_PENALTY
- X_prev_nogap = _mm_set1_epi16(0);
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),NEG_INFINITY_16,LAST_SHORT_INSERT);
#else
X_prev_nogap = _mm_set1_epi16(NEG_INFINITY_16); /* works if we start outside the rlo bounds */
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
#endif
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
} else {
/* second or greater block of 16 */
+#ifdef ZERO_INITIAL_GAP_PENALTY
+ X_prev_nogap = _MM_SETZERO_SI();
+#elif defined(HAVE_AVX2)
+ X_prev_nogap = _mm256_insert_epi16(_mm256_setzero_si256(),matrix[r-1][clo-1],LAST_SHORT_INSERT);
+#else
X_prev_nogap = _mm_set1_epi16(matrix[r-1][clo-1]); /* get H from previous block and previous column */
- X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT);
+ X_prev_nogap = _mm_srli_si128(X_prev_nogap,LAST_SHORT_SHIFT);
+#endif
}
debug15(print_vector_16(E_mask,clo,r,"E_mask"));
- E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ E_c_gap = _MM_MIN_EPI16(E_c_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_c_gap,clo,r,"E_c_gap"));
debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c load"));
/* EGAP */
- T1 = _mm_adds_epi16(H_nogap_c, gap_open);
- dir_vert = _mm_cmpgt_epi16(E_c_gap,T1); /* E > H, for jump early */
+ T1 = _MM_ADDS_EPI16(H_nogap_c, gap_open);
+ dir_vert = _MM_CMPGT_EPI16(E_c_gap,T1); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_Egap)[r][clo]),dir_vert);
+#else
_mm_store_si128((__m128i *) &((*directions_Egap)[r][clo]),dir_vert);
+#endif
debug15(print_vector_16(T1,clo,r,"T1"));
debug15(print_vector_16(dir_vert,clo,r,"dir_Egap"));
- E_c_gap = _mm_max_epi16(E_c_gap, T1); /* Compare H + open with vert */
- E_c_gap = _mm_adds_epi16(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
- E_c_gap = _mm_min_epi16(E_c_gap,_mm_add_epi16(E_mask,E_infinity));
+ E_c_gap = _MM_MAX_EPI16(E_c_gap, T1); /* Compare H + open with vert */
+ E_c_gap = _MM_ADDS_EPI16(E_c_gap, gap_extend); /* Compute scores for Egap (vert + open) */
+ E_c_gap = _MM_MIN_EPI16(E_c_gap,_MM_ADD_EPI16(E_mask,E_infinity));
debug15(print_vector_16(E_c_gap,clo,r,"E"));
/* NOGAP */
- T1 = _mm_srli_si128(H_nogap_c,LAST_SHORT);
+#ifdef HAVE_AVX2
+ T1 = _mm256_insert_epi16(_mm256_setzero_si256(),_mm256_extract_epi16(H_nogap_c,SIMD_NSHORTS-1),LAST_SHORT_INSERT);
+ X_prev_nogap = _mm256_insert_epi16(X_prev_nogap,_mm256_extract_epi16(H_nogap_c,MID_SHORT_INSERT-1),MID_SHORT_INSERT);
+ H_nogap_c = _mm256_slli_si256(H_nogap_c,ONE_SHORT);
+#else
+ T1 = _mm_srli_si128(H_nogap_c,LAST_SHORT_SHIFT);
H_nogap_c = _mm_slli_si128(H_nogap_c,ONE_SHORT);
- H_nogap_c = _mm_or_si128(H_nogap_c, X_prev_nogap);
+#endif
+ H_nogap_c = _MM_OR_SI(H_nogap_c, X_prev_nogap);
X_prev_nogap = T1;
/* Add pairscores. No alternate chars for query sequence */
+#ifdef HAVE_AVX2
+ pairscores_std = _mm256_load_si256((__m256i *) &(pairscores_ptr[clo]));
+ H_nogap_c = _mm256_adds_epi16(H_nogap_c, pairscores_std);
+#else
pairscores_std = _mm_load_si128((__m128i *) &(pairscores_ptr[clo]));
H_nogap_c = _mm_adds_epi16(H_nogap_c, pairscores_std);
+#endif
_mm_clflush(&H_nogap_c); /* Needed for opencc -O3 on AMD */
debug15(print_vector_16(H_nogap_c,clo,r,"H"));
- dir_vert = _mm_cmpgt_epi16(E_c_gap,H_nogap_c); /* E > H, for jump early */
+ dir_vert = _MM_CMPGT_EPI16(E_c_gap,H_nogap_c); /* E > H, for jump early */
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &((*directions_nogap)[r][clo]),dir_vert);
+#else
_mm_store_si128((__m128i *) &((*directions_nogap)[r][clo]),dir_vert);
+#endif
debug15(print_vector_16(dir_vert,clo,r,"dir_nogap"));
- H_nogap_c = _mm_max_epi16(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
+ H_nogap_c = _MM_MAX_EPI16(H_nogap_c, E_c_gap); /* Compare H + pairscores with horiz + extend */
debug15(print_vector_16(H_nogap_c,clo,r,"H_nogap_c store"));
+#ifdef HAVE_AVX2
+ _mm256_store_si256((__m256i *) &(score_column[clo]), H_nogap_c);
+#else
_mm_store_si128((__m128i *) &(score_column[clo]), H_nogap_c);
+#endif
/* Fix gaps along diagonal to prevent going into upper triangle, which can happen with ties between E and H */
@@ -4295,7 +8724,13 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
}
/* No need for F loop here */
+#ifdef HAVE_AVX2
+ save = _mm256_extract_epi16(E_mask,7);
+ E_mask = _mm256_slli_si256(E_mask,ONE_SHORT);
+ E_mask = _mm256_insert_epi16(E_mask,save,8);
+#else
E_mask = _mm_slli_si128(E_mask,ONE_SHORT);
+#endif
}
}
}
@@ -4324,29 +8759,37 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
}
#endif
-#ifdef DEBUG14
- matrix_std = compute_scores_standard(&directions_nogap_std,&directions_Egap_std,
- this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
- rlength,glength,
- goffset,chroffset,chrhigh,watsonp,mismatchtype,
- open,extend,lband,uband,jump_late_p,revp);
+#ifdef DEBUG_AVX2
+ matrix_std = Dynprog_simd_16_lower_nonavx2(&directions_nogap_std,&directions_Egap_std,
+ this,rsequence,gsequence,gsequence_alt,
+ rlength,glength,goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,jump_late_p,revp);
+#elif defined(DEBUG_SIMD)
+ matrix_std = Dynprog_standard(&directions_nogap_std,&directions_Egap_std,&directions_Fgap_std,
+ this,rsequence,/*gsequence (NULL for debugging)*/NULL,/*gsequence_alt*/NULL,
+ rlength,glength,
+ goffset,chroffset,chrhigh,watsonp,mismatchtype,
+ open,extend,lband,/*uband*/0,jump_late_p,revp,/*saturation*/NEG_INFINITY_16,
+ /*upperp*/false,/*lowerp*/true);
+#endif
#ifdef DEBUG2
printf("Banded\n");
- Matrix32_print(matrix_std,rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
- Directions32_print(directions_nogap_std,directions_Egap_std,
- rlength,glength,rsequence,gsequence,gsequence_alt,
- revp);
+ Matrix16_print_ud(matrix,rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
+ Directions16_print_ud(*directions_nogap,*directions_Egap,
+ rlength,glength,rsequence,gsequence,gsequence_alt,
+ revp,lband,/*upperp*/false);
#endif
- banded_matrix16_compare(matrix,matrix_std,rlength,glength,lband,uband,
- rsequence,gsequence,gsequence_alt,
- goffset,chroffset,chrhigh,watsonp,revp);
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
+ banded_matrix16_compare_lower(matrix,matrix_std,rlength,glength,lband,
+ rsequence,gsequence,gsequence_alt,
+ goffset,chroffset,chrhigh,watsonp,revp);
- banded_directions16_compare_nogap(*directions_nogap,directions_nogap_std,rlength,glength,lband,uband);
+ banded_directions16_compare_nogap_lower(*directions_nogap,directions_nogap_std,rlength,glength,lband);
- banded_directions16_compare_Egap(*directions_Egap,directions_Egap_std,rlength,glength,lband,uband);
+ banded_directions16_compare_Egap_lower(*directions_Egap,directions_Egap_std,rlength,glength,lband);
#endif
_mm_free(pairscores[4]);
@@ -4360,20 +8803,90 @@ Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***direc
#endif
+#ifdef DEBUG17
+static char complCode[128] = COMPLEMENT_LC;
+
+static char
+get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T chrhigh,
+ bool watsonp) {
+ char c2, c2_alt;
+ Univcoord_T pos;
+
+#if 0
+ /* If the read has a deletion, then we will extend beyond 0 or genomiclength, so do not restrict. */
+ if (genomicpos < 0) {
+ return '*';
+
+ } else if (genomicpos >= genomiclength) {
+ return '*';
+
+ }
+#endif
+
+ if (watsonp) {
+ if ((pos = chroffset + genomicpos) < chroffset) { /* Must be <, and not <=, or dynamic programming will fail */
+ *g_alt = '*';
+ return '*';
+
+ } else if (pos >= chrhigh) {
+ *g_alt = '*';
+ return '*';
+
+#if 0
+ } else if (genome) {
+ /* Not necessary, because Genome_get_char_blocks should work */
+ debug8(printf("At %u, genomicnt is %c\n",
+ genomicpos,Genome_get_char(genome,pos)));
+ return Genome_get_char(genome,pos);
+#endif
+
+ } else {
+ /* GMAP with user-supplied genomic segment */
+ debug8(printf("At %u, genomicnt is %c\n",
+ genomicpos,Genome_get_char_blocks(pos)));
+ return Genome_get_char_blocks(&(*g_alt),pos);
+ }
+
+ } else {
+ if ((pos = chrhigh - genomicpos) < chroffset) { /* Must be <, and not <=, or dynamic programming will fail */
+ *g_alt = '*';
+ return '*';
+
+ } else if (pos >= chrhigh) {
+ *g_alt = '*';
+ return '*';
+
+#if 0
+ } else if (genome) {
+ /* Not necessary, because Genome_get_char_blocks should work */
+ c2 = Genome_get_char(genome,pos);
+#endif
+
+ } else {
+ /* GMAP with user-supplied genomic segment */
+ c2 = Genome_get_char_blocks(&c2_alt,pos);
+ }
+ debug8(printf("At %u, genomicnt is %c\n",genomicpos,complCode[(int) c2]));
+ *g_alt = complCode[(int) c2_alt];
+ return complCode[(int) c2];
+ }
+}
+#endif
+
+
#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
List_T
Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction8_T **directions_nogap, Direction8_T **directions_Egap, Direction8_T **directions_Fgap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
int querycoord, genomecoord;
Direction8_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG17
char c2_single;
#endif
@@ -4396,10 +8909,9 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
#endif
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4440,7 +8952,7 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG17
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -4503,10 +9015,9 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
assert(r == 0);
dist = c;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4525,14 +9036,13 @@ Dynprog_traceback_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *n
Direction8_T **directions_nogap, Direction8_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
int querycoord, genomecoord;
Direction8_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG17
char c2_single;
#endif
@@ -4549,10 +9059,9 @@ Dynprog_traceback_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *n
/* assert(c != 0); */
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4571,7 +9080,7 @@ Dynprog_traceback_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *n
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG17
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -4622,10 +9131,9 @@ Dynprog_traceback_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *n
assert(r == 0);
dist = c;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4640,15 +9148,12 @@ List_T
Dynprog_traceback_8_lower (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction8_T **directions_nogap, Direction8_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
- int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
- bool add_dashes_p;
int querycoord, genomecoord;
Direction8_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG17
char c2_single;
#endif
@@ -4684,7 +9189,7 @@ Dynprog_traceback_8_lower (List_T pairs, int *nmatches, int *nmismatches, int *n
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG17
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -4752,14 +9257,13 @@ Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens
Direction16_T **directions_nogap, Direction16_T **directions_Egap, Direction16_T **directions_Fgap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
int querycoord, genomecoord;
Direction16_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG17
char c2_single;
#endif
@@ -4781,10 +9285,9 @@ Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens
#endif
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4826,7 +9329,7 @@ Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG17
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -4889,10 +9392,9 @@ Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens
assert(r == 0);
dist = c;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4909,14 +9411,13 @@ Dynprog_traceback_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *
Direction16_T **directions_nogap, Direction16_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
bool add_dashes_p;
int querycoord, genomecoord;
Direction16_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG17
char c2_single;
#endif
@@ -4933,10 +9434,9 @@ Dynprog_traceback_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *
/* assert(c != 0); */
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,r,c+dist,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -4955,7 +9455,7 @@ Dynprog_traceback_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG17
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
@@ -5006,10 +9506,9 @@ Dynprog_traceback_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *
assert(r == 0);
dist = c;
debug(printf("H%d: ",dist));
- pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,
- /*genomesequence*/NULL,/*genomesequenceuc*/NULL,
+ pairs = Pairpool_add_genomeskip(&add_dashes_p,pairs,/*r*/0+LAZY_INDEL,c,dist,/*genomesequence*/NULL,
queryoffset,genomeoffset,pairpool,revp,chroffset,chrhigh,
- cdna_direction,watsonp,dynprogindex,/*use_genomicseg_p*/false);
+ watsonp,dynprogindex);
if (add_dashes_p == true) {
*nopens += 1;
*nindels += dist;
@@ -5024,15 +9523,12 @@ List_T
Dynprog_traceback_16_lower (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction16_T **directions_nogap, Direction16_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
- int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex) {
+ int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, int dynprogindex) {
char c1, c1_uc, c2, c2_alt;
int dist;
- bool add_dashes_p;
int querycoord, genomecoord;
Direction16_T dir;
-#ifdef DEBUG14
+#ifdef DEBUG17
char c2_single;
#endif
@@ -5068,7 +9564,7 @@ Dynprog_traceback_16_lower (List_T pairs, int *nmatches, int *nmismatches, int *
c1_uc = rsequenceuc[querycoord];
c2 = gsequence[genomecoord];
c2_alt = gsequence_alt[genomecoord];
-#ifdef DEBUG14
+#ifdef DEBUG17
c2_single = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
if (c2 != c2_single) {
abort();
diff --git a/src/dynprog_simd.h b/src/dynprog_simd.h
index f2e314b..8d2dd06 100644
--- a/src/dynprog_simd.h
+++ b/src/dynprog_simd.h
@@ -5,6 +5,7 @@
#define SIMD_MAXLENGTH_EPI8 30 /* Previously had 40 = 128/3, but have seen 7-bit overflow empirically at matrices of size 30 */
+/* Define DEBUG_SIMD and DEBUG_AVX2 in dynprog.h */
#define T Dynprog_T
@@ -13,7 +14,7 @@ Dynprog_simd_8 (Direction8_T ***directions_nogap, Direction8_T ***directions_Ega
Direction8_T ***directions_Fgap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
@@ -23,7 +24,7 @@ extern Score8_T **
Dynprog_simd_8_upper (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
@@ -33,7 +34,7 @@ extern Score8_T **
Dynprog_simd_8_lower (Direction8_T ***directions_nogap, Direction8_T ***directions_Egap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
@@ -44,7 +45,7 @@ Dynprog_simd_16 (Direction16_T ***directions_nogap, Direction16_T ***directions_
Direction16_T ***directions_Fgap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
@@ -54,7 +55,7 @@ extern Score16_T **
Dynprog_simd_16_upper (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
@@ -64,7 +65,7 @@ extern Score16_T **
Dynprog_simd_16_lower (Direction16_T ***directions_nogap, Direction16_T ***directions_Egap,
T this, char *rsequence, char *gsequence, char *gsequence_alt,
int rlength, int glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
int goffset, Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#endif
Mismatchtype_T mismatchtype, int open, int extend,
@@ -75,47 +76,41 @@ Dynprog_traceback_8 (List_T pairs, int *nmatches, int *nmismatches, int *nopens,
Direction8_T **directions_nogap, Direction8_T **directions_Egap, Direction8_T **directions_Fgap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex);
extern List_T
Dynprog_traceback_8_upper (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction8_T **directions_nogap, Direction8_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex);
extern List_T
Dynprog_traceback_8_lower (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction8_T **directions_nogap, Direction8_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ int dynprogindex);
extern List_T
Dynprog_traceback_16 (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction16_T **directions_nogap, Direction16_T **directions_Egap, Direction16_T **directions_Fgap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex);
extern List_T
Dynprog_traceback_16_upper (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction16_T **directions_nogap, Direction16_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex);
extern List_T
Dynprog_traceback_16_lower (List_T pairs, int *nmatches, int *nmismatches, int *nopens, int *nindels,
Direction16_T **directions_nogap, Direction16_T **directions_Egap,
int r, int c, char *rsequence, char *rsequenceuc, char *gsequence, char *gsequence_alt,
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex);
+ int dynprogindex);
#undef T
#endif
diff --git a/src/dynprog_single.c b/src/dynprog_single.c
index 3022e28..f06f844 100644
--- a/src/dynprog_single.c
+++ b/src/dynprog_single.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: dynprog_single.c 181922 2016-01-08 00:43:31Z twu $";
+static char rcsid[] = "$Id: dynprog_single.c 184458 2016-02-18 00:06:33Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -9,12 +9,6 @@ static char rcsid[] = "$Id: dynprog_single.c 181922 2016-01-08 00:43:31Z twu $";
#include <string.h>
#include <math.h> /* For ceil, log, pow */
#include <ctype.h> /* For tolower */
-#ifdef HAVE_SSE2
-#include <emmintrin.h>
-#endif
-#ifdef HAVE_SSE4_1
-#include <smmintrin.h>
-#endif
#include "bool.h"
@@ -451,7 +445,7 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
Mismatchtype_T mismatchtype;
int lband, uband;
int open, extend;
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
Score8_T **matrix8;
Direction8_T **directions8_nogap, **directions8_Egap, **directions8_Fgap;
@@ -589,13 +583,13 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
Dynprog_compute_bands(&lband,&uband,rlength,glength,extraband_single,widebandp);
-#if defined(HAVE_SSE4_1) || defined(HAVE_SSE2)
+#if defined(HAVE_SSE2)
/* Use || because we want the minimum length (which determines the diagonal length) to achieve a score less than 128 */
/* Use && because we don't want to overflow in either direction */
if (rlength <= SIMD_MAXLENGTH_EPI8 && glength <= SIMD_MAXLENGTH_EPI8) {
matrix8 = Dynprog_simd_8(&directions8_nogap,&directions8_Egap,&directions8_Fgap,dynprog,
rsequence,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -607,12 +601,12 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
directions8_nogap,directions8_Egap,directions8_Fgap,rlength,glength,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,/*cdna_direction*/0,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
} else {
matrix16 = Dynprog_simd_16(&directions16_nogap,&directions16_Egap,&directions16_Fgap,dynprog,
rsequence,gsequence,gsequence_alt,rlength,glength,
-#ifdef DEBUG14
+#if defined(DEBUG_AVX2) || defined(DEBUG_SIMD)
goffset,chroffset,chrhigh,watsonp,
#endif
mismatchtype,open,extend,
@@ -624,7 +618,7 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
directions16_nogap,directions16_Egap,directions16_Fgap,rlength,glength,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,/*cdna_direction*/0,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
}
#else
@@ -632,7 +626,8 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
matrix = Dynprog_standard(&directions_nogap,&directions_Egap,&directions_Fgap,dynprog,
rsequence,gsequence,gsequence_alt,rlength,glength,
goffset,chroffset,chrhigh,watsonp,mismatchtype,open,extend,
- lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT);
+ lband,uband,jump_late_p,/*revp*/false,/*saturation*/NEG_INFINITY_INT,
+ /*upperp*/true,/*lowerp*/true);
*finalscore = (int) matrix[glength][rlength];
*nmatches = *nmismatches = *nopens = *nindels = 0;
@@ -640,7 +635,7 @@ Dynprog_single_gap (int *dynprogindex, int *finalscore, int *nmatches, int *nmis
directions_nogap,directions_Egap,directions_Fgap,rlength,glength,
rsequence,rsequenceuc,
gsequence,gsequence_alt,roffset,goffset,pairpool,/*revp*/false,
- chroffset,chrhigh,/*cdna_direction*/0,watsonp,*dynprogindex);
+ chroffset,chrhigh,watsonp,*dynprogindex);
#endif
if (homopolymerp == true) {
@@ -852,6 +847,44 @@ make_microexon_pairs_single (int roffsetL, int roffsetR,
#endif
+/************************************************************************/
+
+#ifdef PMAP
+/* Same as in boyer-moore.c */
+/* Handle only cases in iupac table in sequence.c */
+static bool matchtable[26][26] =
+/* A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z */
+ {{1,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,0,0,0,0,1,0,0,0}, /* A */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* B */
+ {0,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,0,0,0,0,0,1,0}, /* C */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* D */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* E */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* F */
+ {0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,1,1,0,0,0,0,0,0,0}, /* G */
+ {1,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,1,1,0,0,1,0,1,0}, /* H = [ACT] */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* I */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* J */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* K */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* L */
+ {1,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,1,0,0,0,1,0,1,0}, /* M = [AC] */
+ {1,0,1,0,0,0,1,1,0,0,0,0,1,1,0,0,0,1,1,1,0,0,1,0,1,0}, /* N = [ACGT] */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* O */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* P */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* Q */
+ {1,0,0,0,0,0,1,1,0,0,0,0,1,1,0,0,0,1,1,0,0,0,1,0,0,0}, /* R = [AG] */
+ {0,0,1,0,0,0,1,1,0,0,0,0,1,1,0,0,0,1,1,0,0,0,0,0,1,0}, /* S = [CG] */
+ {0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,1,0}, /* T */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* U */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* V */
+ {1,0,0,0,0,0,0,1,0,0,0,0,1,1,0,0,0,1,0,1,0,0,1,0,1,0}, /* W = [AT] */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}, /* X */
+ {0,0,1,0,0,0,0,1,0,0,0,0,1,1,0,0,0,0,1,1,0,0,1,0,1,0}, /* Y = [CT] */
+ {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}}; /* Z */
+#endif
+
+/************************************************************************/
+
+
List_T
Dynprog_microexon_int (double *bestprob2, double *bestprob3, int *dynprogindex, int *microintrontype,
char *rsequence, char *rsequenceuc,
@@ -859,7 +892,7 @@ Dynprog_microexon_int (double *bestprob2, double *bestprob3, int *dynprogindex,
int roffset, int goffsetL, int rev_goffsetR, int cdna_direction,
char *queryseq, char *queryuc,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
- Pairpool_T pairpool, double defect_rate) {
+ Pairpool_T pairpool) {
List_T pairs = NULL;
Intlist_T hits = NULL, p;
#ifdef EXTRACT_GENOMICSEG
@@ -868,17 +901,20 @@ Dynprog_microexon_int (double *bestprob2, double *bestprob3, int *dynprogindex,
int bestcL = -1, bestcR = -1, best_middlelength;
int middlelength, cL, cR, mincR, maxcR, leftbound, rightbound, textleft, textright,
best_candidate, candidate, i;
- int span, nmismatches;
+ int nmismatches;
char left1, left2, right2, right1, left1_alt, left2_alt, right2_alt, right1_alt;
char c, c_alt;
char c1_alt, c2_alt, c3_alt, c4_alt;
char intron1, intron2, intron3, intron4, gapchar;
- float pvalue, bestprob = 0.0, prob2, prob3;
+ float bestprob = 0.0, prob2, prob3;
Univcoord_T splicesitepos;
+ /* float pvalue; */
+ /* int span; */
*bestprob2 = *bestprob3 = 0.0;
+#if 0
if (defect_rate < DEFECT_HIGHQ) {
pvalue = MICROEXON_PVALUE_HIGHQ;
} else if (defect_rate < DEFECT_MEDQ) {
@@ -886,6 +922,7 @@ Dynprog_microexon_int (double *bestprob2, double *bestprob3, int *dynprogindex,
} else {
pvalue = MICROEXON_PVALUE_LOWQ;
}
+#endif
#ifdef PMAP
intron1 = 'G';
@@ -926,7 +963,7 @@ Dynprog_microexon_int (double *bestprob2, double *bestprob3, int *dynprogindex,
debug1(printf(" Query sequence is %.*s\n",rlength,rsequence));
- span = rev_goffsetR-goffsetL;
+ /* span = rev_goffsetR-goffsetL; */
debug1(printf(" Genomic span is of length %d\n",span));
#if 0
diff --git a/src/dynprog_single.h b/src/dynprog_single.h
index e183c4b..2b7c016 100644
--- a/src/dynprog_single.h
+++ b/src/dynprog_single.h
@@ -1,4 +1,4 @@
-/* $Id: dynprog_single.h 132731 2014-04-08 21:19:57Z twu $ */
+/* $Id: dynprog_single.h 184458 2016-02-18 00:06:33Z twu $ */
#ifndef DYNPROG_SINGLE_INCLUDED
#define DYNPROG_SINGLE_INCLUDED
@@ -34,7 +34,7 @@ Dynprog_microexon_int (double *bestprob2, double *bestprob3, int *dynprogindex,
int offset1, int offset2L, int revoffset2R, int cdna_direction,
char *queryseq, char *queryuc,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
- Pairpool_T pairpool, double defect_rate);
+ Pairpool_T pairpool);
extern List_T
Dynprog_microexon_5 (int *dynprogindex, int *microintrontype, int *microexonlength,
diff --git a/src/genome-write.c b/src/genome-write.c
index 7cadc41..e4f3792 100644
--- a/src/genome-write.c
+++ b/src/genome-write.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome-write.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: genome-write.c 184187 2016-02-12 20:38:38Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -219,7 +219,7 @@ make_complement_buffered (char *complement, char *sequence, Chrpos_T length) {
and puts alternate strain sequences into altstrain_iit. */
static void
genome_write_file (FILE *refgenome_fp, FILE *input,
- Univ_IIT_T contig_iit, IIT_T altstrain_iit, char *fileroot, bool uncompressedp,
+ Univ_IIT_T contig_iit, char *fileroot, bool uncompressedp,
int index1part, int nmessages) {
char Buffer[BUFFERSIZE], Complement[BUFFERSIZE], *segment;
char *accession, *p;
@@ -396,7 +396,7 @@ genome_write_file (FILE *refgenome_fp, FILE *input,
/* Permits arbitrary ASCII characters. Useful for storing numeric data */
static void
genome_writeraw_file (FILE *refgenome_fp, FILE *input,
- Univ_IIT_T contig_iit, IIT_T altstrain_iit, char *fileroot, int index1part,
+ Univ_IIT_T contig_iit, char *fileroot, int index1part,
int nmessages) {
char Buffer[BUFFERSIZE], Reverse[BUFFERSIZE], *segment;
char *accession, c;
@@ -621,9 +621,8 @@ fill_circular_chromosomes (UINT4 *genomecomp, Univ_IIT_T chromosome_iit, int cir
and puts alternate strain sequences into altstrain_iit. */
static void
genome_write_memory (FILE *refgenome_fp, FILE *input,
- Univ_IIT_T contig_iit, IIT_T altstrain_iit,
- Univ_IIT_T chromosome_iit, int circular_typeint, Genomecomp_T *genomecomp,
- size_t nuint4, char *fileroot, int nmessages) {
+ Univ_IIT_T contig_iit, Univ_IIT_T chromosome_iit, int circular_typeint, Genomecomp_T *genomecomp,
+ size_t nuint4, int nmessages) {
char Buffer[BUFFERSIZE], Complement[BUFFERSIZE], *segment;
char *accession, *p;
Univcoord_T leftposition, rightposition, startposition, endposition,
@@ -636,7 +635,6 @@ genome_write_memory (FILE *refgenome_fp, FILE *input,
#endif
int nbadchars = 0;
int ncontigs = 0;
- size_t i;
while (fgets(Buffer,BUFFERSIZE,input) != NULL) {
if (Buffer[0] == '>') {
@@ -785,7 +783,7 @@ genome_write_memory (FILE *refgenome_fp, FILE *input,
void
Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
- Univ_IIT_T contig_iit, IIT_T altstrain_iit, Univ_IIT_T chromosome_iit,
+ Univ_IIT_T contig_iit, Univ_IIT_T chromosome_iit,
bool uncompressedp, bool rawp, bool writefilep,
Univcoord_T genomelength, int index1part, int nmessages) {
size_t nuint4;
@@ -804,9 +802,9 @@ Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
exit(9);
}
if (rawp == true) {
- genome_writeraw_file(refgenome_fp,input,contig_iit,altstrain_iit,fileroot,index1part,nmessages);
+ genome_writeraw_file(refgenome_fp,input,contig_iit,fileroot,index1part,nmessages);
} else {
- genome_write_file(refgenome_fp,input,contig_iit,altstrain_iit,fileroot,
+ genome_write_file(refgenome_fp,input,contig_iit,fileroot,
/*uncompressedp*/true,index1part,nmessages);
}
fclose(refgenome_fp);
@@ -822,7 +820,7 @@ Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
fprintf(stderr,"Can't open file %s for read/write\n",filename);
exit(9);
}
- genome_write_file(refgenome_fp,input,contig_iit,altstrain_iit,fileroot,
+ genome_write_file(refgenome_fp,input,contig_iit,fileroot,
/*uncompressedp*/false,index1part,nmessages);
fclose(refgenome_fp);
FREE(filename);
@@ -842,7 +840,7 @@ Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
fprintf(stderr,"Can't open file %s for read/write\n",filename);
exit(9);
}
- genome_write_file(refgenome_fp,input,contig_iit,altstrain_iit,fileroot,
+ genome_write_file(refgenome_fp,input,contig_iit,fileroot,
/*uncompressedp*/false,index1part,nmessages);
fclose(refgenome_fp);
@@ -858,8 +856,8 @@ Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
exit(9);
}
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
- genome_write_memory(refgenome_fp,input,contig_iit,altstrain_iit,chromosome_iit,circular_typeint,
- genomecomp,nuint4,fileroot,nmessages);
+ genome_write_memory(refgenome_fp,input,contig_iit,chromosome_iit,circular_typeint,
+ genomecomp,nuint4,nmessages);
fclose(refgenome_fp);
FREE(genomecomp);
}
diff --git a/src/genome-write.h b/src/genome-write.h
index d9592b1..2e3701b 100644
--- a/src/genome-write.h
+++ b/src/genome-write.h
@@ -1,4 +1,4 @@
-/* $Id: genome-write.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: genome-write.h 184187 2016-02-12 20:38:38Z twu $ */
#ifndef GENOME_WRITE_INCLUDED
#define GENOME_WRITE_INCLUDED
@@ -10,7 +10,7 @@
extern void
Genome_write_comp32 (char *genomesubdir, char *fileroot, FILE *input,
- Univ_IIT_T contig_iit, IIT_T altstrain_iit, Univ_IIT_T chromosome_iit,
+ Univ_IIT_T contig_iit, Univ_IIT_T chromosome_iit,
bool uncompressedp, bool rawp, bool writefilep,
Univcoord_T genomelength, int index1part, int nmessages);
diff --git a/src/genome.c b/src/genome.c
index f3a0bbc..bf7cb5c 100644
--- a/src/genome.c
+++ b/src/genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome.c 172736 2015-08-27 16:36:31Z twu $";
+static char rcsid[] = "$Id: genome.c 184156 2016-02-12 18:30:44Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -78,9 +78,11 @@ static char rcsid[] = "$Id: genome.c 172736 2015-08-27 16:36:31Z twu $";
#define T Genome_T
struct T {
- Access_T access;
+ Access_T access; /* For either chars or blocks, whichever is used */
int chars_shmid;
+ key_t chars_key;
int blocks_shmid;
+ key_t blocks_key;
int fd;
size_t len;
@@ -124,9 +126,9 @@ Genome_free (T *old) {
} else if ((*old)->access == ALLOCATED_SHARED) {
if ((*old)->compressedp == true) {
- Access_deallocate((*old)->blocks,(*old)->blocks_shmid);
+ Access_deallocate((*old)->blocks,(*old)->blocks_shmid,(*old)->blocks_key);
} else {
- Access_deallocate((*old)->chars,(*old)->chars_shmid);
+ Access_deallocate((*old)->chars,(*old)->chars_shmid,(*old)->chars_key);
}
#ifdef HAVE_MMAP
@@ -151,6 +153,7 @@ Genome_free (T *old) {
}
+#if 0
void
Genome_shmem_remove (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T genometype,
bool genome_lc_p) {
@@ -204,6 +207,7 @@ Genome_shmem_remove (char *genomesubdir, char *fileroot, char *snps_root, Genome
return;
}
+#endif
T
@@ -270,7 +274,12 @@ Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T ge
} else if (genometype == GENOME_BITS) {
fprintf(stderr,"(bits)...");
}
- new->blocks = (Genomecomp_T *) Access_allocate(&new->blocks_shmid,&new->len,&seconds,filename,sizeof(Genomecomp_T),sharedp);
+ if (sharedp == true) {
+ new->blocks = (Genomecomp_T *) Access_allocate_shared(&new->access,&new->blocks_shmid,&new->blocks_key,
+ &new->fd,&new->len,&seconds,filename,sizeof(Genomecomp_T));
+ } else {
+ new->blocks = (Genomecomp_T *) Access_allocate_private(&new->access,&new->len,&seconds,filename,sizeof(Genomecomp_T));
+ }
if (new->blocks == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B))\n");
exit(9);
@@ -278,11 +287,6 @@ Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T ge
comma = Genomicpos_commafmt(new->len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
FREE(comma);
- if (sharedp == true) {
- new->access = ALLOCATED_SHARED;
- } else {
- new->access = ALLOCATED_PRIVATE;
- }
}
#ifdef HAVE_MMAP
@@ -305,7 +309,7 @@ Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T ge
new->access = MMAPPED;
}
} else if (access == USE_MMAP_ONLY) {
- new->blocks = (Genomecomp_T *) Access_mmap(&new->fd,&new->len,filename,sizeof(Genomecomp_T),/*randomp*/false);
+ new->blocks = (Genomecomp_T *) Access_mmap(&new->fd,&new->len,filename,/*randomp*/false);
if (new->blocks == NULL) {
fprintf(stderr,"Insufficient memory for genome mmap (will use disk file instead)\n");
new->access = FILEIO;
@@ -325,7 +329,12 @@ Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T ge
if (access == USE_ALLOCATE) {
fprintf(stderr,"Allocating memory for uncompressed genome...");
- new->chars = (char *) Access_allocate(&new->chars_shmid,&new->len,&seconds,filename,sizeof(char),sharedp);
+ if (sharedp == true) {
+ new->chars = (char *) Access_allocate_shared(&new->access,&new->chars_shmid,&new->chars_key,
+ &new->fd,&new->len,&seconds,filename,sizeof(char));
+ } else {
+ new->chars = (char *) Access_allocate_private(&new->access,&new->len,&seconds,filename,sizeof(char));
+ }
if (new->chars == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B))\n");
exit(9);
@@ -333,11 +342,6 @@ Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T ge
comma = Genomicpos_commafmt(new->len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
FREE(comma);
- if (sharedp == true) {
- new->access = ALLOCATED_SHARED;
- } else {
- new->access = ALLOCATED_PRIVATE;
- }
}
#ifdef HAVE_MMAP
@@ -356,7 +360,7 @@ Genome_new (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T ge
}
} else if (access == USE_MMAP_ONLY) {
- new->chars = (char *) Access_mmap(&new->fd,&new->len,filename,sizeof(char),/*randomp*/false);
+ new->chars = (char *) Access_mmap(&new->fd,&new->len,filename,/*randomp*/false);
if (new->chars == NULL) {
fprintf(stderr,"Insufficient memory for genome mmap (will use disk file instead)\n");
new->access = FILEIO;
@@ -11129,6 +11133,7 @@ Genome_get_segment_blocks_right (char *segment, char *segmentalt, Univcoord_T le
}
+/* Note: Must call this function with the right coordinate (left + length), not the left coordinate */
void
Genome_get_segment_blocks_left (char *segment, char *segmentalt, Univcoord_T right, Chrpos_T length, Univcoord_T chroffset,
bool revcomp) {
diff --git a/src/genome.h b/src/genome.h
index ec39b70..d4835f2 100644
--- a/src/genome.h
+++ b/src/genome.h
@@ -1,4 +1,4 @@
-/* $Id: genome.h 168395 2015-06-26 17:13:13Z twu $ */
+/* $Id: genome.h 171615 2015-08-11 01:37:18Z twu $ */
#ifndef GENOME_INCLUDED
#define GENOME_INCLUDED
@@ -24,9 +24,11 @@ extern Genomecomp_T *
Genome_blocks (T this);
extern Univcoord_T
Genome_totallength (T this);
+#if 0
extern void
Genome_shmem_remove (char *genomesubdir, char *fileroot, char *snps_root, Genometype_T genometype,
bool genome_lc_p);
+#endif
extern T
Genome_new (char *genomesubdir, char *fileroot, char *snps_root,
Genometype_T genometype, bool genome_lc_p, Access_mode_T access, bool sharedp);
diff --git a/src/genome128_hr.c b/src/genome128_hr.c
index 825dd39..73bc84e 100644
--- a/src/genome128_hr.c
+++ b/src/genome128_hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome128_hr.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: genome128_hr.c 184459 2016-02-18 00:06:56Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -38,13 +38,17 @@ static char rcsid[] = "$Id: genome128_hr.c 168395 2015-06-26 17:13:13Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+/* Skip popcnt, which comes after SSE4.2 */
+#elif defined(HAVE_POPCNT)
#include <immintrin.h>
#elif defined(HAVE_MM_POPCNT)
#include <nmmintrin.h>
#endif
-#if defined(HAVE_LZCNT) || defined(HAVE_TZCNT)
+#if !defined(HAVE_SSE4_2)
+/* Skip lzcnt and tzcnt, which come after SSE4.2 */
+#elif defined(HAVE_LZCNT) || defined(HAVE_TZCNT)
#include <immintrin.h>
#endif
@@ -17624,6 +17628,7 @@ block_diff_cmet_sarray (Genomecomp_T *query_shifted, Genomecomp_T *ref_ptr,
}
}
+#ifdef GSNAP
/* Ignores snp_ptr */
static UINT4
block_diff_cmet_snp_32 (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomecomp_T *ref_ptr,
@@ -17642,8 +17647,10 @@ block_diff_cmet_snp_32 (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Geno
}
}
}
+#endif
+#ifdef GSNAP
/* Ignores snp_ptr */
static Genomediff_T
block_diff_cmet_snp (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomecomp_T *ref_ptr,
@@ -17662,7 +17669,7 @@ block_diff_cmet_snp (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomec
}
}
}
-
+#endif
/************************************************************************
@@ -18088,6 +18095,7 @@ block_diff_atoi_sarray (Genomecomp_T *query_shifted, Genomecomp_T *ref_ptr,
}
}
+#ifdef GSNAP
/* Ignores snp_ptr */
static UINT4
block_diff_atoi_snp_32 (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomecomp_T *ref_ptr,
@@ -18106,7 +18114,9 @@ block_diff_atoi_snp_32 (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Geno
}
}
}
+#endif
+#ifdef GSNAP
/* Ignores snp_ptr */
static Genomediff_T
block_diff_atoi_snp (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomecomp_T *ref_ptr,
@@ -18125,6 +18135,7 @@ block_diff_atoi_snp (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomec
}
}
}
+#endif
/************************************************************************
@@ -18204,6 +18215,7 @@ block_diff_ttoc_sarray (Genomecomp_T *query_shifted, Genomecomp_T *ref_ptr,
}
}
+#ifdef GSNAP
/* Ignores snp_ptr */
static UINT4
block_diff_ttoc_snp_32 (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomecomp_T *ref_ptr,
@@ -18222,7 +18234,9 @@ block_diff_ttoc_snp_32 (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Geno
}
}
}
+#endif
+#ifdef GSNAP
/* Ignores snp_ptr */
static Genomediff_T
block_diff_ttoc_snp (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomecomp_T *ref_ptr,
@@ -18241,7 +18255,7 @@ block_diff_ttoc_snp (Genomecomp_T *query_shifted, Genomecomp_T *snp_ptr, Genomec
}
}
}
-
+#endif
/* query_shifted, (snp_ptr,) ref_ptr, plusp, genestrand, query_unk_mismatch_local_p */
@@ -18431,7 +18445,9 @@ Genome_hr_user_setup (UINT4 *ref_blocks_in,
#define clear_lowbit(diff,relpos) (diff & (diff - 1));
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+#define popcount_ones(diff) (count_bits[diff & 0x0000FFFF] + count_bits[diff >> 16])
+#elif defined(HAVE_POPCNT)
#define popcount_ones(diff) (_popcnt32(diff))
#elif defined(HAVE_MM_POPCNT)
#define popcount_ones(diff) (_mm_popcnt_u32(diff))
@@ -18442,7 +18458,9 @@ Genome_hr_user_setup (UINT4 *ref_blocks_in,
#endif
-#ifdef HAVE_LZCNT
+#if !defined(HAVE_SSE4_2)
+#define count_leading_zeroes(diff) ((diff >> 16) ? clz_table[diff >> 16] : 16 + clz_table[diff])
+#elif defined(HAVE_LZCNT)
#define count_leading_zeroes(diff) _lzcnt_u32(diff)
#elif defined(HAVE_BUILTIN_CLZ)
#define count_leading_zeroes(diff) __builtin_clz(diff)
@@ -18450,7 +18468,9 @@ Genome_hr_user_setup (UINT4 *ref_blocks_in,
#define count_leading_zeroes(diff) ((diff >> 16) ? clz_table[diff >> 16] : 16 + clz_table[diff])
#endif
-#ifdef HAVE_TZCNT
+#if !defined(HAVE_SSE4_2)
+#define count_trailing_zeroes(diff) mod_37_bit_position[(-diff & diff) % 37]
+#elif defined(HAVE_TZCNT)
#define count_trailing_zeroes(diff) _tzcnt_u32(diff)
#elif defined(HAVE_BUILTIN_CTZ)
#define count_trailing_zeroes(diff) __builtin_ctz(diff)
@@ -18463,6 +18483,7 @@ Genome_hr_user_setup (UINT4 *ref_blocks_in,
#define set_start(diff,startdiscard) (diff | ~(~0U << startdiscard))
#define set_end(diff,enddiscard) (diff | (~0U << enddiscard))
+#if defined(DEBUG) || defined(DEBUG5)
static void
print_diff_popcount (UINT4 diff) {
printf("diff: %08X => nmismatches %d\n",diff,popcount_ones(diff));
@@ -18480,6 +18501,7 @@ print_diff_leading_zeroes (UINT4 diff, int offset) {
printf("diff: %08X => offset %d - leading zeroes %d\n",diff,offset,count_leading_zeroes(diff));
return;
}
+#endif
#else /* littleendian and SSE2 */
@@ -18549,37 +18571,23 @@ clear_end (__m128i _diff, int enddiscard) {
}
-#ifdef HAVE_SSE4_1
-
-#ifdef HAVE_POPCNT
-#define popcount_ones(_diff) (_popcnt64(_mm_extract_epi64(_diff,0)) + _popcnt64(_mm_extract_epi64(_diff,1)))
-#elif defined(HAVE_MM_POPCNT)
-#define popcount_ones(_diff) (_mm_popcnt_u64(_mm_extract_epi64(_diff,0)) + _mm_popcnt_u64(_mm_extract_epi64(_diff,1)))
-#else
-#define popcount_ones(_diff) (__builtin_popcountll(_mm_extract_epi64(_diff,0)) + __builtin_popcountll(_mm_extract_epi64(_diff,1)))
-#endif
-
-#elif 0
-/* Naive method for SSE2. Requires four popcount operations. */
+#if !defined(HAVE_SSE4_2)
+#if 0
+/* Naive method for pre-SSE4.2. Requires four popcount operations. */
static int
popcount_ones (__m128i _diff) {
UINT4 diff[4];
_mm_store_si128((__m128i *) diff,_diff);
-#ifdef HAVE_POPCNT
- return _popcnt32(diff[0]) + _popcnt32(diff[1]) + _popcnt32(diff[2]) + _popcnt32(diff[3]);
-#elif defined(HAVE_MM_POPCNT)
- return _mm_popcnt_u32(diff[0]) + _mm_popcnt_u32(diff[1]) + _mm_popcnt_u32(diff[2]) + _mm_popcnt_u32(diff[3]);
-#else
return __builtin_popcount(diff[0]) + __builtin_popcount(diff[1]) + __builtin_popcount(diff[2]) + __builtin_popcount(diff[3]);
-#endif
}
+#endif
+
-#else
/************************************************************************
- * Method for SSE2: Using Harley's method to reduce number of
+ * Method for pre-SSE4.2: Using Harley's method to reduce number of
* popcount operations when we need to compute four 32-bit popcounts
* in a 128-bit register.
*
@@ -18600,15 +18608,16 @@ popcount_ones (__m128i _diff) {
CSA(twos, ones, diff[0], diff[1], diff[2], u, v);
-#ifdef HAVE_POPCNT
- return 2*_popcnt32(twos) + _popcnt32(ones) + _popcnt32(diff[3]);
-#elif defined(HAVE_MM_POPCNT)
- return 2*_mm_popcnt_u32(twos) + _mm_popcnt_u32(ones) + _mm_popcnt_u32(diff[3]);
-#else
return 2*__builtin_popcount(twos) + __builtin_popcount(ones) + __builtin_popcount(diff[3]);
-#endif
}
+
+#elif defined(HAVE_POPCNT)
+#define popcount_ones(_diff) (_popcnt64(_mm_extract_epi64(_diff,0)) + _popcnt64(_mm_extract_epi64(_diff,1)))
+#elif defined(HAVE_MM_POPCNT)
+#define popcount_ones(_diff) (_mm_popcnt_u64(_mm_extract_epi64(_diff,0)) + _mm_popcnt_u64(_mm_extract_epi64(_diff,1)))
+#else
+#define popcount_ones(_diff) (__builtin_popcountll(_mm_extract_epi64(_diff,0)) + __builtin_popcountll(_mm_extract_epi64(_diff,1)))
#endif
@@ -18617,43 +18626,27 @@ count_leading_zeroes (__m128i _diff) {
debug4(printf("Entered count_leading_zeroes with "));
debug4(print_vector_hex(_diff));
-#ifdef HAVE_SSE4_1
+#if defined(HAVE_SSE4_2) && defined(HAVE_LZCNT)
UINT8 x;
-#ifdef HAVE_LZCNT
if ((x = _mm_extract_epi64(_diff,1)) != 0) {
return (int) _lzcnt_u64(x);
} else {
return 64 + (int) _lzcnt_u64(_mm_extract_epi64(_diff,0));
}
-#else
+#elif defined(HAVE_SSE4_1)
+ UINT8 x;
+
if ((x = _mm_extract_epi64(_diff,1)) != 0) {
return __builtin_clzll(x);
} else {
return 64 + __builtin_clzll(_mm_extract_epi64(_diff,0));
}
-#endif
#else
UINT4 x;
-#ifdef HAVE_LZCNT
- if ((x = (_mm_extract_epi16(_diff,7) << 16) | (_mm_extract_epi16(_diff,6) & 0x0000FFFF)) != 0) {
- debug4(printf("word 3 is non-empty, so returning %d\n",_lzcnt_u32(x)));
- return _lzcnt_u32(x);
- } else if ((x = (_mm_extract_epi16(_diff,5) << 16) | (_mm_extract_epi16(_diff,4) & 0x0000FFFF)) != 0) {
- debug4(printf("word 2 is non-empty, so returning 32 + %d\n",_lzcnt_u32(x)));
- return 32 + _lzcnt_u32(x);
- } else if ((x = (_mm_extract_epi16(_diff,3) << 16) | (_mm_extract_epi16(_diff,2) & 0x0000FFFF)) != 0) {
- debug4(printf("word 1 is non-empty, so returning 64 + %d\n",_lzcnt_u32(x)));
- return 64 + _lzcnt_u32(x);
- } else {
- x = (_mm_extract_epi16(_diff,1) << 16) | (_mm_extract_epi16(_diff,0) & 0x0000FFFF);
- debug4(printf("word 0 is non-empty, so returning 96 + %d\n",_lzcnt_u32(x)));
- return 96 + _lzcnt_u32(x);
- }
-#else
if ((x = (_mm_extract_epi16(_diff,7) << 16) | (_mm_extract_epi16(_diff,6) & 0x0000FFFF)) != 0) {
debug4(printf("word 3 is non-empty, so returning %d vs %d\n",__builtin_clz(x),__builtin_clz(((UINT4 *) &_diff)[3])));
return __builtin_clz(x);
@@ -18669,8 +18662,6 @@ count_leading_zeroes (__m128i _diff) {
return 96 + __builtin_clz(x);
}
#endif
-
-#endif
}
static int
@@ -18678,43 +18669,27 @@ count_trailing_zeroes (__m128i _diff) {
debug4(printf("Entered count_trailing_zeroes with "));
debug4(print_vector_hex(_diff));
-#ifdef HAVE_SSE4_1
+#if defined(HAVE_SSE4_2) && defined(HAVE_TZCNT)
UINT8 x;
-#ifdef HAVE_TZCNT
if ((x = _mm_extract_epi64(_diff,0)) != 0) {
return (int) _tzcnt_u64(x);
} else {
return 64 + (int) _tzcnt_u64(_mm_extract_epi64(_diff,1));
}
-#else
+
+#elif defined(HAVE_SSE4_1)
+ UINT8 x;
+
if ((x = _mm_extract_epi64(_diff,0)) != 0) {
return __builtin_ctzll(x);
} else {
return 64 + __builtin_ctzll(_mm_extract_epi64(_diff,1));
}
-#endif
-
#else
UINT4 x;
-#ifdef HAVE_TZCNT
- if ((x = (_mm_extract_epi16(_diff,1) << 16) | (_mm_extract_epi16(_diff,0) & 0x0000FFFF)) != 0) {
- debug4(printf("word 0 is non-empty, so returning %d\n",_tzcnt_u32(x)));
- return _tzcnt_u32(x);
- } else if ((x = (_mm_extract_epi16(_diff,3) << 16) | (_mm_extract_epi16(_diff,2) & 0x0000FFFF)) != 0) {
- debug4(printf("word 1 is non-empty, so returning 32 + %d\n",_tzcnt_u32(x)));
- return 32 + _tzcnt_u32(x);
- } else if ((x = (_mm_extract_epi16(_diff,5) << 16) | (_mm_extract_epi16(_diff,4) & 0x0000FFFF)) != 0) {
- debug4(printf("word 2 is non-empty, so returning 64 + %d\n",_tzcnt_u32(x)));
- return 64 + _tzcnt_u32(x);
- } else {
- x = (_mm_extract_epi16(_diff,7) << 16) | (_mm_extract_epi16(_diff,6) & 0x0000FFFF);
- debug4(printf("word 3 is non-empty, so returning 96 + %d\n",_tzcnt_u32(x)));
- return 96 + _tzcnt_u32(x);
- }
-#else
if ((x = (_mm_extract_epi16(_diff,1) << 16) | (_mm_extract_epi16(_diff,0) & 0x0000FFFF)) != 0) {
debug4(printf("word 0 is non-empty, so returning %d vs %d\n",__builtin_ctz(x),__builtin_ctz(((UINT4 *) &_diff)[0])));
return __builtin_ctz(x);
@@ -18730,8 +18705,6 @@ count_trailing_zeroes (__m128i _diff) {
return 96 + __builtin_ctz(x);
}
#endif
-
-#endif
}
static __m128i
@@ -18871,7 +18844,9 @@ print_diff_leading_zeroes (__m128i _diff, int offset) {
#define clear_lowbit_32(diff,relpos) (diff & (diff - 1));
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+#define popcount_ones_32(diff) (count_bits[diff & 0x0000FFFF] + count_bits[diff >> 16])
+#elif defined(HAVE_POPCNT)
#define popcount_ones_32(diff) (_popcnt32(diff))
#elif defined(HAVE_MM_POPCNT)
#define popcount_ones_32(diff) (_mm_popcnt_u32(diff))
@@ -18881,7 +18856,9 @@ print_diff_leading_zeroes (__m128i _diff, int offset) {
#define popcount_ones_32(diff) (count_bits[diff & 0x0000FFFF] + count_bits[diff >> 16])
#endif
-#ifdef HAVE_LZCNT
+#if !defined(HAVE_SSE4_2)
+#define count_leading_zeroes_32(diff) ((diff >> 16) ? clz_table[diff >> 16] : 16 + clz_table[diff])
+#elif defined(HAVE_LZCNT)
#define count_leading_zeroes_32(diff) _lzcnt_u32(diff)
#elif defined(HAVE_BUILTIN_CLZ)
#define count_leading_zeroes_32(diff) __builtin_clz(diff)
@@ -18889,7 +18866,9 @@ print_diff_leading_zeroes (__m128i _diff, int offset) {
#define count_leading_zeroes_32(diff) ((diff >> 16) ? clz_table[diff >> 16] : 16 + clz_table[diff])
#endif
-#ifdef HAVE_TZCNT
+#if !defined(HAVE_SSE4_2)
+#define count_trailing_zeroes_32(diff) mod_37_bit_position[(-diff & diff) % 37]
+#elif defined(HAVE_TZCNT)
#define count_trailing_zeroes_32(diff) _tzcnt_u32(diff)
#elif defined(HAVE_BUILTIN_CTZ)
#define count_trailing_zeroes_32(diff) __builtin_ctz(diff)
@@ -18907,7 +18886,7 @@ print_diff_leading_zeroes (__m128i _diff, int offset) {
/* Counts matches from pos5 to pos3 up to first mismatch. Modified from mismatches_left */
int
Genome_consecutive_matches_rightward (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -19087,7 +19066,7 @@ Genome_consecutive_matches_rightward (Compress_T query_compress, Univcoord_T lef
/* Counts matches from pos3 to pos5 up to first mismatch. Modified from mismatches_right */
int
Genome_consecutive_matches_leftward (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -19687,7 +19666,7 @@ Genome_consecutive_matches_pair (UINT4 lefta, UINT4 leftb, UINT4 genomelength) {
static int
count_mismatches_limit (Compress_T query_compress, Univcoord_T left,
- int pos5, int pos3, int max_mismatches, bool plusp, int genestrand, bool first_read_p) {
+ int pos5, int pos3, int max_mismatches, bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -19928,7 +19907,7 @@ count_mismatches_limit (Compress_T query_compress, Univcoord_T left,
static int
count_mismatches_limit_snps (Compress_T query_compress, Univcoord_T left, int pos5, int pos3, int max_mismatches,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -20174,7 +20153,7 @@ count_mismatches_limit_snps (Compress_T query_compress, Univcoord_T left, int po
int
Genome_count_mismatches_limit (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- int max_mismatches, bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches, bool plusp, int genestrand) {
#if 0
if (dibasep) {
@@ -20187,9 +20166,9 @@ Genome_count_mismatches_limit (Compress_T query_compress, Univcoord_T left, int
#endif
if (snp_blocks == NULL) {
- return count_mismatches_limit(query_compress,left,pos5,pos3,max_mismatches,plusp,genestrand,first_read_p);
+ return count_mismatches_limit(query_compress,left,pos5,pos3,max_mismatches,plusp,genestrand);
} else {
- return count_mismatches_limit_snps(query_compress,left,pos5,pos3,max_mismatches,plusp,genestrand,first_read_p);
+ return count_mismatches_limit_snps(query_compress,left,pos5,pos3,max_mismatches,plusp,genestrand);
}
}
@@ -20197,7 +20176,7 @@ Genome_count_mismatches_limit (Compress_T query_compress, Univcoord_T left, int
int
Genome_count_mismatches_substring_ref (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -20339,7 +20318,7 @@ Genome_count_mismatches_substring_ref (Compress_T query_compress, Univcoord_T le
static int
count_mismatches_substring_snps (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -20488,7 +20467,7 @@ count_mismatches_substring_snps (Compress_T query_compress, Univcoord_T left, in
inclusive */
int
Genome_count_mismatches_substring (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#if 0
if (dibasep) {
@@ -20498,9 +20477,9 @@ Genome_count_mismatches_substring (Compress_T query_compress, Univcoord_T left,
#endif
if (snp_blocks == NULL) {
- return Genome_count_mismatches_substring_ref(query_compress,left,pos5,pos3,plusp,genestrand,first_read_p);
+ return Genome_count_mismatches_substring_ref(query_compress,left,pos5,pos3,plusp,genestrand);
} else {
- return count_mismatches_substring_snps(query_compress,left,pos5,pos3,plusp,genestrand,first_read_p);
+ return count_mismatches_substring_snps(query_compress,left,pos5,pos3,plusp,genestrand);
}
}
@@ -20549,7 +20528,10 @@ Genome_count_mismatches_fragment_left (Compress_T query_compress, int pos5, int
assert(diff <= 0x0000FFFF);
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+ debug1(printf("nmismatches %08X => %d\n",diff,count_bits[diff]));
+ return count_bits[diff];
+#elif defined(HAVE_POPCNT)
debug1(printf("nmismatches %08X => %d\n",diff,_popcnt32(diff)));
return _popcnt32(diff);
#elif defined(HAVE_MM_POPCNT)
@@ -20609,7 +20591,10 @@ Genome_count_mismatches_fragment_right (Compress_T query_compress, int pos5, int
assert(diff <= 0x0000FFFF);
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+ debug1(printf("nmismatches %08X => %d\n",diff,count_bits[diff]));
+ return count_bits[diff];
+#elif defined(HAVE_POPCNT)
debug1(printf("nmismatches %08X => %d\n",diff,_popcnt32(diff)));
return _popcnt32(diff);
#elif defined(HAVE_MM_POPCNT)
@@ -20984,7 +20969,7 @@ mismatches_left_snps (int *mismatch_positions, int max_mismatches, Compress_T qu
/* If request max_mismatches 3, could return m0, m1, m2, m3, m4 */
int
Genome_mismatches_left (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p) {
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand) {
int nmismatches;
#ifdef DEBUG
int i;
@@ -21027,7 +21012,7 @@ Genome_mismatches_left (int *mismatch_positions, int max_mismatches, Compress_T
/* See note above about why we set query_unk_mismatch_p to false */
int
Genome_mismatches_left_trim (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p) {
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand) {
int nmismatches;
#ifdef DEBUG
int i;
@@ -21425,7 +21410,7 @@ mismatches_right_snps (int *mismatch_positions, int max_mismatches, Compress_T q
/* Returns mismatch_positions[0..nmismatches], where nmismatches <= max_mismatches */
int
Genome_mismatches_right (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p) {
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand) {
int nmismatches;
#ifdef DEBUG
int i;
@@ -21463,7 +21448,7 @@ Genome_mismatches_right (int *mismatch_positions, int max_mismatches, Compress_T
/* See note above about why we set query_unk_mismatch_p to false */
int
Genome_mismatches_right_trim (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p) {
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand) {
int nmismatches;
#ifdef DEBUG
int i;
@@ -21505,7 +21490,7 @@ Genome_mismatches_right_trim (int *mismatch_positions, int max_mismatches, Compr
int
Genome_mark_mismatches_ref (char *genomic, int querylength, Compress_T query_compress,
Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -21718,7 +21703,7 @@ Genome_mark_mismatches_ref (char *genomic, int querylength, Compress_T query_com
static int
mark_mismatches_snps (char *genomic, int querylength, Compress_T query_compress,
Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -21933,7 +21918,7 @@ mark_mismatches_snps (char *genomic, int querylength, Compress_T query_compress,
int
Genome_mark_mismatches (char *genomic, int querylength, Compress_T query_compress,
Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#if 0
if (dibasep) {
@@ -21951,10 +21936,10 @@ Genome_mark_mismatches (char *genomic, int querylength, Compress_T query_compres
if (snp_blocks == NULL) {
return Genome_mark_mismatches_ref(&(*genomic),querylength,query_compress,
- left,pos5,pos3,plusp,genestrand,first_read_p);
+ left,pos5,pos3,plusp,genestrand);
} else {
return mark_mismatches_snps(&(*genomic),querylength,query_compress,
- left,pos5,pos3,plusp,genestrand,first_read_p);
+ left,pos5,pos3,plusp,genestrand);
}
}
@@ -21965,7 +21950,7 @@ Genome_mark_mismatches (char *genomic, int querylength, Compress_T query_compres
static int
trim_left_substring (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -22511,7 +22496,7 @@ trim_left_substring (Compress_T query_compress, Univcoord_T left, int pos5, int
static int
trim_left_substring_snps (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -23062,7 +23047,7 @@ trim_left_substring_snps (Compress_T query_compress, Univcoord_T left, int pos5,
static int
trim_right_substring (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -23609,7 +23594,7 @@ trim_right_substring (Compress_T query_compress, Univcoord_T left, int pos5, int
static int
trim_right_substring_snps (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#ifdef DEBUG14
int answer;
#endif
@@ -24157,7 +24142,7 @@ trim_right_substring_snps (Compress_T query_compress, Univcoord_T left, int pos5
int
Genome_trim_left (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#if 0
if (dibasep) {
/* Not implemented */
@@ -24166,15 +24151,15 @@ Genome_trim_left (Compress_T query_compress, Univcoord_T left, int pos5, int pos
#endif
if (snp_blocks == NULL) {
- return trim_left_substring(query_compress,left,pos5,pos3,plusp,genestrand,first_read_p);
+ return trim_left_substring(query_compress,left,pos5,pos3,plusp,genestrand);
} else {
- return trim_left_substring_snps(query_compress,left,pos5,pos3,plusp,genestrand,first_read_p);
+ return trim_left_substring_snps(query_compress,left,pos5,pos3,plusp,genestrand);
}
}
int
Genome_trim_right (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p) {
+ bool plusp, int genestrand) {
#if 0
if (dibasep) {
/* Not implemented */
@@ -24183,9 +24168,9 @@ Genome_trim_right (Compress_T query_compress, Univcoord_T left, int pos5, int po
#endif
if (snp_blocks == NULL) {
- return trim_right_substring(query_compress,left,pos5,pos3,plusp,genestrand,first_read_p);
+ return trim_right_substring(query_compress,left,pos5,pos3,plusp,genestrand);
} else {
- return trim_right_substring_snps(query_compress,left,pos5,pos3,plusp,genestrand,first_read_p);
+ return trim_right_substring_snps(query_compress,left,pos5,pos3,plusp,genestrand);
}
}
diff --git a/src/genome128_hr.h b/src/genome128_hr.h
index c3866cb..dd99cba 100644
--- a/src/genome128_hr.h
+++ b/src/genome128_hr.h
@@ -1,4 +1,4 @@
-/* $Id: genome128_hr.h 166739 2015-06-02 01:23:18Z twu $ */
+/* $Id: genome128_hr.h 184179 2016-02-12 20:14:39Z twu $ */
#ifndef GENOME128_HR_INCLUDED
#define GENOME128_HR_INCLUDED
#include "types.h"
@@ -18,22 +18,22 @@ Genome_hr_user_setup (UINT4 *ref_blocks_in,
extern int
Genome_consecutive_matches_rightward (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_consecutive_matches_leftward (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_consecutive_matches_pair (UINT4 lefta, UINT4 leftb, UINT4 genomelength);
extern int
Genome_count_mismatches_limit (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- int max_mismatches, bool plusp, int genestrand, bool first_read_p);
+ int max_mismatches, bool plusp, int genestrand);
extern int
Genome_count_mismatches_substring_ref (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_count_mismatches_substring (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_count_mismatches_fragment_left (Compress_T query_compress, int pos5, int pos3,
@@ -44,33 +44,33 @@ Genome_count_mismatches_fragment_right (Compress_T query_compress, int pos5, int
extern int
Genome_mismatches_left (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p);
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
extern int
Genome_mismatches_left_trim (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p);
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
extern int
Genome_mismatches_right (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p);
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
extern int
Genome_mismatches_right_trim (int *mismatch_positions, int max_mismatches, Compress_T query_compress,
- Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand, bool first_read_p);
+ Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
extern int
Genome_mark_mismatches_ref (char *genomic, int querylength, Compress_T query_compress,
Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_mark_mismatches (char *genomic, int querylength, Compress_T query_compress,
Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_trim_left (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
extern int
Genome_trim_right (Compress_T query_compress, Univcoord_T left, int pos5, int pos3,
- bool plusp, int genestrand, bool first_read_p);
+ bool plusp, int genestrand);
#endif
diff --git a/src/genome_sites.c b/src/genome_sites.c
index 708e3b9..32f041f 100644
--- a/src/genome_sites.c
+++ b/src/genome_sites.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: genome_sites.c 153955 2014-11-24 17:54:45Z twu $";
+static char rcsid[] = "$Id: genome_sites.c 184186 2016-02-12 20:38:12Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -24670,6 +24670,7 @@ static const Genomecomp_T antiacceptor_bits[] =
/* Code starts here */
+#if 0
static void
write_chars_comp (UINT4 high, UINT4 low, UINT4 flags) {
char Buffer[33];
@@ -24707,8 +24708,10 @@ write_chars_comp (UINT4 high, UINT4 low, UINT4 flags) {
printf("%s",Buffer);
return;
}
+#endif
+#if 0
static void
Genome_print_blocks (Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos) {
/* Chrpos_T length = endpos - startpos; */
@@ -24760,6 +24763,62 @@ Genome_print_blocks (Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T end
return;
}
+#endif
+
+
+#if 0
+static void
+Genome_print_blocks_chrpos (Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T endpos, Univcoord_T chroffset) {
+ /* Chrpos_T length = endpos - startpos; */
+ Univcoord_T startblock, endblock, ptr;
+ int startdiscard, enddiscard;
+ Genomecomp_T high, low, flags;
+ int i;
+
+ /* sequence = (char *) CALLOC(length+1,sizeof(char)); */
+
+ ptr = startblock = startpos/32U*3;
+ endblock = endpos/32U*3;
+ startdiscard = startpos % 32;
+ enddiscard = endpos % 32;
+
+ /* high: 9F61B62A low: 6D68A157 flags: 00000000 */
+ printf(" \t");
+ printf("%llu\t%llu\t",(unsigned long long) startblock,(unsigned long long) startblock/3*32U - chroffset);
+ for (i = 0; i < startdiscard; i++) {
+ printf("*");
+ }
+ printf("\n");
+
+ for (ptr = startblock ; ptr <= endblock; ptr += 3) {
+#ifdef WORDS_BIGENDIAN
+ high = Bigendian_convert_uint(blocks[ptr]);
+ low = Bigendian_convert_uint(blocks[ptr+1]);
+ flags = Bigendian_convert_uint(blocks[ptr+2]);
+#else
+ high = blocks[ptr]; low = blocks[ptr+1]; flags = blocks[ptr+2];
+#endif
+ printf("high: %08X low: %08X flags: %08X\t",high,low,flags);
+ printf("%llu\t%llu\t",(unsigned long long) ptr,(unsigned long long) ptr/3*32U - chroffset);
+ write_chars_comp(high,low,flags);
+ printf("\n");
+ }
+
+ /* high: 9F61B62A low: 6D68A157 flags: 00000000 */
+ printf(" \t");
+ printf("%llu\t%llu\t",(unsigned long long) endblock+3,(unsigned long long) (endblock+3)/3*32U - chroffset);
+ for (i = 0; i < enddiscard; i++) {
+ printf(" ");
+ }
+ for ( ; i < 32; i++) {
+ printf("*");
+ }
+ printf("\n");
+
+
+ return;
+}
+#endif
@@ -25273,7 +25332,7 @@ prev_dinucleotide_position (Univcoord_T pos, Univcoord_T prevpos,
printf("\n\n");
printf("Genome (in prev_dinucleotide_position): chroffset %llu, pos %llu, prevpos %llu\n",
(unsigned long long) chroffset,(unsigned long long) (pos-chroffset),(unsigned long long) (prevpos-chroffset));
- Genome_print_blocks(ref_blocks,prevpos-chroffset,pos-chroffset);
+ Genome_print_blocks_chrpos(ref_blocks,prevpos,pos,chroffset);
printf("\n");
);
@@ -25991,45 +26050,31 @@ last_dinucleotide_positions_rev (int *last_position, Univcoord_T genomicstart,
#endif
+#if 0
Univcoord_T
-Genome_prev_donor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset) {
+Genome_prev_donor_position (Univcoord_T pos, Univcoord_T prevpos) {
debug3(printf("==> Looking for donor GT\n"));
- return prev_dinucleotide_position(pos+1,prevpos,
-#ifdef DEBUG3A
- chroffset,
-#endif
- donor_gt_bits,/*splicepos_offset*/-1);
+ return prev_dinucleotide_position(pos+1,prevpos,donor_gt_bits,/*splicepos_offset*/-1);
}
Univcoord_T
-Genome_prev_acceptor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset) {
+Genome_prev_acceptor_position (Univcoord_T pos, Univcoord_T prevpos) {
debug3(printf("==> Looking for acceptor AG\n"));
- return prev_dinucleotide_position(pos-1,prevpos-2,
-#ifdef DEBUG3A
- chroffset,
-#endif
- acceptor_bits,/*splicepos_offset*/2);
+ return prev_dinucleotide_position(pos-1,prevpos-2,acceptor_bits,/*splicepos_offset*/2);
}
Univcoord_T
-Genome_prev_antidonor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset) {
+Genome_prev_antidonor_position (Univcoord_T pos, Univcoord_T prevpos) {
debug3(printf("==> Looking for antidonor AC\n"));
- return prev_dinucleotide_position(pos-1,prevpos-2,
-#ifdef DEBUG3A
- chroffset,
-#endif
- antidonor_ac_bits,/*splicepos_offset*/2);
+ return prev_dinucleotide_position(pos-1,prevpos-2,antidonor_ac_bits,/*splicepos_offset*/2);
}
Univcoord_T
-Genome_prev_antiacceptor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset) {
+Genome_prev_antiacceptor_position (Univcoord_T pos, Univcoord_T prevpos) {
debug3(printf("==> Looking for antiacceptor CT\n"));
- return prev_dinucleotide_position(pos+1,prevpos,
-#ifdef DEBUG3A
- chroffset,
-#endif
- antiacceptor_bits,/*splicepos_offset*/-1);
+ return prev_dinucleotide_position(pos+1,prevpos,antiacceptor_bits,/*splicepos_offset*/-1);
}
+#endif
bool
diff --git a/src/genome_sites.h b/src/genome_sites.h
index 49cd010..2eecea7 100644
--- a/src/genome_sites.h
+++ b/src/genome_sites.h
@@ -1,4 +1,4 @@
-/* $Id: genome_sites.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: genome_sites.h 184184 2016-02-12 20:30:43Z twu $ */
#ifndef GENOME_SITES_INCLUDED
#define GENOME_SITES_INCLUDED
@@ -37,14 +37,16 @@ Genome_antisense_canonicalp (Univcoord_T donor_rightbound, Univcoord_T donor_lef
Univcoord_T chroffset);
+#if 0
extern Univcoord_T
-Genome_prev_donor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset);
+Genome_prev_donor_position (Univcoord_T pos, Univcoord_T prevpos);
extern Univcoord_T
-Genome_prev_acceptor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset);
+Genome_prev_acceptor_position (Univcoord_T pos, Univcoord_T prevpos);
extern Univcoord_T
-Genome_prev_antidonor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset);
+Genome_prev_antidonor_position (Univcoord_T pos, Univcoord_T prevpos);
extern Univcoord_T
-Genome_prev_antiacceptor_position (Univcoord_T pos, Univcoord_T prevpos, Univcoord_T chroffset);
+Genome_prev_antiacceptor_position (Univcoord_T pos, Univcoord_T prevpos);
+#endif
#endif
diff --git a/src/get-genome.c b/src/get-genome.c
index 10c3288..84c4ad8 100644
--- a/src/get-genome.c
+++ b/src/get-genome.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: get-genome.c 170023 2015-07-17 16:47:21Z twu $";
+static char rcsid[] = "$Id: get-genome.c 184460 2016-02-18 00:07:13Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -213,6 +213,7 @@ print_two_coords (Univcoord_T left, Chrpos_T length, Univ_IIT_T chromosome_iit)
/* Retrieval functions */
+#if 0
static int
translate_chromosomepos_universal (Univcoord_T *genomicstart, Chrpos_T *genomiclength,
char *chromosome, Univcoord_T left, Chrpos_T length,
@@ -233,7 +234,10 @@ translate_chromosomepos_universal (Univcoord_T *genomicstart, Chrpos_T *genomicl
return rc;
}
+#endif
+
+#if 0
static int
translate_chromosomepos_segment (Univcoord_T *segmentstart, Chrpos_T *segmentlength,
char *chromosome, Univcoord_T left, Chrpos_T length,
@@ -254,8 +258,10 @@ translate_chromosomepos_segment (Univcoord_T *segmentstart, Chrpos_T *segmentlen
return rc;
}
+#endif
+#if 0
static int
translate_contig (Univcoord_T *genomicstart, Chrpos_T *genomiclength,
char *contig, Univcoord_T left, Chrpos_T length, Univ_IIT_T contig_iit) {
@@ -275,8 +281,10 @@ translate_contig (Univcoord_T *genomicstart, Chrpos_T *genomiclength,
return rc;
}
+#endif
+#if 0
static bool
parse_query (char **divstring, Chrpos_T *coordstart, Chrpos_T *coordend, bool *revcomp,
char *query_original, char *filename) {
@@ -353,8 +361,10 @@ parse_query (char **divstring, Chrpos_T *coordstart, Chrpos_T *coordend, bool *r
}
}
}
+#endif
+#if 0
/* This code is duplicated in gmap.c */
static IIT_T global_altstrain_iit;
@@ -387,6 +397,7 @@ index_compare (const void *a, const void *b) {
}
}
}
+#endif
static void
@@ -541,8 +552,7 @@ print_sequence (Genome_T genome, Genome_T genomealt, Univcoord_T genomicstart, C
strlen(fileroot)+strlen(".altstrain.iit")+1,sizeof(char));
sprintf(iitfile,"%s/%s.altstrain.iit",genomesubdir,fileroot);
global_altstrain_iit = altstrain_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,
- /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false,
- /*labels_read_p*/false);
+ /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false);
FREE(iitfile);
} else {
global_altstrain_iit = altstrain_iit = (IIT_T) NULL;
@@ -650,7 +660,7 @@ parse_and_get_matches (int *nmatches, char **divstring, Chrpos_T *coordstart, Ch
*divstring = (char *) NULL;
if (*iit == NULL) {
if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_NONE,/*divstring*/NULL,
- /*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*add_iit_p*/true)) == NULL) {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
exit(9);
}
@@ -660,8 +670,7 @@ parse_and_get_matches (int *nmatches, char **divstring, Chrpos_T *coordstart, Ch
} else if (typestring == NULL) {
/* Treat query as coordinates, without a typestring */
if (*iit == NULL) {
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,
- /*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
exit(9);
}
@@ -680,8 +689,7 @@ parse_and_get_matches (int *nmatches, char **divstring, Chrpos_T *coordstart, Ch
fprintf(stderr,"No such type as %s. Ignoring the type.\n",typestring);
/* Treat query as coordinates, without a typestring */
if (*iit == NULL) {
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,
- /*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
exit(9);
}
@@ -699,8 +707,7 @@ parse_and_get_matches (int *nmatches, char **divstring, Chrpos_T *coordstart, Ch
} else {
/* Treat query as coordinates, with a typestring */
if (*iit == NULL) {
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,
- /*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
exit(9);
}
@@ -740,8 +747,7 @@ get_matches (int *nmatches, int *sign, char *divstring, Chrpos_T coordstart, Chr
if (*iit == NULL) {
/* This call can give a warning if there are no entries in the map IIT file for the given div */
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,divstring,
- /*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,divstring,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
exit(9);
}
@@ -790,6 +796,7 @@ get_matches (int *nmatches, int *sign, char *divstring, Chrpos_T coordstart, Chr
}
+#if 0
static int *
get_matches_multiple_typed (int *nmatches, char **divstring, Chrpos_T *coordstart, Chrpos_T *coordend,
int **leftflanks, int *nleftflanks, int **rightflanks, int *nrightflanks,
@@ -802,8 +809,7 @@ get_matches_multiple_typed (int *nmatches, char **divstring, Chrpos_T *coordstar
abort();
}
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true,
- /*labels_read_p*/false)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"File %s appears to be an invalid IIT file\n",filename);
exit(9);
}
@@ -816,9 +822,11 @@ get_matches_multiple_typed (int *nmatches, char **divstring, Chrpos_T *coordstar
return matches;
}
+#endif
static char complCode[128] = COMPLEMENT_LC;
+#if 0
static void
make_complement_buffered (char *complement, char *sequence, Chrpos_T length) {
int i, j;
@@ -829,6 +837,7 @@ make_complement_buffered (char *complement, char *sequence, Chrpos_T length) {
complement[length] = '\0';
return;
}
+#endif
static void
make_complement_inplace (char *sequence, Chrpos_T length) {
@@ -1071,14 +1080,14 @@ main (int argc, char *argv[]) {
char *divstring, *divstring2;
Univ_IIT_T chromosome_iit, contig_iit;
IIT_T map_iit = NULL;
- char Buffer[BUFFERLEN], subsetname[BUFFERLEN], *segment;
+ char Buffer[BUFFERLEN], *segment;
char coords[BUFFERLEN], typestring[BUFFERLEN];
int fieldint = -1;
int *matches, nmatches, ndivs, i, *leftflanks, *rightflanks, nleftflanks = 0, nrightflanks = 0;
int sign;
- int circular_typeint;
+ /* int circular_typeint; */
bool *circularp = NULL;
bool any_circular_p;
@@ -1189,7 +1198,7 @@ main (int argc, char *argv[]) {
chromosome_iit = Univ_IIT_read(iitfile,/*readonlyp*/true,/*add_iit_p*/false);
FREE(iitfile);
- circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
+ /* circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular"); */
circularp = Univ_IIT_circularp(&any_circular_p,chromosome_iit);
genome = Genome_new(genomesubdir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_OLIGOS,
@@ -1440,12 +1449,11 @@ main (int argc, char *argv[]) {
} else {
/* Must have been a label */
#if 0
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_NONE,/*divstring*/NULL,
- /*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_NONE,/*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
}
#endif
if ((map_iit = IIT_read(iitfile,/*name*/NULL,true,/*divread*/READ_NONE,/*divstring*/NULL,
- /*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*add_iit_p*/true)) == NULL) {
fprintf(stderr,"Cannot open IIT file %s\n",iitfile);
exit(9);
}
@@ -1502,8 +1510,7 @@ main (int argc, char *argv[]) {
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
if ((map_iit = IIT_read(iitfile,/*name*/map_iitfile,/*readonlyp*/true,
- /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false,
- /*labels_read_p*/false)) == NULL) {
+ /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false)) == NULL) {
fprintf(stderr,"Map file %s.iit not found in %s. Available files:\n",map_iitfile,mapdir);
Datadir_list_directory(stderr,mapdir);
fprintf(stderr,"Either install file %s.iit or specify a full directory path\n",map_iitfile);
diff --git a/src/gmap.c b/src/gmap.c
index 655682f..717550b 100644
--- a/src/gmap.c
+++ b/src/gmap.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gmap.c 173190 2015-09-01 18:59:44Z twu $";
+static char rcsid[] = "$Id: gmap.c 186739 2016-03-30 23:55:14Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -22,13 +22,22 @@ static char rcsid[] = "$Id: gmap.c 173190 2015-09-01 18:59:44Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+/* Skip popcnt */
+#elif defined(HAVE_POPCNT)
#include <immintrin.h>
#endif
-#if defined(HAVE_MM_POPCNT)
+
+#if !defined(HAVE_SSE4_2)
+/* Skip mm_popcnt */
+#elif defined(HAVE_MM_POPCNT)
#include <nmmintrin.h>
#endif
-#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
+
+
+#if !defined(HAVE_SSE4_2)
+/* Skip lzcnt/tzcnt */
+#elif defined(HAVE_LZCNT) || defined(HAVE_TZCNT)
#include <immintrin.h>
#endif
@@ -167,11 +176,16 @@ static char rcsid[] = "$Id: gmap.c 173190 2015-09-01 18:59:44Z twu $";
************************************************************************/
static Univ_IIT_T chromosome_iit = NULL;
+static Univ_IIT_T altscaffold_iit = NULL;
static Univcoord_T genomelength;
static int circular_typeint = -1;
static int nchromosomes;
static bool *circularp = NULL;
static bool any_circular_p;
+
+static bool *altlocp = NULL;
+static Univcoord_T *alias_starts = NULL;
+static Univcoord_T *alias_ends = NULL;
static Univ_IIT_T contig_iit = NULL;
static Genome_T genomecomp = NULL;
static Genome_T genomecomp_alt = NULL;
@@ -279,6 +293,12 @@ static int part_interval = 1;
/* Compute options */
static int min_matches;
+#ifdef USE_MPI
+ int nbeyond;
+#else
+ bool multiple_sequences_p = false;
+#endif
+
static bool sharedp = true;
static Access_mode_T offsetsstrm_access = USE_ALLOCATE;
static bool expand_offsets_p = false;
@@ -360,7 +380,7 @@ static bool require_splicedir_p = false;
static bool gff3_separators_p = true;
/* SAM */
-#ifndef PMAP
+/* Applicable to PMAP? */
static bool sam_paired_p = false;
static bool user_quality_shift = false;
static int quality_shift = 0;
@@ -369,7 +389,6 @@ static char *sam_read_group_id = NULL;
static char *sam_read_group_name = NULL;
static char *sam_read_group_library = NULL;
static char *sam_read_group_platform = NULL;
-#endif
static bool sam_insert_0M_p = false;
static bool orderedp = false;
@@ -410,7 +429,6 @@ static bool novelsplicingp = true; /* Can be disabled with --nosplicing flag */
static bool knownsplicingp = false;
static bool distances_observed_p = false;
static Chrpos_T shortsplicedist = 2000000;
-static int min_extra_end; /* If knownsplicing, then equals shortsplicedist */
static char *user_splicingdir = (char *) NULL;
static char *splicing_file = (char *) NULL;
static IIT_T splicing_iit = NULL;
@@ -734,39 +752,13 @@ check_compiler_assumptions () {
#endif
- fprintf(stderr,"Checking compiler assumptions for popcnt: ");
- fprintf(stderr,"%08X ",x);
-#ifdef HAVE_LZCNT
- fprintf(stderr,"_lzcnt_u32=%d ",_lzcnt_u32(x));
-#endif
-#ifdef HAVE_BUILTIN_CLZ
- fprintf(stderr,"__builtin_clz=%d ",__builtin_clz(x));
-#endif
-#ifdef HAVE_BMI1
- fprintf(stderr,"_tzcnt_u32=%d ",_tzcnt_u32(x));
-#endif
-#ifdef HAVE_BUILTIN_CTZ
- fprintf(stderr,"__builtin_ctz=%d ",__builtin_ctz(x));
-#endif
-
-#ifdef HAVE_POPCNT
- fprintf(stderr,"_popcnt32=%d ",_popcnt32(x));
-#endif
-#if defined(HAVE_MM_POPCNT)
- fprintf(stderr,"_mm_popcnt_u32=%d ",_mm_popcnt_u32(x));
-#endif
-#if defined(HAVE_BUILTIN_POPCOUNT)
- fprintf(stderr,"__builtin_popcount=%d ",__builtin_popcount(x));
-#endif
-
- fprintf(stderr,"\n");
-
#ifdef HAVE_SSE2
fprintf(stderr,"Checking compiler assumptions for SSE2: ");
fprintf(stderr,"%08X %08X",x,y);
a = _mm_xor_si128(_mm_set1_epi32(x),_mm_set1_epi32(y));
z = _mm_cvtsi128_si32(a);
fprintf(stderr," xor=%08X\n",z);
+#endif
#ifdef HAVE_SSE4_1
if ((negx = (char) x) > 0) {
@@ -794,8 +786,34 @@ check_compiler_assumptions () {
fprintf(stderr,"compiler zero extends\n");
}
}
+#endif
+
+#ifdef HAVE_SSE4_2
+ fprintf(stderr,"Checking compiler options for SSE4.2: ");
+ fprintf(stderr,"%08X ",x);
+#ifdef HAVE_LZCNT
+ fprintf(stderr,"_lzcnt_u32=%d ",_lzcnt_u32(x));
+#endif
+#ifdef HAVE_BUILTIN_CLZ
+ fprintf(stderr,"__builtin_clz=%d ",__builtin_clz(x));
+#endif
+#ifdef HAVE_TZCNT
+ fprintf(stderr,"_tzcnt_u32=%d ",_tzcnt_u32(x));
+#endif
+#ifdef HAVE_BUILTIN_CTZ
+ fprintf(stderr,"__builtin_ctz=%d ",__builtin_ctz(x));
+#endif
+#ifdef HAVE_POPCNT
+ fprintf(stderr,"_popcnt32=%d ",_popcnt32(x));
#endif
+#if defined(HAVE_MM_POPCNT)
+ fprintf(stderr,"_mm_popcnt_u32=%d ",_mm_popcnt_u32(x));
+#endif
+#if defined(HAVE_BUILTIN_POPCOUNT)
+ fprintf(stderr,"__builtin_popcount=%d ",__builtin_popcount(x));
+#endif
+ fprintf(stderr,"\n");
#endif
@@ -820,7 +838,7 @@ evaluate_query (bool *poorp, bool *repetitivep, char *queryuc_ptr, int queryleng
Oligoindex_set_inquery(&diagnostic->query_badoligos,&diagnostic->query_repoligos,
&diagnostic->query_trimoligos,&diagnostic->query_trim_start,
&diagnostic->query_trim_end,oligoindex,queryuc_ptr,
- querylength);
+ /*querystart*/0,/*queryend*/querylength);
*poorp = false;
*repetitivep = false;
#else
@@ -864,59 +882,79 @@ evaluate_query (bool *poorp, bool *repetitivep, char *queryuc_ptr, int queryleng
static Stage3_T *
-stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T stage3list,
- bool mergedp, bool chimerap, bool remove_overlaps_p) {
+stage3array_from_list (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
+ List_T stage3list, bool mergedp, bool chimerap, bool remove_overlaps_p) {
Stage3_T *array1, *array0, x, y;
bool *eliminate;
- int norig, i, j;
+ int norig_primary, norig_altloc, i_primary, i_altloc, i, j;
int threshold_score;
- debug2(printf("Entering stage3array_from_list\n"));
+ Univcoord_T alias_start, alias_end;
+
+ debug2(printf("Entering stage3array_from_list with %d entries\n",List_length(stage3list)));
/* Stage3_recompute_goodness(stage3list); -- No longer necessary */
Stage3_compute_mapq(stage3list);
- if ((norig = List_length(stage3list)) == 0) {
+ if (stage3list == NULL) {
*first_absmq = 0;
*second_absmq = 0;
return (Stage3_T *) NULL;
} else if (mergedp == true) {
debug2(printf("mergedp is true\n"));
+ Stage3_count_paths(&norig_primary,&norig_altloc,stage3list);
array0 = (Stage3_T *) List_to_array(stage3list,NULL);
List_free(&stage3list);
*first_absmq = 0;
*second_absmq = 0;
- *npaths = norig;
+ *npaths_primary = norig_primary;
+ *npaths_altloc = norig_altloc;
return array0;
} else if (chimerap == true) {
debug2(printf("chimerap is true\n"));
+ Stage3_count_paths(&norig_primary,&norig_altloc,stage3list);
array0 = (Stage3_T *) List_to_array(stage3list,NULL);
List_free(&stage3list);
*first_absmq = Stage3_absmq_score(array0[0]);
- if (norig <= 2) {
+ if (norig_primary + norig_altloc <= 2) {
*second_absmq = 0;
} else {
- qsort(&(array0[2]),norig-2,sizeof(Stage3_T),Stage3_cmp);
+ qsort(&(array0[2]),norig_primary + norig_altloc - 2,sizeof(Stage3_T),Stage3_cmp);
*second_absmq = Stage3_absmq_score(array0[2]);
}
- *npaths = norig;
+ *npaths_primary = norig_primary;
+ *npaths_altloc = norig_altloc;
return array0;
} else if (remove_overlaps_p == false) {
+ debug2(printf("remove_overlaps_p is false\n"));
+ Stage3_count_paths(&norig_primary,&norig_altloc,stage3list);
array0 = (Stage3_T *) List_to_array(stage3list,NULL);
List_free(&stage3list);
- qsort(array0,norig,sizeof(Stage3_T),Stage3_cmp);
+ qsort(array0,norig_primary + norig_altloc,sizeof(Stage3_T),Stage3_cmp);
threshold_score = Stage3_goodness(array0[0]) - suboptimal_score;
+ if (Stage3_altloc_chr(&alias_start,&alias_end,array0[0]) == false) {
+ i_primary = 1;
+ i_altloc = 0;
+ } else {
+ i_primary = 0;
+ i_altloc = 1;
+ }
i = 1;
- while (i < norig && Stage3_goodness(array0[i]) >= threshold_score) {
+ while (i < norig_primary + norig_altloc && Stage3_goodness(array0[i]) >= threshold_score) {
+ if (Stage3_altloc_chr(&alias_start,&alias_end,array0[i]) == false) {
+ i_primary++;
+ } else {
+ i_altloc++;
+ }
i++;
}
- *npaths = i;
-
+ *npaths_primary = i_primary;
+ *npaths_altloc = i_altloc;
*first_absmq = Stage3_absmq_score(array0[0]);
- if (*npaths < 2) {
+ if ((*npaths_primary) + (*npaths_altloc) < 2) {
*second_absmq = 0;
} else {
*second_absmq = Stage3_absmq_score(array0[1]);
@@ -925,17 +963,19 @@ stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T
return array0;
} else {
- eliminate = (bool *) CALLOCA(norig,sizeof(bool));
+ debug2(printf("remove_overlaps_p is true\n"));
+ Stage3_count_paths(&norig_primary,&norig_altloc,stage3list);
+ eliminate = (bool *) CALLOCA(norig_primary + norig_altloc,sizeof(bool));
/* Initial sort to remove subsumed alignments */
- array0 = (Stage3_T *) MALLOCA(norig * sizeof(Stage3_T));
+ array0 = (Stage3_T *) MALLOCA((norig_primary + norig_altloc) * sizeof(Stage3_T));
List_fill_array_and_free((void **) array0,&stage3list);
- qsort(array0,norig,sizeof(Stage3_T),Stage3_cmp);
- for (i = 0; i < norig; i++) {
+ qsort(array0,norig_primary + norig_altloc,sizeof(Stage3_T),Stage3_cmp);
+ for (i = 0; i < norig_primary + norig_altloc; i++) {
x = array0[i];
debug(printf("%d: chr %d:%u..%u, goodness %d, matches %d, npairs %d\n",
i,Stage3_chrnum(x),Stage3_chrstart(x),Stage3_chrend(x),Stage3_goodness(x),Stage3_matches(x),Stage3_npairs(x)));
- for (j = i+1; j < norig; j++) {
+ for (j = i+1; j < norig_primary + norig_altloc; j++) {
y = array0[j];
if (Stage3_overlap(x,y)) {
eliminate[j] = true;
@@ -943,16 +983,20 @@ stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T
}
}
- *npaths = 0;
- for (i = 0; i < norig; i++) {
+ *npaths_primary = *npaths_altloc = 0;
+ for (i = 0; i < norig_primary + norig_altloc; i++) {
if (eliminate[i] == false) {
- (*npaths)++;
+ if (Stage3_altloc_chr(&alias_start,&alias_end,array0[i]) == false) {
+ (*npaths_primary)++;
+ } else {
+ (*npaths_altloc)++;
+ }
}
}
- array1 = (Stage3_T *) MALLOC_OUT((*npaths) * sizeof(Stage3_T)); /* Return value */
+ array1 = (Stage3_T *) MALLOC_OUT(((*npaths_primary) + (*npaths_altloc)) * sizeof(Stage3_T)); /* Return value */
j = 0;
- for (i = 0; i < norig; i++) {
+ for (i = 0; i < norig_primary + norig_altloc; i++) {
x = array0[i];
if (eliminate[i] == true) {
Stage3_free(&x);
@@ -964,14 +1008,26 @@ stage3array_from_list (int *npaths, int *first_absmq, int *second_absmq, List_T
FREEA(eliminate);
threshold_score = Stage3_goodness(array1[0]) - suboptimal_score;
+ if (Stage3_altloc_chr(&alias_start,&alias_end,array0[0]) == false) {
+ i_primary = 1;
+ i_altloc = 0;
+ } else {
+ i_primary = 0;
+ i_altloc = 1;
+ }
i = 1;
- while (i < *npaths && Stage3_goodness(array1[i]) >= threshold_score) {
+ while (i < (*npaths_primary) + (*npaths_altloc) && Stage3_goodness(array1[i]) >= threshold_score) {
+ if (Stage3_altloc_chr(&alias_start,&alias_end,array1[i]) == false) {
+ i_primary++;
+ } else {
+ i_altloc++;
+ }
i++;
}
- *npaths = i;
-
+ *npaths_primary = i_primary;
+ *npaths_altloc = i_altloc;
*first_absmq = Stage3_absmq_score(array1[0]);
- if (*npaths < 2) {
+ if ((*npaths_primary) + (*npaths_altloc) < 2) {
*second_absmq = 0;
} else {
*second_absmq = Stage3_absmq_score(array1[1]);
@@ -993,7 +1049,8 @@ update_stage3list (List_T stage3list, Sequence_T queryseq,
Chrpos_T chrstart, Chrpos_T chrend, bool watsonp, int genestrand,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
Stopwatch_T worker_stopwatch) {
- int stage2_source, stage2_indexsize;
+ /* int stage2_source, stage2_indexsize; */
+ /* double stage3_runtime; */
#ifdef PMAP
Sequence_T genomicuc = NULL;
@@ -1015,7 +1072,6 @@ update_stage3list (List_T stage3list, Sequence_T queryseq,
Splicetype_T ambig_splicetype_5, ambig_splicetype_3;
double ambig_prob_5, ambig_prob_3;
double min_splice_prob;
- double stage3_runtime;
#ifdef PMAP
int subseq_offset;
#endif
@@ -1054,11 +1110,10 @@ update_stage3list (List_T stage3list, Sequence_T queryseq,
debug2(printf("Beginning Stage2_compute with chrstart %u and chrend %u and query_subseq_offset %d\n",
chrstart,chrend,Sequence_subseq_offset(queryseq)));
- all_stage2results = Stage2_compute(&stage2_source,&stage2_indexsize,
- Sequence_trimpointer(queryseq),Sequence_trimpointer(queryuc),
+ all_stage2results = Stage2_compute(Sequence_trimpointer(queryseq),Sequence_trimpointer(queryuc),
Sequence_trimlength(queryseq),/*query_offset*/0,
chrstart,chrend,chroffset,chrhigh,/*plusp*/watsonp,genestrand,
- stage2_alloc,oligoindices_major,/*proceed_pctcoverage*/0.3,
+ stage2_alloc,/*proceed_pctcoverage*/0.3,oligoindices_major,
pairpool,diagpool,cellpool,
/*localp*/true,/*skip_repetitive_p*/true,
/*favor_right_p*/false,/*max_nalignments*/MAX_NALIGNMENTS,debug_graphic_p,
@@ -1069,7 +1124,7 @@ update_stage3list (List_T stage3list, Sequence_T queryseq,
for (p = all_stage2results; p != NULL; p = List_next(p)) {
stage2 = (Stage2_T) List_head(p);
- Stopwatch_start(worker_stopwatch);
+ /* Stopwatch_start(worker_stopwatch); */
#ifdef PMAP
subseq_offset = Sequence_subseq_offset(queryseq); /* in nucleotides */
#endif
@@ -1100,19 +1155,19 @@ update_stage3list (List_T stage3list, Sequence_T queryseq,
maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
sense_try,sense_filter,oligoindices_minor,diagpool,cellpool);
- stage3_runtime = Stopwatch_stop(worker_stopwatch);
+ /* stage3_runtime = Stopwatch_stop(worker_stopwatch); */
if (pairarray == NULL) {
/* Skip */
} else if (matches < min_matches) {
FREE_OUT(pairarray);
} else if ((stage3 = Stage3_new(pairarray,pairs,npairs,goodness,cdna_direction,sensedir,
- stage2_source,stage2_indexsize,matches,unknowns,mismatches,
+ matches,unknowns,mismatches,
qopens,qindels,topens,tindels,ncanonical,nsemicanonical,nnoncanonical,
chrnum,chroffset,chrhigh,chrlength,watsonp,
/*querylength*/Sequence_fulllength(queryseq),
/*skiplength*/Sequence_skiplength(queryseq),
/*trimlength*/Sequence_trimlength(queryseq),
- stage3_runtime,straintype,strain,altstrain_iit)) != NULL) {
+ straintype,strain,altstrain_iit)) != NULL) {
stage3list = List_push(stage3list,(void *) stage3);
}
@@ -1166,7 +1221,7 @@ index_compare (const void *a, const void *b) {
static Stage3_T *
-stage3_from_usersegment (int *npaths, int *first_absmq, int *second_absmq,
+stage3_from_usersegment (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
Sequence_T queryseq, Sequence_T queryuc,
#ifdef PMAP
Sequence_T queryntseq,
@@ -1217,11 +1272,11 @@ stage3_from_usersegment (int *npaths, int *first_absmq, int *second_absmq,
#endif
if (stage3list == NULL) {
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
return NULL;
} else {
- return stage3array_from_list(&(*npaths),&(*first_absmq),&(*second_absmq),stage3list,
- /*mergedp*/false,/*chimerap*/false,/*remove_overlaps_p*/true);
+ return stage3array_from_list(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),
+ stage3list,/*mergedp*/false,/*chimerap*/false,/*remove_overlaps_p*/true);
}
}
@@ -3872,7 +3927,7 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
List_T gregions = NULL, stage3list;
Stage3_T *stage3array;
- int npaths, first_absmq, second_absmq;
+ int npaths_primary, npaths_altloc, first_absmq, second_absmq;
#ifdef PMAP
Sequence_T queryntseq;
#endif
@@ -3891,7 +3946,8 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
if (Sequence_fulllength_given(queryseq) <= 0) {
result = Result_new(jobid,/*mergedp*/false,(Chimera_T) NULL,(Stage3_T *) NULL,
- /*npaths*/0,/*first_absmq*/0,/*second_absmq*/0,/*diagnostic*/NULL,EMPTY_SEQUENCE);
+ /*npaths_primary*/0,/*npaths_altloc*/0,/*first_absmq*/0,/*second_absmq*/0,
+ /*diagnostic*/NULL,EMPTY_SEQUENCE);
} else if (Sequence_fulllength_given(queryseq) <
#ifdef PMAP
@@ -3901,7 +3957,8 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
#endif
) {
result = Result_new(jobid,/*mergedp*/false,(Chimera_T) NULL,(Stage3_T *) NULL,
- /*npaths*/0,/*first_absmq*/0,/*second_absmq*/0,/*diagnostic*/NULL,SHORT_SEQUENCE);
+ /*npaths_primary*/0,/*npaths_altloc*/0,/*first_absmq*/0,/*second_absmq*/0,
+ /*diagnostic*/NULL,SHORT_SEQUENCE);
} else { /* Sequence_fulllength_given(queryseq) > 0 */
queryuc = Sequence_uppercase(queryseq);
@@ -3915,10 +3972,12 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
#ifndef PMAP
if (poorp == true && prune_poor_p == true) {
result = Result_new(jobid,/*mergedp*/false,(Chimera_T) NULL,(Stage3_T *) NULL,
- /*npaths*/0,/*first_absmq*/0,/*second_absmq*/0,diagnostic,POOR_SEQUENCE);
+ /*npaths_primary*/0,/*npaths_altloc*/0,/*first_absmq*/0,/*second_absmq*/0,
+ diagnostic,POOR_SEQUENCE);
} else if (repetitivep == true && prune_repetitive_p == true) {
result = Result_new(jobid,/*mergedp*/false,(Chimera_T) NULL,(Stage3_T *) NULL,
- /*npaths*/0,/*first_absmq*/0,/*second_absmq*/0,diagnostic,REPETITIVE);
+ /*npaths_primary*/0,/*npaths_altloc*/0,/*first_absmq*/0,/*second_absmq*/0,
+ diagnostic,REPETITIVE);
}
#endif
@@ -3930,13 +3989,14 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
Sequence_trim(queryuc,diagnostic->query_trim_start,diagnostic->query_trim_end);
#endif
#endif
- stage3array = stage3_from_usersegment(&npaths,&first_absmq,&second_absmq,queryseq,queryuc,
+ stage3array = stage3_from_usersegment(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,queryseq,queryuc,
#ifdef PMAP
queryntseq,
#endif
usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,worker_stopwatch);
- result = Result_new(jobid,/*mergedp*/false,(Chimera_T) NULL,stage3array,npaths,first_absmq,second_absmq,diagnostic,NO_FAILURE);
+ result = Result_new(jobid,/*mergedp*/false,(Chimera_T) NULL,stage3array,npaths_primary,npaths_altloc,
+ first_absmq,second_absmq,diagnostic,NO_FAILURE);
} else { /* Not user segment and not maponly */
#ifndef PMAP
@@ -3950,8 +4010,7 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
debug(printf("Calling stage 1\n"));
if (mode == CMET_NONSTRANDED) {
gregions = Stage1_compute_nonstranded(&lowidentityp,queryuc,indexdb_fwd,indexdb_fwd,
- /*indexdb_size_threshold*/400,chromosome_iit,
- chrsubset_start,chrsubset_end,matchpool,
+ chromosome_iit,chrsubset_start,chrsubset_end,matchpool,
stutterhits,diagnostic,worker_stopwatch,/*nbest*/10);
} else {
gregions = Stage1_compute(&lowidentityp,queryuc,indexdb_fwd,indexdb_rev,
@@ -3962,7 +4021,8 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
debug(printf("Got %d gregions\n",List_length(gregions)));
if (stage1debug == true) {
- result = Result_new_stage1debug(jobid,gregions,diagnostic,NO_FAILURE);
+ /* result = Result_new_stage1debug(jobid,gregions,diagnostic,NO_FAILURE); */
+ abort();
} else {
debug(printf("Applying stage 3\n"));
stage3list = apply_stage3(&mergedp,&chimera,gregions,queryseq,queryuc,
@@ -3972,20 +4032,23 @@ process_request (Filestring_T *fp_failedinput, double *worker_runtime, Request_T
usersegment,stage2_alloc,oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,worker_stopwatch);
if (diag_debug == true) {
+#if 0
result = Result_new_diag_debug(jobid,/*diagonals*/stage3list,diagnostic,NO_FAILURE);
+#endif
+ abort();
} else if (stage3list == NULL) {
- result = Result_new(jobid,mergedp,chimera,/*stage3array*/NULL,/*npaths*/0,/*first_absmq*/0,/*second_absmq*/0,
- diagnostic,NO_FAILURE);
+ result = Result_new(jobid,mergedp,chimera,/*stage3array*/NULL,/*npaths_primary*/0,/*npaths_altloc*/0,
+ /*first_absmq*/0,/*second_absmq*/0,diagnostic,NO_FAILURE);
} else if (chimera == NULL) {
- stage3array = stage3array_from_list(&npaths,&first_absmq,&second_absmq,stage3list,mergedp,
- /*chimerap*/false,/*remove_overlaps_p*/true);
- result = Result_new(jobid,mergedp,/*chimera*/NULL,stage3array,npaths,first_absmq,second_absmq,
- diagnostic,NO_FAILURE);
+ stage3array = stage3array_from_list(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,
+ stage3list,mergedp,/*chimerap*/false,/*remove_overlaps_p*/true);
+ result = Result_new(jobid,mergedp,/*chimera*/NULL,stage3array,npaths_primary,npaths_altloc,
+ first_absmq,second_absmq,diagnostic,NO_FAILURE);
} else {
- stage3array = stage3array_from_list(&npaths,&first_absmq,&second_absmq,stage3list,mergedp,
- /*chimerap*/true,/*remove_overlaps_p*/false);
- result = Result_new(jobid,mergedp,chimera,stage3array,npaths,first_absmq,second_absmq,
- diagnostic,NO_FAILURE);
+ stage3array = stage3array_from_list(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,
+ stage3list,mergedp,/*chimerap*/true,/*remove_overlaps_p*/false);
+ result = Result_new(jobid,mergedp,chimera,stage3array,npaths_primary,npaths_altloc,
+ first_absmq,second_absmq,diagnostic,NO_FAILURE);
}
}
@@ -4027,7 +4090,8 @@ signal_handler (int sig) {
fprintf(stderr,"Signal received: SIGILL\n");
fprintf(stderr,"An illegal instruction means that this program is being run on a computer\n");
fprintf(stderr," with different features than the computer used to compile the program\n");
- fprintf(stderr,"You may need to re-compile the program with fewer features by doing something like\n");
+ fprintf(stderr,"You may need to re-compile the program on the same computer type as the target machine\n");
+ fprintf(stderr," or re-compile with fewer features by doing something like\n");
fprintf(stderr," ./configure --disable-simd\n");
break;
case SIGINT: fprintf(stderr,"Signal received: SIGINT\n"); break;
@@ -4666,7 +4730,7 @@ align_relative (FILE *input, char **files, int nfiles, int nextchar,
Chimera_T chimera = NULL;
List_T gregions, stage3list;
Stage3_T *stage3array, stage3, stage3ref;
- int npaths, i;
+ int npaths_primary, npaths_altloc, i;
oligoindices_major = Oligoindex_array_new_major(&noligoindices_major);
oligoindices_minor = Oligoindex_array_new_minor(&noligoindices_minor);
@@ -4705,20 +4769,21 @@ align_relative (FILE *input, char **files, int nfiles, int nextchar,
oligoindices_major,oligoindices_minor,
matchpool,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,stopwatch);
if (stage3list == NULL) {
- npaths = 0;
+ npaths_primary = npaths_altloc = 0;
stage3array = (Stage3_T *) NULL;
} else {
- stage3array = stage3array_from_list(&npaths,stage3list,/*mergedp*/false,/*chimerap*/false,/*remove_overlaps_p*/true);
+ stage3array = stage3array_from_list(&npaths_primary,&npaths_altloc,stage3list,/*mergedp*/false,
+ /*chimerap*/false,/*remove_overlaps_p*/true);
}
Diagnostic_free(&diagnostic);
/* chimera should be NULL */
- for (i = 1; i < npaths; i++) {
+ for (i = 1; i < npaths_primary + npaths_altloc; i++) {
stage3 = stage3array[i];
Stage3_free(&stage3);
}
- if (npaths > 0) {
+ if (npaths_primary + npaths_altloc > 0) {
stage3ref = stage3array[0];
#ifdef PMAP
Stage3_translate_cdna(stage3ref,queryseq,strictp);
@@ -4799,11 +4864,11 @@ align_relative (FILE *input, char **files, int nfiles, int nextchar,
print_npaths(fp,0,diagnostic,/*usersegment*/NULL,chrsubset,/*chimera*/NULL,REPETITIVE);
} else {
#endif /* PMAP */
- stage3array = stage3_from_usersegment(&npaths,queryseq,queryuc,genomicseg,
+ stage3array = stage3_from_usersegment(&npaths_primary,&npaths_altloc,queryseq,queryuc,genomicseg,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,stopwatch);
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
print_npaths(fp,0,diagnostic,/*usersegment*/NULL,chrsubset,/*chimera*/NULL,NO_FAILURE);
} else if (printtype == COORDS) {
Stage3_print_coordinates(fp,stage3array[0],chromosome_iit,invertmode);
@@ -4820,7 +4885,7 @@ align_relative (FILE *input, char **files, int nfiles, int nextchar,
invertmode,nointronlenp,wraplength,
/*snps_p*/snp_blocks ? true : false,
/*maxmutations*/1000000);
- for (i = 0; i < npaths; i++) {
+ for (i = 0; i < npaths_primary + npaths_altloc; i++) {
stage3 = stage3array[i];
Stage3_free(&stage3);
}
@@ -5279,8 +5344,8 @@ parse_command_line (int argc, char *argv[], int optind) {
#else
case 'k':
required_index1part = atoi(check_valid_int(optarg));
- if (required_index1part > 16) {
- fprintf(stderr,"The value for k-mer size must be 16 or less\n");
+ if (required_index1part > MAXIMUM_KMER) {
+ fprintf(stderr,"The value for k-mer size must be %d or less\n",MAXIMUM_KMER);
return 9;
}
break;
@@ -5737,11 +5802,6 @@ open_input_stream (int *nread, Sequence_T *usersegment, int argc, char **argv) {
int
main (int argc, char *argv[]) {
-#ifdef USE_MPI
- int nbeyond;
-#else
- bool multiple_sequences_p = false;
-#endif
int cmdline_status;
char *genomesubdir = NULL, *snpsdir = NULL, *modedir = NULL, *mapdir = NULL, *iitfile = NULL, *fileroot = NULL;
@@ -5814,7 +5874,7 @@ main (int argc, char *argv[]) {
check_compiler_assumptions();
if (exception_raise_p == false) {
- fprintf(stderr,"Allowing signals and exceptions to pass through\n");
+ fprintf(stderr,"Allowing signals and exceptions to pass through. If using shared memory, need to remove segments manually.\n");
Except_inactivate();
} else {
#ifdef HAVE_SIGACTION
@@ -5871,8 +5931,8 @@ main (int argc, char *argv[]) {
#endif
} else {
- /* multiple_sequences_p = false; */
/* fprintf(stderr,"Note: only 1 sequence detected. Ignoring batch (-B) command\n"); */
+ multiple_sequences_p = false;
expand_offsets_p = false;
#ifdef HAVE_MMAP
offsetsstrm_access = USE_MMAP_ONLY;
@@ -5905,13 +5965,29 @@ main (int argc, char *argv[]) {
exit(9);
#endif
} else {
+ FREE(iitfile);
nchromosomes = Univ_IIT_total_nintervals(chromosome_iit);
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
circularp = Univ_IIT_circularp(&any_circular_p,chromosome_iit);
+
+ iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
+ strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
+ sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
+ if ((altscaffold_iit = Univ_IIT_read(iitfile,/*readonlyp*/true,/*add_iit_p*/false)) == NULL) {
+ /* fprintf(stderr,"No altscaffold file found\n"); */
+ altlocp = (bool *) CALLOC(nchromosomes+1,sizeof(bool));
+ alias_starts = (Univcoord_T *) CALLOC(nchromosomes+1,sizeof(Univcoord_T));
+ alias_ends = (Univcoord_T *) CALLOC(nchromosomes+1,sizeof(Univcoord_T));
+
+ } else {
+ fprintf(stderr,"Found altscaffold file found\n");
+ altlocp = Univ_IIT_altlocp(&alias_starts,&alias_ends,chromosome_iit,altscaffold_iit);
+ Univ_IIT_free(&altscaffold_iit);
+ }
+ FREE(iitfile);
}
- genomelength = Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false);
- FREE(iitfile);
+ genomelength = Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false);
}
#ifdef USE_MPI
@@ -5929,7 +6005,7 @@ main (int argc, char *argv[]) {
strlen(map_iitfile)+strlen(".iit")+1,sizeof(char));
sprintf(iitfile,"%s/%s.iit",mapdir,map_iitfile);
if ((map_iit = IIT_read(iitfile,/*name*/map_iitfile,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"Map file %s.iit not found in %s. Available files:\n",map_iitfile,mapdir);
Datadir_list_directory(stderr,mapdir);
fprintf(stderr,"Either install file %s.iit or specify a directory for the IIT file\n",iitfile);
@@ -5949,13 +6025,13 @@ main (int argc, char *argv[]) {
if (splicing_file != NULL) {
if (user_splicingdir == NULL) {
if ((splicing_iit = IIT_read(splicing_file,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/false)) != NULL) {
fprintf(stderr,"Reading splicing file %s locally...",splicing_file);
} else {
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
sprintf(iitfile,"%s/%s",user_splicingdir,splicing_file);
if ((splicing_iit = IIT_read(splicing_file,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/false)) != NULL) {
fprintf(stderr,"Reading splicing file %s locally...",splicing_file);
FREE(iitfile);
}
@@ -5968,7 +6044,7 @@ main (int argc, char *argv[]) {
strlen(splicing_file)+1,sizeof(char));
sprintf(iitfile,"%s/%s",mapdir,splicing_file);
if ((splicing_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading splicing file %s...",iitfile);
FREE(iitfile);
FREE(mapdir);
@@ -6010,6 +6086,10 @@ main (int argc, char *argv[]) {
dbversion = (char *) NULL;
genomecomp_blocks = Compress_create_blocks_comp(Sequence_fullpointer(global_usersegment),Sequence_fulllength(global_usersegment));
genomebits_blocks = Compress_create_blocks_bits(genomecomp_blocks,Sequence_fulllength(global_usersegment));
+ altlocp = (bool *) MALLOC(sizeof(bool));
+ altlocp[0] = false;
+ alias_starts = (Univcoord_T *) CALLOC(1,sizeof(Univcoord_T));
+ alias_ends = (Univcoord_T *) CALLOC(1,sizeof(Univcoord_T));
if (Sequence_fulllength(global_usersegment) > 1000000) {
fprintf(stderr,"Genomic sequence is unusually long (%d bp). GMAP handles genomes better when\n",
@@ -6034,8 +6114,12 @@ main (int argc, char *argv[]) {
genomecomp = Genome_new(genomesubdir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_OLIGOS,
uncompressedp,genome_access,sharedp);
- genomebits = Genome_new(genomesubdir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_BITS,
- uncompressedp,genome_access,sharedp);
+ if ((genomebits = Genome_new(genomesubdir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_BITS,
+ uncompressedp,genome_access,sharedp)) == NULL) {
+ genomebits_blocks = (Genomecomp_T *) NULL;
+ } else {
+ genomebits_blocks = Genome_blocks(genomebits);
+ }
if (snps_root == NULL) {
genomecomp_alt = genomebits_alt = (Genome_T) NULL;
} else {
@@ -6049,12 +6133,14 @@ main (int argc, char *argv[]) {
genomesubdir,fileroot,FWD_FILESUFFIX,/*snps_root*/NULL,
&alphabet,&alphabet_size,required_alphabet,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp);
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p);
indexdb_rev = Indexdb_new_genome(&index1part_aa,&index1interval,
genomesubdir,fileroot,REV_FILESUFFIX,/*snps_root*/NULL,
&alphabet,&alphabet_size,required_alphabet,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp);
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p);
if (indexdb_fwd == NULL || indexdb_rev == NULL) {
fprintf(stderr,"Cannot find offsets file %s.%s*offsets or %s.%s*offsets.\n",
@@ -6113,7 +6199,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metct",/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metct index file. Need to run cmetindex first\n");
exit(9);
}
@@ -6122,7 +6208,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metga",/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metga index file. Need to run cmetindex first\n");
exit(9);
}
@@ -6138,7 +6224,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6147,7 +6233,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6163,7 +6249,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6172,7 +6258,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6183,7 +6269,7 @@ main (int argc, char *argv[]) {
genomesubdir,fileroot,IDX_FILESUFFIX,/*snps_root*/NULL,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find offsets file %s.%s*offsets, needed for GSNAP\n",fileroot,IDX_FILESUFFIX);
exit(9);
}
@@ -6248,7 +6334,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metct",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metct index file. Need to run cmetindex first\n");
exit(9);
}
@@ -6256,7 +6342,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metga",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metga index file. Need to run cmetindex first\n");
exit(9);
}
@@ -6272,7 +6358,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6280,7 +6366,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6296,7 +6382,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6304,7 +6390,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp)) == NULL) {
+ sharedp,multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -6314,7 +6400,7 @@ main (int argc, char *argv[]) {
snpsdir,fileroot,/*idx_filesuffix*/"ref",snps_root,
required_index1part,required_index1interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- sharedp);
+ sharedp,multiple_sequences_p);
if (indexdb_fwd == NULL) {
fprintf(stderr,"Cannot find snps index file for %s in directory %s\n",snps_root,snpsdir);
exit(9);
@@ -6344,7 +6430,7 @@ main (int argc, char *argv[]) {
} else {
/* TODO: Handle case for observed distances */
/* min_extra_end no longer used by gregion.c */
- min_extra_end = shortsplicedist;
+ /* min_extra_end = shortsplicedist; */
splicing_divint_crosstable = Univ_IIT_divint_crosstable(chromosome_iit,splicing_iit);
if ((donor_typeint = IIT_typeint(splicing_iit,"donor")) >= 0 &&
@@ -6443,12 +6529,12 @@ main (int argc, char *argv[]) {
Oligoindex_pmap_setup(genomecomp);
Oligop_setup(alphabet,alphabet_size,index1part_aa);
Indexdb_setup(index1part_aa);
- Stage1_setup(index1part_aa,maxextension,maxtotallen_bound,min_extra_end,circular_typeint);
+ Stage1_setup(index1part_aa,maxextension,maxtotallen_bound,circular_typeint);
#else
Oligoindex_hr_setup(Genome_blocks(genomecomp),mode);
Oligo_setup(index1part);
Indexdb_setup(index1part);
- Stage1_setup(index1part,maxextension,maxtotallen_bound,min_extra_end,circular_typeint);
+ Stage1_setup(index1part,maxextension,maxtotallen_bound,circular_typeint);
#endif
}
@@ -6466,8 +6552,8 @@ main (int argc, char *argv[]) {
/*print_nsnpdiffs_p*/genomecomp_alt ? true : false,genomelength);
Stage3_setup(/*splicingp*/novelsplicingp == true || knownsplicingp == true,novelsplicingp,
require_splicedir_p,splicing_iit,splicing_divint_crosstable,
- donor_typeint,acceptor_typeint,
- splicesites,min_intronlength,max_deletionlength,/*min_indel_end_matches*/6,
+ donor_typeint,acceptor_typeint,splicesites,altlocp,alias_starts,alias_ends,
+ min_intronlength,max_deletionlength,/*min_indel_end_matches*/6,
maxpeelback_distalmedial,nullgap,extramaterial_end,extramaterial_paired,
extraband_single,extraband_end,extraband_paired,
ngap,maxintronlen,/*output_sam_p*/printtype == SAM ? true : false,
@@ -6717,6 +6803,11 @@ main (int argc, char *argv[]) {
if (contig_iit != NULL) {
Univ_IIT_free(&contig_iit);
}
+ if (altlocp != NULL) {
+ FREE(alias_ends);
+ FREE(alias_starts);
+ FREE(altlocp);
+ }
if (circularp != NULL) {
FREE(circularp);
}
diff --git a/src/gmap_select.c b/src/gmap_select.c
new file mode 100644
index 0000000..9a3e335
--- /dev/null
+++ b/src/gmap_select.c
@@ -0,0 +1,195 @@
+#include "bool.h"
+#include "cpuid.h"
+#include <errno.h>
+#include <sys/stat.h> /* For fstat */
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <string.h>
+#include <libgen.h>
+#include <unistd.h>
+
+static bool
+file_exists_p (char *filename) {
+ struct stat sb;
+
+ if (stat(filename,&sb) == 0) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+int
+main (int argc, char *argv[]) {
+ bool sse2_support_p;
+ bool ssse3_support_p;
+ bool sse4_1_support_p;
+ bool sse4_2_support_p;
+ bool avx2_support_p;
+ char *dir, **new_argv;
+ int i;
+ int rc;
+
+ CPUID_support(&sse2_support_p,&ssse3_support_p,&sse4_1_support_p,&sse4_2_support_p,&avx2_support_p);
+
+ new_argv = (char **) malloc((argc + 1) * sizeof(char *));
+ for (i = 1; i < argc; i++) {
+ new_argv[i] = argv[i];
+ }
+ new_argv[argc] = (char *) NULL;
+
+ if (index(argv[0],'/') == NULL) {
+ /* Depend on path */
+ /* Cannot use file_exists_p, since it won't search PATH */
+
+ if (avx2_support_p == true) {
+ new_argv[0] = "gmap.avx2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = "gmap.sse42";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = "gmap.sse41";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = "gmap.ssse3";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = "gmap.sse2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = "gmap.nosimd";
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv);
+ return rc;
+ }
+
+ } else {
+ dir = dirname(argv[0]);
+
+ if (avx2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.avx2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmap.avx2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse42") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmap.sse42",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse41") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmap.sse41",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.ssse3") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmap.ssse3",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.sse2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmap.sse2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmap.nosimd") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmap.nosimd",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an non-SIMD machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+ }
+
+ fprintf(stderr,"Error: appropriate GMAP version not found\n");
+ free(new_argv);
+ return -1;
+}
+
diff --git a/src/gmapindex.c b/src/gmapindex.c
index ec0be93..15bce5e 100644
--- a/src/gmapindex.c
+++ b/src/gmapindex.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gmapindex.c 167265 2015-06-11 00:04:50Z twu $";
+static char rcsid[] = "$Id: gmapindex.c 186742 2016-03-31 00:44:01Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -46,6 +46,7 @@ typedef Tableuint_T Table_chrpos_T;
#include "sarray-write.h"
#include "bytecoding.h"
#include "bitpack64-write.h"
+#include "parserange.h"
#ifdef HAVE_SSE2
#include <emmintrin.h>
@@ -53,13 +54,21 @@ typedef Tableuint_T Table_chrpos_T;
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+/* Skip popcnt */
+#elif defined(HAVE_POPCNT)
#include <immintrin.h>
#endif
-#if defined(HAVE_MM_POPCNT)
+
+#if !defined(HAVE_SSE4_2)
+/* Skip mm_popcnt */
+#elif defined(HAVE_MM_POPCNT)
#include <nmmintrin.h>
#endif
-#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
+
+#if !defined(HAVE_SSE4_2)
+/* Skip lzcnt and tzcnt */
+#elif defined(HAVE_LZCNT) || defined(HAVE_TZCNT)
#include <immintrin.h>
#endif
@@ -104,6 +113,8 @@ static char *sortfilename = NULL;
static bool huge_offsets_p = false;
+#if 0
+/* Using non-SIMD code, so no need to check compiler assumptions */
static void
check_compiler_assumptions () {
unsigned int x = rand(), y = rand();
@@ -124,7 +135,7 @@ check_compiler_assumptions () {
#ifdef HAVE_BUILTIN_CLZ
fprintf(stderr,"__builtin_clz=%d ",__builtin_clz(x));
#endif
-#ifdef HAVE_BMI1
+#ifdef HAVE_TZCNT
fprintf(stderr,"_tzcnt_u32=%d ",_tzcnt_u32(x));
#endif
#ifdef HAVE_BUILTIN_CTZ
@@ -185,6 +196,7 @@ check_compiler_assumptions () {
return;
}
+#endif
#if 0
@@ -312,16 +324,19 @@ static void
store_accession (Table_T accsegmentpos_table, Table_chrpos_T chrlength_table, Tableuint_T chrorder_table,
char *accession, char *chr_string, Chrpos_T chrpos1,
Chrpos_T chrpos2, bool revcompp, Chrpos_T seglength,
- int contigtype, unsigned int universal_coord, bool circularp) {
+ int contigtype, unsigned int universal_coord, bool circularp,
+ Chrpos_T alt_scaffold_start, Chrpos_T alt_scaffold_end) {
Chrom_T chrom;
Segmentpos_T segmentpos;
unsigned int order;
if (chrorder_table != NULL) {
order = Tableuint_get(chrorder_table,chr_string);
- chrom = Chrom_from_string(chr_string,mitochondrial_string,order,circularp);
+ chrom = Chrom_from_string(chr_string,mitochondrial_string,order,circularp,
+ alt_scaffold_start,alt_scaffold_end);
} else {
- chrom = Chrom_from_string(chr_string,mitochondrial_string,/*order*/universal_coord,circularp);
+ chrom = Chrom_from_string(chr_string,mitochondrial_string,/*order*/universal_coord,circularp,
+ alt_scaffold_start,alt_scaffold_end);
}
segmentpos = Segmentpos_new(chrom,chrpos1,chrpos2,revcompp,seglength,contigtype);
@@ -406,12 +421,15 @@ skip_sequence (Chrpos_T seglength) {
static bool
process_sequence_aux (Chrpos_T *seglength, Table_T accsegmentpos_table, Table_chrpos_T chrlength_table,
- Tableuint_T chrorder_table, char *fileroot, int ncontigs) {
+ Tableuint_T chrorder_table, Table_T alt_scaffold_info_table,
+ char *fileroot, int ncontigs) {
char Buffer[BUFFERSIZE], accession_p[BUFFERSIZE], *accession,
- chrpos_string[BUFFERSIZE], *chr_string, *coords, *ptr, *p;
- Chrpos_T chrpos1, chrpos2, lower, upper;
+ chrpos_string[BUFFERSIZE], primary_string[BUFFERSIZE], *chr_string, *coords, *ptr, *p;
+ Chrpos_T chrpos1, chrpos2, lower, upper, primary_chrstart, primary_chrend;
Univcoord_T universal_coord = 0U;
bool revcompp, circularp;
+ Chrpos_T alt_scaffold_start, alt_scaffold_end;
+ char *alt_scaffold_chr, *altscaffold_info, *primary_chr;
int nitems;
/* Store sequence info */
@@ -497,8 +515,12 @@ process_sequence_aux (Chrpos_T *seglength, Table_T accsegmentpos_table, Table_ch
while (*p != '\0' && isspace((int) *p)) { p++; } /* Skip past third space */
circularp = false;
+ alt_scaffold_start = alt_scaffold_end = 0;
if (*p == '\0') {
/* circularp = false; */
+ if (ncontigs < nmessages) {
+ fprintf(stderr," => primary (linear) chromosome");
+ }
} else {
if ((ptr = rindex(p,'\n')) != NULL) {
while (isspace((int) *ptr)) { ptr--; } /* Erase empty space */
@@ -506,16 +528,56 @@ process_sequence_aux (Chrpos_T *seglength, Table_T accsegmentpos_table, Table_ch
*ptr = '\0';
}
if (!strcmp(p,"circular")) {
- fprintf(stderr,"%s is a circular chromosome\n",chr_string);
+ if (ncontigs < nmessages) {
+ fprintf(stderr," => circular chromosome");
+ }
circularp = true;
+ } else if (!strcmp(p,"linear")) {
+ /* Ignore. Not a altloc chromosome. */
+ if (ncontigs < nmessages) {
+ fprintf(stderr," => primary (linear) chromosome");
+ }
+
} else {
- fprintf(stderr,"%s has an unrecognized tag %s\n",chr_string,p);
+ /* Alternate scaffold. Store primary information as a new type. */
+ if (ncontigs < nmessages) {
+ fprintf(stderr," => alternate scaffold for segment %s",p);
+ }
+
+ if (sscanf(p,"%u..%u",&alt_scaffold_start,&alt_scaffold_end) == 2) {
+ while (*p != '\0' && *p != ',') {
+ p++;
+ }
+ if (*p == '\0') {
+ fprintf(stderr,"Expected to find a comma in the altscaffold tag\n");
+ } else {
+ p++;
+ if (Parserange_simple(&primary_chr,&revcompp,&primary_chrstart,&primary_chrend,p) == false) {
+ fprintf(stderr,"Cannot parse %s\n",p);
+ abort();
+ } else {
+ sprintf(primary_string,"%u..%u,%s:%u..%u\n",
+ alt_scaffold_start,alt_scaffold_end,primary_chr,primary_chrstart,primary_chrend);
+ }
+ altscaffold_info = (char *) CALLOC(strlen(primary_string)+1,sizeof(char));
+ strcpy(altscaffold_info,primary_string);
+
+ alt_scaffold_chr = (char *) CALLOC(strlen(chr_string)+1,sizeof(char));
+ strcpy(alt_scaffold_chr,chr_string);
+
+ Table_put(alt_scaffold_info_table,(void *) alt_scaffold_chr,(void *) altscaffold_info);
+ }
+ }
}
}
/* The '>' character was already stripped off by the last call to count_sequence() */
accession = (char *) CALLOC(strlen(accession_p)+1,sizeof(char));
strcpy(accession,accession_p);
+
+ if (ncontigs < nmessages) {
+ fprintf(stderr,"\n");
+ }
}
if (rawp == true) {
@@ -536,7 +598,8 @@ process_sequence_aux (Chrpos_T *seglength, Table_T accsegmentpos_table, Table_ch
store_accession(accsegmentpos_table,chrlength_table,chrorder_table,
accession,chr_string,lower,upper,revcompp,
- *seglength,/*contigtype*/0,universal_coord,circularp);
+ *seglength,/*contigtype*/0,universal_coord,circularp,
+ alt_scaffold_start,alt_scaffold_end);
return true;
}
@@ -556,7 +619,7 @@ write_chromosome_file (char *genomesubdir, char *fileroot, Table_chrpos_T chrlen
int typeint;
Chrom_T *chroms;
Univcoord_T chroffset = 0;
- Chrpos_T chrlength;
+ Chrpos_T chrlength, alt_scaffold_start, alt_scaffold_end;
List_T divlist = NULL;
List_T intervallist = NULL, chrtypelist = NULL, labellist = NULL, annotlist = NULL, p;
Table_T intervaltable, labeltable, annottable;
@@ -598,6 +661,8 @@ write_chromosome_file (char *genomesubdir, char *fileroot, Table_chrpos_T chrlen
textfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".chromosome")+1,sizeof(char));
sprintf(textfile,"%s/%s.chromosome",genomesubdir,fileroot);
+ fprintf(stderr,"Writing chromosome file %s\n",textfile);
+
/* Use binary, not text, so files are Unix-compatible */
if ((textfp = FOPEN_WRITE_BINARY(textfile)) == NULL) {
fprintf(stderr,"Can't write to file %s\n",textfile);
@@ -617,8 +682,10 @@ write_chromosome_file (char *genomesubdir, char *fileroot, Table_chrpos_T chrlen
fprintf(chrsubsetfp,">all\n");
fprintf(chrsubsetfp,"\n");
- chrtypelist = List_push(chrtypelist,"circular");
- chrtypelist = List_push(chrtypelist,"");
+ chrtypelist = List_push(chrtypelist,"circular"); /* typeint 1 */
+ chrtypelist = List_push(chrtypelist,""); /* typeint 0 */
+
+
for (i = 0; i < n; i++) {
#ifdef HAVE_64_BIT
chrlength = (Chrpos_T) Tableuint8_get(chrlength_table,chroms[i]);
@@ -664,6 +731,9 @@ write_chromosome_file (char *genomesubdir, char *fileroot, Table_chrpos_T chrlen
if (Chrom_circularp(chroms[i]) == true) {
chroffset += (Univcoord_T) chrlength;
chroffset += (Univcoord_T) chrlength;
+ } else if (Chrom_altlocp(&alt_scaffold_start,&alt_scaffold_end,chroms[i]) == true) {
+ /* Handle same as primary, non-circular */
+ chroffset += chrlength;
} else {
chroffset += (Univcoord_T) chrlength;
}
@@ -691,6 +761,7 @@ write_chromosome_file (char *genomesubdir, char *fileroot, Table_chrpos_T chrlen
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
sprintf(iitfile,"%s/%s.chromosome.iit",genomesubdir,fileroot);
+ fprintf(stderr,"Writing chromosome IIT file %s\n",iitfile);
IIT_write_univ(iitfile,divlist,chrtypelist,
intervaltable,labeltable,annottable,
coord_values_8p,/*label_pointers_8p*/false,/*annot_pointers_8p*/false);
@@ -720,8 +791,128 @@ write_chromosome_file (char *genomesubdir, char *fileroot, Table_chrpos_T chrlen
return;
}
+static void
+write_alt_scaffold_file (char *genomesubdir, char *fileroot, Table_T alt_scaffold_info_table,
+ Univ_IIT_T chromosome_iit, bool coord_values_8p) {
+ char *iitfile, Buffer[1024];
+ char **alt_chrs, *altloc_chr, *altscaffold_info, primary_chr[1024], *p, *q;
+ char *divstring, *annot;
+ Univinterval_T interval;
+ Univcoord_T chroffset;
+ Chrpos_T alt_scaffold_start, alt_scaffold_end, primary_start, primary_end;
+ int n, i;
+ int index;
+ List_T intervallist = NULL, labellist = NULL, annotlist = NULL, chrtypelist = NULL, divlist = NULL;
+ Table_T intervaltable, labeltable, annottable;
+ /* bool revcompp; */
+
+
+ if ((n = Table_length(alt_scaffold_info_table)) == 0) {
+ printf("No alternate scaffolds observed\n");
+
+ } else {
+ alt_chrs = (char **) Table_keys(alt_scaffold_info_table,0U);
+
+ for (i = 0; i < n; i++) {
+ altloc_chr = alt_chrs[i];
+ if ((index = Univ_IIT_find_linear(chromosome_iit,altloc_chr)) < 0) {
+ fprintf(stderr,"Error: Could not find alternate chromosome %s in IIT file\n",altloc_chr);
+ abort();
+ } else {
+ interval = Univ_IIT_interval(chromosome_iit,index);
+ chroffset = Univinterval_low(interval);
+ }
+
+ altscaffold_info = (char *) Table_get(alt_scaffold_info_table,(void *) altloc_chr);
+#if 0
+ fprintf(textfp,"\t%s",altscaffold_info); /* contains a tab character */
+#endif
+ if (sscanf(altscaffold_info,"%u..%u",&alt_scaffold_start,&alt_scaffold_end) < 2) {
+ fprintf(stderr,"Could not parse altscaffold_info %s\n",altscaffold_info);
+ abort();
+ } else {
+ p = altscaffold_info;
+ while (*p != '\0' && *p != ',') {
+ p++;
+ }
+ if (*p == '\0') {
+ fprintf(stderr,"Expected to find a comma in the altscaffold tag\n");
+ } else {
+ p++;
+ q = p;
+ while (*q != '\0' && *q != ':') {
+ q++;
+ }
+ strncpy(primary_chr,p,q-p);
+ primary_chr[q-p] = '\0';
+ q++;
+ p = q;
+
+ if (sscanf(p,"%u..%u\n",&primary_start,&primary_end) < 2) {
+ fprintf(stderr,"Could not parse altscaffold_info %s\n",p);
+ abort();
+ } else if ((index = Univ_IIT_find_linear(chromosome_iit,primary_chr)) < 0) {
+ fprintf(stderr,"Warning: Could not find primary chromosome %s in IIT file, so ignoring alt scaffold %s:%u..%u\n",
+ primary_chr,altloc_chr,alt_scaffold_start,alt_scaffold_end);
+ } else {
+ intervallist = List_push(intervallist,
+ (void *) Univinterval_new(chroffset + alt_scaffold_start-1U, /* zero-based */
+ chroffset + alt_scaffold_end,
+ /*type*/0));
+ labellist = List_push(labellist,(void *) altloc_chr);
+
+ sprintf(Buffer,"%s:%u..%u",primary_chr,primary_start,primary_end);
+ annot = (char *) CALLOC(strlen(Buffer)+1,sizeof(char));
+ strcpy(annot,Buffer);
+ annotlist = List_push(annotlist,(void *) annot);
+ }
+ }
+ }
+ }
+
+ /* Write alt_scaffold IIT file */
+ divstring = (char *) CALLOC(1,sizeof(char));
+ divstring[0] = '\0';
+ divlist = List_push(NULL,divstring);
+
+ intervaltable = Table_new(65522,Table_string_compare,Table_string_hash);
+ labeltable = Table_new(65522,Table_string_compare,Table_string_hash);
+ annottable = Table_new(65522,Table_string_compare,Table_string_hash);
+
+ Table_put(intervaltable,(void *) divstring,intervallist);
+ Table_put(labeltable,(void *) divstring,labellist);
+ Table_put(annottable,(void *) divstring,annotlist);
+
+ chrtypelist = List_push(chrtypelist,""); /* typeint 0 */
+
+ iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
+ strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
+ sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
+ fprintf(stderr,"Writing altscaffold IIT file %s\n",iitfile);
+ IIT_write_univ(iitfile,divlist,chrtypelist,
+ intervaltable,labeltable,annottable,
+ coord_values_8p,/*label_pointers_8p*/false,/*annot_pointers_8p*/false);
+ FREE(iitfile);
+
+ List_free(&chrtypelist); /* chrtypelist has a single static string */
+
+ List_free(&divlist);
+ FREE(divstring);
+
+ Table_free(&annottable);
+ Table_free(&labeltable);
+ Table_free(&intervaltable);
+
+ List_free(&annotlist);
+ }
+
+ return;
+}
+
+
static Table_T current_accsegmentpos_table;
+#if 0
/* x is really a char ** */
static int
bysegmentpos_compare_alpha (const void *x, const void *y) {
@@ -732,6 +923,8 @@ bysegmentpos_compare_alpha (const void *x, const void *y) {
return Segmentpos_compare_alpha(&a,&b);
}
+#endif
+
static int
bysegmentpos_compare (const void *x, const void *y) {
@@ -991,6 +1184,32 @@ accsegmentpos_table_gc (Table_T *accsegmentpos_table) {
return;
}
+static void
+alt_scaffold_info_table_gc (Table_T *alt_scaffold_info_table) {
+ int n, i = 0;
+ char *altloc_chr, *altscaffold_info;
+ void **keys, **values;
+
+ if ((n = Table_length(*alt_scaffold_info_table)) > 0) {
+ keys = Table_keys(*alt_scaffold_info_table,NULL);
+ values = Table_values(*alt_scaffold_info_table,NULL);
+ for (i = 0; i < n; i++) {
+ altloc_chr = (char *) keys[i];
+ FREE(altloc_chr);
+ }
+ for (i = 0; i < n; i++) {
+ altscaffold_info = (char *) values[i];
+ FREE(altscaffold_info);
+ }
+ FREE(values);
+ FREE(keys);
+ }
+
+ Table_free(&(*alt_scaffold_info_table));
+ return;
+}
+
+
#if 0
static char *
remove_slashes (char *buffer) {
@@ -1043,8 +1262,7 @@ int getopt (int argc, char *const argv[], const char *optstring);
int
main (int argc, char *argv[]) {
int ncontigs;
- Table_T accsegmentpos_table;
- int shmid;
+ Table_T accsegmentpos_table, alt_scaffold_info_table;
FILE *fp;
char *key, **keys, chrname[1024], chrname_alt[1024], Buffer[1024];
@@ -1073,7 +1291,7 @@ main (int argc, char *argv[]) {
char *indexijptrsfile, *indexijcompfile;
#endif
UINT4 start, end;
- UINT4 *SA, *lcp, *child;
+ UINT4 *SA;
UINT4 nbytes;
Filenames_T filenames;
Chrpos_T seglength;
@@ -1082,12 +1300,14 @@ main (int argc, char *argv[]) {
unsigned char *discrim_chars;
unsigned char *lcp_bytes;
UINT4 *lcp_guide, *lcp_exceptions;
- int n_lcp_exceptions;
+ UINT4 n_lcp_exceptions;
unsigned char *lcpchilddc;
+ unsigned char *child_bytes;
UINT4 *child_guide, *child_exceptions;
- int n_child_exceptions;
+ UINT4 n_child_exceptions;
+ Access_T lcpguide_access, lcpexc_access, childguide_access, childexc_access;
int sa_fd, lcpchilddc_fd;
size_t sa_len, lcpchilddc_len, lcpguide_len, lcpexc_len, childguide_len, childexc_len;
double seconds;
@@ -1163,7 +1383,7 @@ main (int argc, char *argv[]) {
case 'm': mask_lowercase_p = true; break;
- case '9': check_compiler_assumptions(); return 0; break;
+ case '9': /* check_compiler_assumptions(); */ return 0; break;
default: fprintf(stderr,"Unknown flag %c\n",c); exit(9);
@@ -1237,6 +1457,8 @@ main (int argc, char *argv[]) {
#else
chrlength_table = Tableuint_new(65522,Chrom_compare_table,Chrom_hash_table);
#endif
+ alt_scaffold_info_table = Table_new(65522,Table_string_compare,Table_string_hash);
+
#if 0
/* No longer supporting strains */
@@ -1253,8 +1475,11 @@ main (int argc, char *argv[]) {
contigtypelist = List_push(NULL,typestring);
ncontigs = 0;
- totalnts = 0;
- while (process_sequence_aux(&seglength,accsegmentpos_table,chrlength_table,chrorder_table,fileroot,ncontigs) == true) {
+ totalnts = 0U;
+
+ while (process_sequence_aux(&seglength,accsegmentpos_table,chrlength_table,
+ chrorder_table,alt_scaffold_info_table,
+ fileroot,ncontigs) == true) {
if (totalnts + seglength < totalnts) {
/* Exceeds 32 bits */
fprintf(stderr,"The total length of genomic sequence exceeds 2^32 = 4,294,967,296 bp, which the GMAP index format cannot handle\n");
@@ -1284,6 +1509,18 @@ main (int argc, char *argv[]) {
write_chromosome_file(destdir,fileroot,chrlength_table,coord_values_8p);
write_contig_file(destdir,fileroot,accsegmentpos_table,chrlength_table,contigtypelist,coord_values_8p);
+ /* Note: We are using destdir here, not sourcedir */
+ chromosomefile = (char *) CALLOC(strlen(destdir)+strlen("/")+
+ strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
+ sprintf(chromosomefile,"%s/%s.chromosome.iit",destdir,fileroot);
+ if ((chromosome_iit = Univ_IIT_read(chromosomefile,/*readonlyp*/true,/*add_iit_p*/false)) == NULL) {
+ fprintf(stderr,"IIT file %s is not valid\n",chromosomefile);
+ exit(9);
+ }
+ write_alt_scaffold_file(destdir,fileroot,alt_scaffold_info_table,chromosome_iit,coord_values_8p);
+ Univ_IIT_free(&chromosome_iit);
+ FREE(chromosomefile);
+
for (p = contigtypelist; p != NULL; p = List_next(p)) {
typestring = (char *) List_head(p);
FREE(typestring);
@@ -1293,6 +1530,8 @@ main (int argc, char *argv[]) {
chrlength_table_gc(&chrlength_table);
accsegmentpos_table_gc(&accsegmentpos_table);
+ alt_scaffold_info_table_gc(&alt_scaffold_info_table);
+
if (chrorder_table != NULL) {
keys = (char **) Tableuint_keys(chrorder_table,NULL);
for (i = 0; i < Tableuint_length(chrorder_table); i++) {
@@ -1306,7 +1545,8 @@ main (int argc, char *argv[]) {
/* Usage: cat <fastafile> | gmapindex [-F <sourcedir>] [-D <destdir>] -d <dbname> -G
Requires <fastafile> in appropriate format and <sourcedir>/<dbname>.chromosome.iit
and <sourcedir>/<dbname>.contig.iit files.
- Creates <destdir>/<dbname>.genomecomp (in blocks of 32) */
+ Creates <destdir>/<dbname>.genomecomp (horizontal format in blocks of 32).
+ Then the unshuffle command creates another version (vertical format in blocks of 128). */
chromosomefile = (char *) CALLOC(strlen(sourcedir)+strlen("/")+
strlen(fileroot)+strlen(".chromosome.iit")+1,sizeof(char));
@@ -1329,7 +1569,7 @@ main (int argc, char *argv[]) {
if (Univ_IIT_ntypes(contig_iit) == 1) {
/* index1part needed only if writing an uncompressed genome using a file */
- Genome_write_comp32(destdir,fileroot,stdin,contig_iit,/*altstrain_iit*/NULL,
+ Genome_write_comp32(destdir,fileroot,stdin,contig_iit,
chromosome_iit,genome_lc_p,rawp,writefilep,
genomelength,index1part,nmessages);
} else if (Univ_IIT_ntypes(contig_iit) > 1) {
@@ -1399,7 +1639,7 @@ main (int argc, char *argv[]) {
Indexdb_write_offsets(destdir,interval_char,fp,chromosome_iit,
index1part,index1interval,
- genome_lc_p,fileroot,mask_lowercase_p,compression_types);
+ genome_lc_p,fileroot,mask_lowercase_p);
} else {
fprintf(stderr,"Offset compression types:");
if ((compression_types & BITPACK64_COMPRESSION) != 0) {
@@ -1409,7 +1649,7 @@ main (int argc, char *argv[]) {
Indexdb_write_offsets_huge(destdir,interval_char,fp,chromosome_iit,
index1part,index1interval,
- genome_lc_p,fileroot,mask_lowercase_p,compression_types);
+ genome_lc_p,fileroot,mask_lowercase_p);
}
if (argc > 0) {
@@ -1480,13 +1720,13 @@ main (int argc, char *argv[]) {
filenames->offsets_filename,fp,chromosome_iit,
index1part,index1interval,genomelength,
genome_lc_p,writefilep,fileroot,mask_lowercase_p,
- compression_type,coord_values_8p);
+ coord_values_8p);
} else {
Indexdb_write_positions_huge(positionsfile_high,positionsfile_low,filenames->pages_filename,filenames->pointers_filename,
filenames->offsets_filename,fp,chromosome_iit,
index1part,index1interval,genomelength,
genome_lc_p,writefilep,fileroot,mask_lowercase_p,
- compression_type,coord_values_8p);
+ coord_values_8p);
}
if (argc > 0) {
@@ -1601,6 +1841,7 @@ main (int argc, char *argv[]) {
sprintf(rankfile,"%s/%s.rank",destdir,fileroot);
permuted_sarray_file = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".permuted_sarray")+1,sizeof(char));
sprintf(permuted_sarray_file,"%s/%s.permuted_sarray",destdir,fileroot);
+#if 0
lcp = Sarray_compute_lcp(rankfile,permuted_sarray_file,sarrayfile,n);
FREE(permuted_sarray_file);
FREE(rankfile);
@@ -1614,27 +1855,37 @@ main (int argc, char *argv[]) {
sprintf(lcpguidefile,"%s/%s.salcpguide1024",destdir,fileroot);
lcp_bytes = Bytecoding_write_exceptions_only(lcpexcfile,lcpguidefile,lcp,genomelength,/*guide_interval*/1024);
-
FREE(lcpguidefile);
FREE(lcpexcfile);
FREE(lcp); /* Use lcp_bytes, which are more memory-efficient than lcp */
+#else
+ lcp_bytes = Sarray_compute_lcp_bytes(&lcp_exceptions,&n_lcp_exceptions,rankfile,permuted_sarray_file,sarrayfile,n);
+ FREE(permuted_sarray_file);
+ FREE(rankfile);
+
+ Genome_free(&genomebits);
+
+ /* Write lcp exceptions/guide */
+ lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".salcpexc")+1,sizeof(char));
+ sprintf(lcpexcfile,"%s/%s.salcpexc",destdir,fileroot);
+ lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".salcpguide1024")+1,sizeof(char));
+ sprintf(lcpguidefile,"%s/%s.salcpguide1024",destdir,fileroot);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,lcpexcfile,lcpguidefile,lcp_bytes,lcp_exceptions,n_lcp_exceptions,
+ genomelength,/*guide_interval*/1024);
+ FREE(lcpguidefile);
+ FREE(lcpexcfile);
+#endif
fprintf(stderr,"Building DC array\n");
- /* Assume we have lcp_bytes already in memory. Don't need to use guide for speed. */
+ /* Assume we have lcp_bytes and lcp_exceptions already in memory. Don't need to use guide for speed. */
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s.salcpguide1024",destdir,fileroot);
- lcp_guide = (UINT4 *) Access_allocate(&shmid,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4),/*sharedp*/false);
+ lcp_guide = (UINT4 *) Access_allocate_private(&lcpguide_access,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4));
FREE(lcpguidefile);
- lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".salcpexc")+1,sizeof(char));
- sprintf(lcpexcfile,"%s/%s.salcpexc",destdir,fileroot);
- lcp_exceptions = (UINT4 *) Access_allocate(&shmid,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4),/*sharedp*/false);
- n_lcp_exceptions = lcpexc_len/(sizeof(UINT4) + sizeof(UINT4));
- FREE(lcpexcfile);
-
genomecomp = Genome_new(sourcedir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_OLIGOS,
/*uncompressedp*/false,/*access*/USE_MMAP_ONLY,/*sharedp*/false);
@@ -1648,6 +1899,7 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Building child array\n");
+#if 0
/* Compute child array (relative values) */
child = Sarray_compute_child(lcp_bytes,lcp_guide,lcp_exceptions,n);
FREE(lcp_exceptions);
@@ -1667,6 +1919,30 @@ main (int argc, char *argv[]) {
FREE(lcpchilddcfile);
FREE(child);
+#else
+ /* Compute child array (relative values, directly to bytes and exceptions) */
+ child_bytes = Sarray_compute_child_bytes(&child_exceptions,&n_child_exceptions,lcp_bytes,lcp_guide,lcp_exceptions,n);
+ FREE(lcp_exceptions);
+ FREE(lcp_guide);
+
+ childexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".sachildexc")+1,sizeof(char));
+ sprintf(childexcfile,"%s/%s.sachildexc",destdir,fileroot);
+ childguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".sachildguide1024")+1,sizeof(char));
+ sprintf(childguidefile,"%s/%s.sachildguide1024",destdir,fileroot);
+ Bytecoding_write_bytes(/*bytesfile*/NULL,childexcfile,childguidefile,child_bytes,child_exceptions,n_child_exceptions,
+ genomelength,/*guide_interval*/1024);
+ FREE(childguidefile);
+ FREE(childexcfile);
+ FREE(child_exceptions);
+
+ /* Write combined lcpchilddc file */
+ lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(".salcpchilddc")+1,sizeof(char));
+ sprintf(lcpchilddcfile,"%s/%s.salcpchilddc",destdir,fileroot);
+ Bytecoding_interleave_lcpchilddc(lcpchilddcfile,child_bytes,discrim_chars,lcp_bytes,genomelength);
+ FREE(lcpchilddcfile);
+ FREE(child_bytes);
+#endif
+
FREE(discrim_chars);
FREE(lcp_bytes);
}
@@ -1789,40 +2065,44 @@ main (int argc, char *argv[]) {
sarrayfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("sarray")+1,sizeof(char));
sprintf(sarrayfile,"%s/%s%ssarray",destdir,fileroot,mode_prefix);
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/true);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/true);
FREE(sarrayfile);
lcpchilddcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("salcpchilddc")+1,sizeof(char));
sprintf(lcpchilddcfile,"%s/%s%ssalcpchilddc",destdir,fileroot,mode_prefix);
- lcpchilddc = (unsigned char *) Access_mmap(&lcpchilddc_fd,&lcpchilddc_len,lcpchilddcfile,
- sizeof(unsigned char),/*randomp*/true);
+ lcpchilddc = (unsigned char *) Access_mmap(&lcpchilddc_fd,&lcpchilddc_len,lcpchilddcfile,/*randomp*/true);
FREE(lcpchilddcfile);
lcpguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("salcpguide1024")+1,sizeof(char));
sprintf(lcpguidefile,"%s/%s%ssalcpguide1024",destdir,fileroot,mode_prefix);
- lcp_guide = (UINT4 *) Access_allocate(&shmid,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4),/*sharedp*/false);
+ lcp_guide = (UINT4 *) Access_allocate_private(&lcpguide_access,&lcpguide_len,&seconds,lcpguidefile,sizeof(UINT4));
FREE(lcpguidefile);
lcpexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("salcpexc")+1,sizeof(char));
sprintf(lcpexcfile,"%s/%s%ssalcpexc",destdir,fileroot,mode_prefix);
- lcp_exceptions = (UINT4 *) Access_allocate(&shmid,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4),/*sharedp*/false);
+ lcp_exceptions = (UINT4 *) Access_allocate_private(&lcpexc_access,&lcpexc_len,&seconds,lcpexcfile,sizeof(UINT4));
n_lcp_exceptions = lcpexc_len/(sizeof(UINT4) + sizeof(UINT4));
FREE(lcpexcfile);
childguidefile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("sachildguide1024")+1,sizeof(char));
sprintf(childguidefile,"%s/%s%ssachildguide1024",destdir,fileroot,mode_prefix);
- child_guide = (UINT4 *) Access_allocate(&shmid,&childguide_len,&seconds,childguidefile,sizeof(UINT4),/*sharedp*/false);
+ child_guide = (UINT4 *) Access_allocate_private(&childguide_access,&childguide_len,&seconds,childguidefile,sizeof(UINT4));
FREE(childguidefile);
childexcfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("sachildexc")+1,sizeof(char));
sprintf(childexcfile,"%s/%s%ssachildexc",destdir,fileroot,mode_prefix);
- child_exceptions = (UINT4 *) Access_allocate(&shmid,&childexc_len,&seconds,childexcfile,sizeof(UINT4),/*sharedp*/false);
+ child_exceptions = (UINT4 *) Access_allocate_private(&childexc_access,&childexc_len,&seconds,childexcfile,sizeof(UINT4));
n_child_exceptions = childexc_len/(sizeof(UINT4) + sizeof(UINT4));
FREE(childexcfile);
Sarray_child_uncompress(genomecomp,lcpchilddc,lcp_guide,lcp_exceptions,n_lcp_exceptions,
child_guide,child_exceptions,n_child_exceptions,SA,genomelength,start,end);
+ FREE(child_exceptions); /* Not using shared */
+ FREE(child_guide); /* Not using shared */
+ FREE(lcp_exceptions); /* Not using shared */
+ FREE(lcp_guide); /* Not using shared */
+
Genome_free(&genomecomp);
munmap((void *) lcpchilddc,lcpchilddc_len);
diff --git a/src/gmapl_select.c b/src/gmapl_select.c
new file mode 100644
index 0000000..0b908ca
--- /dev/null
+++ b/src/gmapl_select.c
@@ -0,0 +1,195 @@
+#include "bool.h"
+#include "cpuid.h"
+#include <errno.h>
+#include <sys/stat.h> /* For fstat */
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <string.h>
+#include <libgen.h>
+#include <unistd.h>
+
+static bool
+file_exists_p (char *filename) {
+ struct stat sb;
+
+ if (stat(filename,&sb) == 0) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+int
+main (int argc, char *argv[]) {
+ bool sse2_support_p;
+ bool ssse3_support_p;
+ bool sse4_1_support_p;
+ bool sse4_2_support_p;
+ bool avx2_support_p;
+ char *dir, **new_argv;
+ int i;
+ int rc;
+
+ CPUID_support(&sse2_support_p,&ssse3_support_p,&sse4_1_support_p,&sse4_2_support_p,&avx2_support_p);
+
+ new_argv = (char **) malloc((argc + 1) * sizeof(char *));
+ for (i = 1; i < argc; i++) {
+ new_argv[i] = argv[i];
+ }
+ new_argv[argc] = (char *) NULL;
+
+ if (index(argv[0],'/') == NULL) {
+ /* Depend on path */
+ /* Cannot use file_exists_p, since it won't search PATH */
+
+ if (avx2_support_p == true) {
+ new_argv[0] = "gmapl.avx2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = "gmapl.sse42";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = "gmapl.sse41";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = "gmapl.ssse3";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = "gmapl.sse2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = "gmapl.nosimd";
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv);
+ return rc;
+ }
+
+ } else {
+ dir = dirname(argv[0]);
+
+ if (avx2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.avx2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmapl.avx2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse42") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmapl.sse42",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse41") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmapl.sse41",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.ssse3") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmapl.ssse3",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.sse2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmapl.sse2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gmapl.nosimd") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gmapl.nosimd",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an non-SIMD machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+ }
+
+ fprintf(stderr,"Error: appropriate GMAPL version not found\n");
+ free(new_argv);
+ return -1;
+}
+
diff --git a/src/gregion.c b/src/gregion.c
index c197605..d5df0d0 100644
--- a/src/gregion.c
+++ b/src/gregion.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gregion.c 151507 2014-10-22 19:37:48Z twu $";
+static char rcsid[] = "$Id: gregion.c 184461 2016-02-18 00:07:47Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -313,8 +313,8 @@ Gregion_new (int nexons, Univcoord_T genomicstart, Univcoord_T genomicend,
debug5(printf(" Testing bound5+extension5 = %d - %u < %d + %d, bound3 = %d + %u > %d - %d\n",
new->querystart,new->extension5,trimstart,SUFFICIENT_SUPPORT,
new->queryend,new->extension3,trimend,SUFFICIENT_SUPPORT));
- if (new->querystart - new->extension5 < trimstart + SUFFICIENT_SUPPORT &&
- new->queryend + new->extension3 > trimend - SUFFICIENT_SUPPORT) {
+ if (new->querystart - new->extension5 < (Chrpos_T) (trimstart + SUFFICIENT_SUPPORT) &&
+ new->queryend + new->extension3 > (Chrpos_T) (trimend - SUFFICIENT_SUPPORT)) {
new->sufficient_support_p = true;
} else {
new->sufficient_support_p = false;
@@ -657,8 +657,7 @@ Gregion_sufficient_support (T this) {
void
-Gregion_extend (T this, Chrpos_T extension5, Chrpos_T extension3, int querylength,
- int min_extra_end) {
+Gregion_extend (T this, Chrpos_T extension5, Chrpos_T extension3, int querylength) {
Chrpos_T left, right;
int extra_end;
@@ -739,8 +738,8 @@ Gregion_extend (T this, Chrpos_T extension5, Chrpos_T extension3, int querylengt
debug5(printf(" Testing bound5+extension5 = %d - %u < %d + %d, bound3 = %d + %u > %d - %d\n",
this->querystart,this->extension5,this->trimstart,SUFFICIENT_SUPPORT,
this->queryend,this->extension3,this->trimend,SUFFICIENT_SUPPORT));
- if (this->querystart - this->extension5 < this->trimstart + SUFFICIENT_SUPPORT &&
- this->queryend + this->extension3 > this->trimend - SUFFICIENT_SUPPORT) {
+ if (this->querystart - this->extension5 < (Chrpos_T) (this->trimstart + SUFFICIENT_SUPPORT) &&
+ this->queryend + this->extension3 > (Chrpos_T) (this->trimend - SUFFICIENT_SUPPORT)) {
this->sufficient_support_p = true;
} else {
this->sufficient_support_p = false;
diff --git a/src/gregion.h b/src/gregion.h
index 8b54a0f..95fcba7 100644
--- a/src/gregion.h
+++ b/src/gregion.h
@@ -1,4 +1,4 @@
-/* $Id: gregion.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: gregion.h 184461 2016-02-18 00:07:47Z twu $ */
#ifndef GREGION_INCLUDED
#define GREGION_INCLUDED
@@ -107,8 +107,7 @@ extern bool
Gregion_sufficient_support (T this);
extern void
-Gregion_extend (T this, Chrpos_T extension5, Chrpos_T extension3, int querylength,
- int min_extra_end);
+Gregion_extend (T this, Chrpos_T extension5, Chrpos_T extension3, int querylength);
extern int
Gregion_cmp (const void *a, const void *b);
diff --git a/src/gsnap.c b/src/gsnap.c
index add5511..9b339b7 100644
--- a/src/gsnap.c
+++ b/src/gsnap.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gsnap.c 186090 2016-03-17 22:21:17Z twu $";
+static char rcsid[] = "$Id: gsnap.c 186727 2016-03-30 23:02:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -24,13 +24,22 @@ static char rcsid[] = "$Id: gsnap.c 186090 2016-03-17 22:21:17Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+/* Skip popcnt */
+#elif defined(HAVE_POPCNT)
#include <immintrin.h>
#endif
-#if defined(HAVE_MM_POPCNT)
+
+#if !defined(HAVE_SSE4_2)
+/* Skip mm_popcnt */
+#elif defined(HAVE_MM_POPCNT)
#include <nmmintrin.h>
#endif
-#if defined(HAVE_LZCNT) || defined(HAVE_BMI1)
+
+
+#if !defined(HAVE_SSE4_2)
+/* Skip lzcnt/tzcnt */
+#elif defined(HAVE_LZCNT) || defined(HAVE_TZCNT)
#include <immintrin.h>
#endif
@@ -180,6 +189,11 @@ static int circular_typeint = -1;
static int nchromosomes = 0;
static bool *circularp = NULL;
static bool any_circular_p;
+
+static bool *altlocp = NULL;
+static Univcoord_T *alias_starts = NULL;
+static Univcoord_T *alias_ends = NULL;
+
static Indexdb_T indexdb = NULL;
static Indexdb_T indexdb2 = NULL; /* For cmet or atoi */
static Genome_T genomecomp = NULL;
@@ -244,7 +258,10 @@ static int trim_mismatch_score = -3;
static int trim_indel_score = -2; /* was -4 */
+static bool multiple_sequences_p;
static bool sharedp = true;
+static bool preload_shared_memory_p = false;
+static bool unload_shared_memory_p = false;
static bool expand_offsets_p = false;
/* Note: sarray aux files (like lcpchilddc) are always allocated */
@@ -267,7 +284,8 @@ static Access_mode_T guideexc_access = USE_ALLOCATE;
static Access_mode_T indexij_access = USE_ALLOCATE;
#endif
-static int pairmax;
+static int pairmax_linear;
+static int pairmax_circular;
static int pairmax_dna = 1000;
static int pairmax_rna = 200000;
static int expected_pairlength = 200;
@@ -307,7 +325,7 @@ static int indel_penalty_middle = 2;
static int indel_penalty_end = 2;
static bool allow_end_indels_p = true;
-static int max_middle_insertions = 9;
+static int max_middle_insertions = -1;
static int max_middle_deletions = 30;
static int max_end_insertions = 3;
static int max_end_deletions = 6;
@@ -323,6 +341,8 @@ static int min_shortend = 2;
/* static bool find_novel_doublesplices_p = true; */
static int antistranded_penalty = 0; /* Most RNA-Seq is non-stranded */
+static int end_detail = 1; /* 2 (high), 1 (medium), or 0 (low) */
+
static Width_T index1part;
static Width_T required_index1part = 0;
static Width_T index1interval;
@@ -491,6 +511,8 @@ static struct option long_options[] = {
/* Compute options */
{"use-shared-memory", required_argument, 0, 0}, /* sharedp */
+ {"preload-shared-memory", no_argument, 0, 0}, /* preload_shared_memory_p */
+ {"unload-shared-memory", no_argument, 0, 0}, /* unload_shared_memory_p */
#ifdef HAVE_MMAP
{"batch", required_argument, 0, 'B'}, /* offsetsstrm_access, positions_access, genome_access */
#endif
@@ -536,6 +558,7 @@ static struct option long_options[] = {
{"ambig-splice-noclip", no_argument, 0, 0}, /* amb_clip_p */
{"genes", required_argument, 0, 'g'}, /* genes_iit */
{"favor-multiexon", no_argument, 0, 0}, /* favor_multiexon_p */
+ {"end-detail", required_argument, 0, 0}, /* end_detail */
{"local-splice-penalty", required_argument, 0, 'e'}, /* localsplicing_penalty */
{"distant-splice-penalty", required_argument, 0, 'E'}, /* distantsplicing_penalty */
@@ -755,34 +778,6 @@ check_compiler_assumptions () {
#endif
#endif
-
- fprintf(stderr,"Checking compiler assumptions for popcnt: ");
- fprintf(stderr,"%08X ",x);
-#ifdef HAVE_LZCNT
- fprintf(stderr,"_lzcnt_u32=%d ",_lzcnt_u32(x));
-#endif
-#ifdef HAVE_BUILTIN_CLZ
- fprintf(stderr,"__builtin_clz=%d ",__builtin_clz(x));
-#endif
-#ifdef HAVE_BMI1
- fprintf(stderr,"_tzcnt_u32=%d ",_tzcnt_u32(x));
-#endif
-#ifdef HAVE_BUILTIN_CTZ
- fprintf(stderr,"__builtin_ctz=%d ",__builtin_ctz(x));
-#endif
-
-#ifdef HAVE_POPCNT
- fprintf(stderr,"_popcnt32=%d ",_popcnt32(x));
-#endif
-#if defined(HAVE_MM_POPCNT)
- fprintf(stderr,"_mm_popcnt_u32=%d ",_mm_popcnt_u32(x));
-#endif
-#if defined(HAVE_BUILTIN_POPCOUNT)
- fprintf(stderr,"__builtin_popcount=%d ",__builtin_popcount(x));
-#endif
-
- fprintf(stderr,"\n");
-
#ifdef HAVE_SSE2
/* With -mavx, compiler may use assembly instructions for _mm_set1_epi32 that don't work on non-AVX machines */
fprintf(stderr,"Checking compiler assumptions for SSE2: ");
@@ -790,6 +785,8 @@ check_compiler_assumptions () {
a = _mm_xor_si128(_mm_set1_epi32(x),_mm_set1_epi32(y));
z = _mm_cvtsi128_si32(a);
fprintf(stderr," xor=%08X\n",z);
+#endif
+
#ifdef HAVE_SSE4_1
if ((negx = (char) x) > 0) {
@@ -817,9 +814,36 @@ check_compiler_assumptions () {
fprintf(stderr,"compiler zero extends\n");
}
}
+#endif
+
+#ifdef HAVE_SSE4_2
+ fprintf(stderr,"Checking compiler assumptions for SSE4.2 options: ");
+ fprintf(stderr,"%08X ",x);
+#ifdef HAVE_LZCNT
+ fprintf(stderr,"_lzcnt_u32=%d ",_lzcnt_u32(x));
+#endif
+#ifdef HAVE_BUILTIN_CLZ
+ fprintf(stderr,"__builtin_clz=%d ",__builtin_clz(x));
+#endif
+#ifdef HAVE_TZCNT
+ fprintf(stderr,"_tzcnt_u32=%d ",_tzcnt_u32(x));
+#endif
+#ifdef HAVE_BUILTIN_CTZ
+ fprintf(stderr,"__builtin_ctz=%d ",__builtin_ctz(x));
+#endif
+
+#ifdef HAVE_POPCNT
+ fprintf(stderr,"_popcnt32=%d ",_popcnt32(x));
+#endif
+#if defined(HAVE_MM_POPCNT)
+ fprintf(stderr,"_mm_popcnt_u32=%d ",_mm_popcnt_u32(x));
+#endif
+#if defined(HAVE_BUILTIN_POPCOUNT)
+ fprintf(stderr,"__builtin_popcount=%d ",__builtin_popcount(x));
#endif
+ fprintf(stderr,"\n");
#endif
fprintf(stderr,"Finished checking compiler assumptions\n");
@@ -845,7 +869,7 @@ process_request (Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2,
Stage3end_T *stage3array, *stage3array5, *stage3array3;
Stage3pair_T *stage3pairarray;
- int npaths, npaths5, npaths3, i;
+ int npaths_primary, npaths_altloc, npaths5_primary, npaths5_altloc, npaths3_primary, npaths3_altloc, i;
int first_absmq, second_absmq, first_absmq5, second_absmq5, first_absmq3, second_absmq3;
Pairtype_T final_pairtype;
@@ -864,25 +888,24 @@ process_request (Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2,
}
if (queryseq2 == NULL) {
- stage3array = Stage1_single_read(&npaths,&first_absmq,&second_absmq,
+ stage3array = Stage1_single_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,
queryseq1,indexdb,indexdb2,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
/*keep_floors_p*/true);
- result = Result_single_read_new(jobid,(void **) stage3array,npaths,first_absmq,second_absmq);
+ result = Result_single_read_new(jobid,(void **) stage3array,npaths_primary,npaths_altloc,first_absmq,second_absmq);
fp = Output_filestring_fromresult(&(*fp_failedinput_1),&(*fp_failedinput_2),result,request);
*worker_runtime = worker_stopwatch == NULL ? 0.00 : Stopwatch_stop(worker_stopwatch);
Result_free(&result);
return fp;
- } else if ((stage3pairarray = Stage1_paired_read(&npaths,&first_absmq,&second_absmq,&final_pairtype,
- &stage3array5,&npaths5,&first_absmq5,&second_absmq5,
- &stage3array3,&npaths3,&first_absmq3,&second_absmq3,
+ } else if ((stage3pairarray = Stage1_paired_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,&final_pairtype,
+ &stage3array5,&npaths5_primary,&npaths5_altloc,&first_absmq5,&second_absmq5,
+ &stage3array3,&npaths3_primary,&npaths3_altloc,&first_absmq3,&second_absmq3,
queryseq1,queryseq2,indexdb,indexdb2,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
@@ -890,9 +913,9 @@ process_request (Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,/*keep_floors_p*/true)) != NULL) {
+ pairmax_linear,/*keep_floors_p*/true)) != NULL) {
/* Paired or concordant hits found */
- result = Result_paired_read_new(jobid,(void **) stage3pairarray,npaths,first_absmq,second_absmq,
+ result = Result_paired_read_new(jobid,(void **) stage3pairarray,npaths_primary,npaths_altloc,first_absmq,second_absmq,
final_pairtype);
fp = Output_filestring_fromresult(&(*fp_failedinput_1),&(*fp_failedinput_2),result,request);
*worker_runtime = worker_stopwatch == NULL ? 0.00 : Stopwatch_stop(worker_stopwatch);
@@ -902,8 +925,8 @@ process_request (Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2,
} else if (chop_primers_p == false || Shortread_chop_primers(queryseq1,queryseq2) == false) {
/* No paired or concordant hits found, and no adapters found */
/* Report ends as unpaired */
- result = Result_paired_as_singles_new(jobid,(void **) stage3array5,npaths5,first_absmq5,second_absmq5,
- (void **) stage3array3,npaths3,first_absmq3,second_absmq3);
+ result = Result_paired_as_singles_new(jobid,(void **) stage3array5,npaths5_primary,npaths5_altloc,first_absmq5,second_absmq5,
+ (void **) stage3array3,npaths3_primary,npaths3_altloc,first_absmq3,second_absmq3);
fp = Output_filestring_fromresult(&(*fp_failedinput_1),&(*fp_failedinput_2),result,request);
*worker_runtime = worker_stopwatch == NULL ? 0.00 : Stopwatch_stop(worker_stopwatch);
Result_free(&result);
@@ -911,19 +934,19 @@ process_request (Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2,
} else {
/* Try with potential primers chopped. queryseq1 and queryseq2 altered by Shortread_chop_primers. */
- for (i = 0; i < npaths5; i++) {
+ for (i = 0; i < npaths5_primary + npaths5_altloc; i++) {
Stage3end_free(&(stage3array5[i]));
}
FREE_OUT(stage3array5);
- for (i = 0; i < npaths3; i++) {
+ for (i = 0; i < npaths3_primary + npaths3_altloc; i++) {
Stage3end_free(&(stage3array3[i]));
}
FREE_OUT(stage3array3);
- if ((stage3pairarray = Stage1_paired_read(&npaths,&first_absmq,&second_absmq,&final_pairtype,
- &stage3array5,&npaths5,&first_absmq5,&second_absmq5,
- &stage3array3,&npaths3,&first_absmq3,&second_absmq3,
+ if ((stage3pairarray = Stage1_paired_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,&final_pairtype,
+ &stage3array5,&npaths5_primary,&npaths5_altloc,&first_absmq5,&second_absmq5,
+ &stage3array3,&npaths3_primary,&npaths3_altloc,&first_absmq3,&second_absmq3,
queryseq1,queryseq2,indexdb,indexdb2,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
@@ -931,15 +954,15 @@ process_request (Filestring_T *fp_failedinput_1, Filestring_T *fp_failedinput_2,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,/*keep_floors_p*/false)) != NULL) {
+ pairmax_linear,/*keep_floors_p*/false)) != NULL) {
/* Paired or concordant hits found, after chopping adapters */
- result = Result_paired_read_new(jobid,(void **) stage3pairarray,npaths,first_absmq,second_absmq,
+ result = Result_paired_read_new(jobid,(void **) stage3pairarray,npaths_primary,npaths_altloc,first_absmq,second_absmq,
final_pairtype);
} else {
/* No paired or concordant hits found, after chopping adapters */
- result = Result_paired_as_singles_new(jobid,(void **) stage3array5,npaths5,first_absmq5,second_absmq5,
- (void **) stage3array3,npaths3,first_absmq3,second_absmq3);
+ result = Result_paired_as_singles_new(jobid,(void **) stage3array5,npaths5_primary,npaths5_altloc,first_absmq5,second_absmq5,
+ (void **) stage3array3,npaths3_primary,npaths3_altloc,first_absmq3,second_absmq3);
}
fp = Output_filestring_fromresult(&(*fp_failedinput_1),&(*fp_failedinput_2),result,request);
@@ -970,7 +993,8 @@ signal_handler (int sig) {
fprintf(stderr,"Signal received: SIGILL\n");
fprintf(stderr,"An illegal instruction means that this program is being run on a computer\n");
fprintf(stderr," with different features than the computer used to compile the program\n");
- fprintf(stderr,"You may need to re-compile the program with fewer features by doing something like\n");
+ fprintf(stderr,"You may need to re-compile the program on the same computer type as the target machine\n");
+ fprintf(stderr," or re-compile with fewer features by doing something like\n");
fprintf(stderr," ./configure --disable-simd\n");
break;
case SIGINT: fprintf(stderr,"Signal received: SIGINT\n"); break;
@@ -1653,6 +1677,12 @@ parse_command_line (int argc, char *argv[], int optind) {
return 9;
}
+ } else if (!strcmp(long_name,"preload-shared-memory")) {
+ preload_shared_memory_p = true;
+
+ } else if (!strcmp(long_name,"unload-shared-memory")) {
+ unload_shared_memory_p = true;
+
} else if (!strcmp(long_name,"expand-offsets")) {
if (!strcmp(optarg,"1")) {
expand_offsets_p = true;
@@ -1889,6 +1919,18 @@ parse_command_line (int argc, char *argv[], int optind) {
} else if (!strcmp(long_name,"favor-multiexon")) {
favor_multiexon_p = true;
+ } else if (!strcmp(long_name,"end-detail")) {
+ if (!strcmp(optarg,"high")) {
+ end_detail = 2;
+ } else if (!strcmp(optarg,"medium")) {
+ end_detail = 1;
+ } else if (!strcmp(optarg,"low")) {
+ end_detail = 0;
+ } else {
+ fprintf(stderr,"--end-detail must be high, medium, or low");
+ return 9;
+ }
+
} else if (!strcmp(long_name,"merge-distant-samechr")) {
merge_samechr_p = true;
@@ -2042,8 +2084,8 @@ parse_command_line (int argc, char *argv[], int optind) {
case 'k':
required_index1part = atoi(check_valid_int(optarg));
- if (required_index1part > 16) {
- fprintf(stderr,"The value for k-mer size must be 16 or less\n");
+ if (required_index1part > MAXIMUM_KMER) {
+ fprintf(stderr,"The value for k-mer size must be %d or less\n",MAXIMUM_KMER);
return 9;
}
break;
@@ -2278,25 +2320,29 @@ parse_command_line (int argc, char *argv[], int optind) {
if (novelsplicingp == true && knownsplicingp == true) {
fprintf(stderr,"Novel splicing (-N) and known splicing (-s) both turned on => assume reads are RNA-Seq\n");
find_dna_chimeras_p = false;
- pairmax = pairmax_rna;
+ pairmax_linear = pairmax_rna;
+ pairmax_circular = pairmax_dna;
shortsplicedist_known = shortsplicedist;
} else if (knownsplicingp == true) {
fprintf(stderr,"Known splicing (-s) turned on => assume reads are RNA-Seq\n");
find_dna_chimeras_p = false;
- pairmax = pairmax_rna;
+ pairmax_linear = pairmax_rna;
+ pairmax_circular = pairmax_dna;
shortsplicedist_known = shortsplicedist;
} else if (novelsplicingp == true) {
fprintf(stderr,"Novel splicing (-N) turned on => assume reads are RNA-Seq\n");
find_dna_chimeras_p = false;
- pairmax = pairmax_rna;
+ pairmax_linear = pairmax_rna;
+ pairmax_circular = pairmax_dna;
shortsplicedist_known = 0;
} else {
/* Appears to be DNA-Seq */
fprintf(stderr,"Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic)\n");
- pairmax = pairmax_dna;
+ pairmax_linear = pairmax_dna;
+ pairmax_circular = pairmax_dna;
shortsplicedist = shortsplicedist_known = 0U;
shortsplicedist_novelend = 0U;
}
@@ -2371,7 +2417,15 @@ open_input_streams_parser (int *nextchar, int *nchars1, int *nchars2, char ***fi
#endif
/* Open input stream and peek at first char */
- if (argc == 0) {
+ if (preload_shared_memory_p == true || unload_shared_memory_p == true) {
+ /* Ignore any input */
+ *input = stdin;
+ *files = (char **) NULL;
+ *nfiles = 0;
+ *nextchar = EOF;
+ return false;
+
+ } else if (argc == 0) {
#ifdef USE_MPI
fprintf(stderr,"For mpi_gsnap, cannot read from stdin\n");
exit(9);
@@ -2514,7 +2568,10 @@ open_input_streams_worker (char ***files, int *nfiles,
#endif
/* Open input stream and peek at first char */
- if (argc == 0) {
+ if (preload_shared_memory_p == true || unload_shared_memory_p == true) {
+ /* Ignore input */
+
+ } else if (argc == 0) {
fprintf(stderr,"For mpi_gsnap, cannot read from stdin\n");
exit(9);
@@ -2625,8 +2682,9 @@ open_input_streams_worker (char ***files, int *nfiles,
static Univ_IIT_T
chromosome_iit_setup (int *nchromosomes, int *circular_typeint, bool *any_circular_p, bool **circularp,
char *genomesubdir, char *fileroot) {
- Univ_IIT_T chromosome_iit = NULL;
+ Univ_IIT_T chromosome_iit = NULL, altscaffold_iit = NULL;
char *iitfile = NULL;
+ int i;
/* Prepare genomic data */
@@ -2643,11 +2701,28 @@ chromosome_iit_setup (int *nchromosomes, int *circular_typeint, bool *any_circul
exit(9);
#endif
} else {
+ FREE(iitfile);
*nchromosomes = Univ_IIT_total_nintervals(chromosome_iit);
*circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
*circularp = Univ_IIT_circularp(&(*any_circular_p),chromosome_iit);
+
+ iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
+ strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
+ sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
+ if ((altscaffold_iit = Univ_IIT_read(iitfile,/*readonlyp*/true,/*add_iit_p*/false)) == NULL) {
+ /* fprintf(stderr,"No altscaffold file found\n"); */
+ altlocp = (bool *) CALLOC((*nchromosomes)+1,sizeof(bool));
+ alias_starts = (Univcoord_T *) CALLOC((*nchromosomes)+1,sizeof(Univcoord_T));
+ alias_ends = (Univcoord_T *) CALLOC((*nchromosomes)+1,sizeof(Univcoord_T));
+
+ } else {
+ fprintf(stderr,"Found altscaffold file found\n");
+ altlocp = Univ_IIT_altlocp(&alias_starts,&alias_ends,chromosome_iit,altscaffold_iit);
+ Univ_IIT_free(&altscaffold_iit);
+ }
+
+ FREE(iitfile);
}
- FREE(iitfile);
return chromosome_iit;
}
@@ -2667,16 +2742,16 @@ worker_setup (char *genomesubdir, char *fileroot) {
#ifndef LARGE_GENOMES
if (use_sarray_p == true) {
if (mode == STANDARD) {
- if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,/*snps_root*/NULL,sarray_access,lcp_access,
+ if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,sarray_access,lcp_access,
guideexc_access,indexij_access,sharedp,mode,/*fwdp*/true)) == NULL) {
use_sarray_p = false;
} else {
sarray_rev = sarray_fwd;
}
} else {
- if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,/*snps_root*/NULL,sarray_access,lcp_access,
+ if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,sarray_access,lcp_access,
guideexc_access,indexij_access,sharedp,mode,/*fwdp*/true)) == NULL ||
- (sarray_rev = Sarray_new(genomesubdir,fileroot,/*snps_root*/NULL,sarray_access,lcp_access,
+ (sarray_rev = Sarray_new(genomesubdir,fileroot,sarray_access,lcp_access,
guideexc_access,indexij_access,sharedp,mode,/*fwdp*/false)) == NULL) {
use_sarray_p = false;
}
@@ -2693,7 +2768,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
genomesubdir,fileroot,/*idx_filesuffix*/"dibase",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find offsets file %s.%s*offsets, needed for GSNAP color mode\n",fileroot,"dibase");
exit(9);
}
@@ -2710,7 +2786,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"metct",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metct index file. Need to run cmetindex first\n");
exit(9);
}
@@ -2718,7 +2795,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"metga",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metga index file. Need to run cmetindex first\n");
exit(9);
}
@@ -2733,7 +2811,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2iag",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -2741,7 +2820,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2itc",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -2756,7 +2836,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2itc",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -2764,7 +2845,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2iag",/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -2775,7 +2857,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
genomesubdir,fileroot,IDX_FILESUFFIX,/*snps_root*/NULL,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find offsets file %s.%s*offsets, needed for GSNAP\n",fileroot,IDX_FILESUFFIX);
exit(9);
}
@@ -2805,16 +2888,16 @@ worker_setup (char *genomesubdir, char *fileroot) {
if (use_sarray_p == true) {
fprintf(stderr,"Note: Suffix arrays will bias against SNP-tolerant alignment. For bias-free alignment, set --use-sarray=0\n");
if (mode == STANDARD) {
- if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,/*snps_root*/NULL,sarray_access,lcp_access,
+ if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,sarray_access,lcp_access,
guideexc_access,indexij_access,sharedp,mode,/*fwdp*/true)) == NULL) {
use_sarray_p = false;
} else {
sarray_rev = sarray_fwd;
}
} else {
- if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,/*snps_root*/NULL,sarray_access,lcp_access,
+ if ((sarray_fwd = Sarray_new(genomesubdir,fileroot,sarray_access,lcp_access,
guideexc_access,indexij_access,sharedp,mode,/*fwdp*/true)) == NULL ||
- (sarray_rev = Sarray_new(genomesubdir,fileroot,/*snps_root*/NULL,sarray_access,lcp_access,
+ (sarray_rev = Sarray_new(genomesubdir,fileroot,sarray_access,lcp_access,
guideexc_access,indexij_access,sharedp,mode,/*fwdp*/false)) == NULL) {
use_sarray_p = false;
}
@@ -2837,14 +2920,16 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"metct",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metct index file. Need to run cmetindex first\n");
exit(9);
}
if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"metga",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find metga index file. Need to run cmetindex first\n");
exit(9);
}
@@ -2859,14 +2944,16 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2iag",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2itc",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -2881,14 +2968,16 @@ worker_setup (char *genomesubdir, char *fileroot) {
if ((indexdb = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2itc",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
if ((indexdb2 = Indexdb_new_genome(&index1part,&index1interval,
modedir,fileroot,/*idx_filesuffix*/"a2iag",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp)) == NULL) {
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -2897,7 +2986,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
indexdb = Indexdb_new_genome(&index1part,&index1interval,
snpsdir,fileroot,/*idx_filesuffix*/"ref",snps_root,
required_index1part,required_index1interval,
- expand_offsets_p,offsetsstrm_access,positions_access,sharedp);
+ expand_offsets_p,offsetsstrm_access,positions_access,sharedp,
+ multiple_sequences_p);
if (indexdb == NULL) {
fprintf(stderr,"Cannot find snps index file for %s in directory %s\n",snps_root,snpsdir);
exit(9);
@@ -2910,7 +3000,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
sprintf(iitfile,"%s/%s",mapdir,snps_root);
fprintf(stderr,"Reading SNPs file %s/%s...",mapdir,snps_root);
if ((snps_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"SNPs file %s.iit not found in %s.\n",snps_root,mapdir);
if (user_snpsdir == NULL) {
fprintf(stderr,"Available files:\n");
@@ -2950,7 +3040,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
if (genes_file != NULL) {
if ((genes_iit = IIT_read(genes_file,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading genes file %s locally...",genes_file);
} else {
mapdir = Datadir_find_mapdir(/*user_mapdir*/NULL,genomesubdir,fileroot);
@@ -2958,7 +3048,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
strlen(genes_file)+1,sizeof(char));
sprintf(iitfile,"%s/%s",mapdir,genes_file);
if ((genes_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading genes file %s...",iitfile);
FREE(iitfile);
FREE(mapdir);
@@ -2976,14 +3066,14 @@ worker_setup (char *genomesubdir, char *fileroot) {
if (splicing_file != NULL) {
if (user_splicingdir == NULL) {
if ((splicing_iit = IIT_read(splicing_file,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading splicing file %s locally...",splicing_file);
}
} else {
iitfile = (char *) CALLOC(strlen(user_splicingdir)+strlen("/")+strlen(splicing_file)+1,sizeof(char));
sprintf(iitfile,"%s/%s",user_splicingdir,splicing_file);
if ((splicing_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading splicing file %s...",iitfile);
FREE(iitfile);
}
@@ -2995,7 +3085,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
strlen(splicing_file)+1,sizeof(char));
sprintf(iitfile,"%s/%s",mapdir,splicing_file);
if ((splicing_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading splicing file %s...",iitfile);
FREE(iitfile);
FREE(mapdir);
@@ -3107,14 +3197,14 @@ worker_setup (char *genomesubdir, char *fileroot) {
if (tally_root != NULL) {
if (user_tallydir == NULL) {
if ((tally_iit = IIT_read(tally_root,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading tally file %s.iit locally...",tally_root);
}
} else {
iitfile = (char *) CALLOC(strlen(user_tallydir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
sprintf(iitfile,"%s/%s",user_tallydir,tally_root);
if ((tally_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading tally file %s...",iitfile);
FREE(iitfile);
}
@@ -3124,7 +3214,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(tally_root)+1,sizeof(char));
sprintf(iitfile,"%s/%s",genomesubdir,tally_root);
if ((tally_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading tally file %s...",iitfile);
FREE(iitfile);
} else {
@@ -3145,14 +3235,14 @@ worker_setup (char *genomesubdir, char *fileroot) {
if (runlength_root != NULL) {
if (user_runlengthdir == NULL) {
if ((runlength_iit = IIT_read(runlength_root,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading runlength file %s.iit locally...",runlength_root);
}
} else {
iitfile = (char *) CALLOC(strlen(user_runlengthdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
sprintf(iitfile,"%s/%s",user_runlengthdir,runlength_root);
if ((runlength_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading runlength file %s...",iitfile);
FREE(iitfile);
}
@@ -3162,7 +3252,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+strlen(runlength_root)+1,sizeof(char));
sprintf(iitfile,"%s/%s",genomesubdir,runlength_root);
if ((runlength_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) != NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) != NULL) {
fprintf(stderr,"Reading runlength file %s...",iitfile);
FREE(iitfile);
} else {
@@ -3212,8 +3302,8 @@ worker_setup (char *genomesubdir, char *fileroot) {
Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false));
Stage3_setup(/*splicingp*/novelsplicingp == true || knownsplicingp == true,novelsplicingp,
/*require_splicedir_p*/true,splicing_iit,splicing_divint_crosstable,
- donor_typeint,acceptor_typeint,
- splicesites,min_intronlength,max_deletionlength,min_indel_end_matches,
+ donor_typeint,acceptor_typeint,splicesites,altlocp,alias_starts,alias_ends,
+ min_intronlength,max_deletionlength,min_indel_end_matches,
maxpeelback_distalmedial,nullgap,extramaterial_end,extramaterial_paired,
extraband_single,extraband_end,extraband_paired,
ngap,/*maxintronlen*/shortsplicedist,
@@ -3241,7 +3331,7 @@ worker_setup (char *genomesubdir, char *fileroot) {
genomecomp,genomecomp_alt,mode,maxpaths_search,
splicesites,splicetypes,splicedists,nsplicesites,
novelsplicingp,knownsplicingp,find_dna_chimeras_p,distances_observed_p,
- subopt_levels,max_middle_insertions,max_middle_deletions,
+ subopt_levels,min_indel_end_matches,max_middle_insertions,max_middle_deletions,
shortsplicedist,shortsplicedist_known,shortsplicedist_novelend,min_intronlength,
min_distantsplicing_end_matches,min_distantsplicing_identity,
nullgap,maxpeelback,maxpeelback_distalmedial,
@@ -3258,11 +3348,12 @@ worker_setup (char *genomesubdir, char *fileroot) {
Stage3hr_setup(invert_first_p,invert_second_p,genomecomp,chromosome_iit,nchromosomes,circular_typeint,
genes_iit,genes_divint_crosstable,
tally_iit,tally_divint_crosstable,runlength_iit,runlength_divint_crosstable,
- distances_observed_p,pairmax,
+ distances_observed_p,pairmax_linear,pairmax_circular,
expected_pairlength,pairlength_deviation,
localsplicing_penalty,indel_penalty_middle,antistranded_penalty,
- favor_multiexon_p,gmap_min_nconsecutive,index1part,index1interval,novelsplicingp,
- merge_samechr_p,circularp,failedinput_root,print_m8_p,want_random_p);
+ favor_multiexon_p,gmap_min_nconsecutive,end_detail,subopt_levels,
+ novelsplicingp,shortsplicedist,
+ merge_samechr_p,circularp,altlocp,alias_starts,alias_ends,failedinput_root,print_m8_p,want_random_p);
SAM_setup(add_paired_nomappers_p,paired_flag_means_concordant_p,
quiet_if_excessive_p,maxpaths_report,failedinput_root,fastq_format_p,hide_soft_clips_p,
clip_overlap_p,merge_overlap_p,sam_multiple_primaries_p,
@@ -3361,6 +3452,12 @@ worker_cleanup () {
IIT_free(&snps_iit);
}
+ if (altlocp != NULL) {
+ FREE(alias_ends);
+ FREE(alias_starts);
+ FREE(altlocp);
+ }
+
if (circularp != NULL) {
FREE(circularp);
}
@@ -3378,7 +3475,6 @@ worker_cleanup () {
int
main (int argc, char *argv[]) {
int nchars1 = 0, nchars2 = 0;
- bool multiple_sequences_p;
int cmdline_status;
char *genomesubdir, *fileroot, *dbversion;
@@ -3451,7 +3547,7 @@ main (int argc, char *argv[]) {
check_compiler_assumptions();
if (exception_raise_p == false) {
- fprintf(stderr,"Allowing signals and exceptions to pass through\n");
+ fprintf(stderr,"Allowing signals and exceptions to pass through. If using shared memory, need to remove segments manually.\n");
Except_inactivate();
} else {
#ifdef HAVE_SIGACTION
@@ -3617,7 +3713,18 @@ main (int argc, char *argv[]) {
}
#endif
- if (multiple_sequences_p == true) {
+ if (preload_shared_memory_p == true || unload_shared_memory_p == true) {
+#ifdef HAVE_MMAP
+ /* To avoid time-consuming pre-load */
+ sarray_access = USE_MMAP_ONLY;
+ lcp_access = USE_MMAP_ONLY;
+#else
+ /* No choice, since mmap is not available */
+ sarray_access = USE_ALLOCATE;
+ lcp_access = USE_ALLOCATE;
+#endif
+
+ } else if (multiple_sequences_p == true) {
#if 0
if (offsetsstrm_access != USE_ALLOCATE || genome_access != USE_ALLOCATE ||
sarray_access != USE_ALLOCATE || lcp_access != USE_ALLOCATE) {
@@ -3722,9 +3829,14 @@ main (int argc, char *argv[]) {
}
#else
+ Access_setup(preload_shared_memory_p,unload_shared_memory_p);
worker_setup(genomesubdir,fileroot);
FREE(genomesubdir);
FREE(fileroot);
+ if (preload_shared_memory_p == true || unload_shared_memory_p == true) {
+ worker_cleanup();
+ return 0;
+ }
outbuffer = Outbuffer_new(output_buffer_size,nread);
Inbuffer_set_outbuffer(inbuffer,outbuffer);
@@ -3979,6 +4091,11 @@ is still designed to be fast.\n\
\n\
--use-shared-memory=INT If 1 (default), then allocated memory is shared among all processes\n\
on this node. If 0, then each process has private allocated memory\n\
+ --preload-shared-memory Load files indicated by --batch mode into shared memory for use by other\n\
+ GMAP/GSNAP processes on this node, and then exit. Ignore any input files.\n\
+ --unload-shared-memory Unload files indicated by --batch mode into shared memory, or allow them\n\
+ to be unloaded when existing GMAP/GSNAP processes on this node are finished\n\
+ with them. Ignore any input files.\n\
--expand-offsets=INT Whether to expand the genomic offsets index\n\
Values: 0 (no, default), or 1 (yes).\n\
Expansion gives faster alignment, but requires more memory\n\
@@ -4050,8 +4167,8 @@ is still designed to be fast.\n\
--indel-endlength=INT Minimum length at end required for indel alignments (default %d)\n\
",min_indel_end_matches);
fprintf(stdout,"\
- -y, --max-middle-insertions=INT Maximum number of middle insertions allowed (default %d)\n\
-",max_middle_insertions);
+ -y, --max-middle-insertions=INT Maximum number of middle insertions allowed (default is readlength - indel-endlength)\n\
+");
fprintf(stdout,"\
-z, --max-middle-deletions=INT Maximum number of middle deletions allowed (default %d)\n\
",max_middle_deletions);
@@ -4081,6 +4198,11 @@ is still designed to be fast.\n\
will give false positive indels at the ends of reads\n\
",trim_indel_score);
fprintf(stdout,"\
+ --end-detail=STRING Amount of alignment detail at ends of read: high, medium (default), or low\n\
+ Warning: high detail at ends will slow down speed of program by a\n\
+ factor of 3 or so. Medium detail does not incur much slow down, though\n\
+");
+ fprintf(stdout,"\
-V, --snpsdir=STRING Directory for SNPs index files (created using snpindex) (default is\n\
location of genome index files specified using -D and -d)\n \
-v, --use-snps=STRING Use database containing known SNPs (in <STRING>.iit, built\n\
@@ -4258,6 +4380,8 @@ is still designed to be fast.\n\
fprintf(stdout,"\
--pairmax-dna=INT Max total genomic length for DNA-Seq paired reads, or other reads\n\
without splicing (default %d). Used if -N or -s is not specified.\n\
+ This value is also used for circular chromosomes when splicing in\n\
+ linear chromosomes is allowed\n\
",pairmax_dna);
fprintf(stdout,"\
--pairmax-rna=INT Max total genomic length for RNA-Seq paired reads, or other reads\n\
diff --git a/src/gsnap_select.c b/src/gsnap_select.c
new file mode 100644
index 0000000..303c7d4
--- /dev/null
+++ b/src/gsnap_select.c
@@ -0,0 +1,195 @@
+#include "bool.h"
+#include "cpuid.h"
+#include <errno.h>
+#include <sys/stat.h> /* For fstat */
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <string.h>
+#include <libgen.h>
+#include <unistd.h>
+
+static bool
+file_exists_p (char *filename) {
+ struct stat sb;
+
+ if (stat(filename,&sb) == 0) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+int
+main (int argc, char *argv[]) {
+ bool sse2_support_p;
+ bool ssse3_support_p;
+ bool sse4_1_support_p;
+ bool sse4_2_support_p;
+ bool avx2_support_p;
+ char *dir, **new_argv;
+ int i;
+ int rc;
+
+ CPUID_support(&sse2_support_p,&ssse3_support_p,&sse4_1_support_p,&sse4_2_support_p,&avx2_support_p);
+
+ new_argv = (char **) malloc((argc + 1) * sizeof(char *));
+ for (i = 1; i < argc; i++) {
+ new_argv[i] = argv[i];
+ }
+ new_argv[argc] = (char *) NULL;
+
+ if (index(argv[0],'/') == NULL) {
+ /* Depend on path */
+ /* Cannot use file_exists_p, since it won't search PATH */
+
+ if (avx2_support_p == true) {
+ new_argv[0] = "gsnap.avx2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = "gsnap.sse42";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = "gsnap.sse41";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = "gsnap.ssse3";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = "gsnap.sse2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = "gsnap.nosimd";
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv);
+ return rc;
+ }
+
+ } else {
+ dir = dirname(argv[0]);
+
+ if (avx2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.avx2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnap.avx2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse42") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnap.sse42",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse41") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnap.sse41",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.ssse3") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnap.ssse3",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.sse2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnap.sse2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnap.nosimd") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnap.nosimd",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an non-SIMD machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+ }
+
+ fprintf(stderr,"Error: appropriate GSNAP version not found\n");
+ free(new_argv);
+ return -1;
+}
+
diff --git a/src/gsnapl_select.c b/src/gsnapl_select.c
new file mode 100644
index 0000000..642a851
--- /dev/null
+++ b/src/gsnapl_select.c
@@ -0,0 +1,195 @@
+#include "bool.h"
+#include "cpuid.h"
+#include <errno.h>
+#include <sys/stat.h> /* For fstat */
+#include <stdio.h>
+#include <stdlib.h>
+#include <strings.h>
+#include <string.h>
+#include <libgen.h>
+#include <unistd.h>
+
+static bool
+file_exists_p (char *filename) {
+ struct stat sb;
+
+ if (stat(filename,&sb) == 0) {
+ return true;
+ } else {
+ return false;
+ }
+}
+
+int
+main (int argc, char *argv[]) {
+ bool sse2_support_p;
+ bool ssse3_support_p;
+ bool sse4_1_support_p;
+ bool sse4_2_support_p;
+ bool avx2_support_p;
+ char *dir, **new_argv;
+ int i;
+ int rc;
+
+ CPUID_support(&sse2_support_p,&ssse3_support_p,&sse4_1_support_p,&sse4_2_support_p,&avx2_support_p);
+
+ new_argv = (char **) malloc((argc + 1) * sizeof(char *));
+ for (i = 1; i < argc; i++) {
+ new_argv[i] = argv[i];
+ }
+ new_argv[argc] = (char *) NULL;
+
+ if (index(argv[0],'/') == NULL) {
+ /* Depend on path */
+ /* Cannot use file_exists_p, since it won't search PATH */
+
+ if (avx2_support_p == true) {
+ new_argv[0] = "gsnapl.avx2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = "gsnapl.sse42";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = "gsnapl.sse41";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = "gsnapl.ssse3";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = "gsnapl.sse2";
+ if ((rc = execvp(new_argv[0],new_argv)) == -1 && errno == ENOENT) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ } else {
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = "gsnapl.nosimd";
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv);
+ return rc;
+ }
+
+ } else {
+ dir = dirname(argv[0]);
+
+ if (avx2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.avx2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnapl.avx2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an AVX2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse42") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnapl.sse42",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse4_1_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse41") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnapl.sse41",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE4.1 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (ssse3_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.ssse3") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnapl.ssse3",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSSE3 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (sse2_support_p == true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.sse2") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnapl.sse2",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an SSE2 machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+
+ if (true) {
+ new_argv[0] = (char *) malloc((strlen(dir) + strlen("/") + strlen("gsnapl.nosimd") + 1) * sizeof(char));
+ sprintf(new_argv[0],"%s/gsnapl.nosimd",dir);
+ if (file_exists_p(new_argv[0]) == false) {
+ fprintf(stderr,"Note: %s does not exist. May want to compile package on an non-SIMD machine\n",new_argv[0]);
+ free(new_argv[0]);
+ } else {
+ rc = execvp(new_argv[0],new_argv);
+ free(new_argv[0]);
+ free(new_argv);
+ return rc;
+ }
+ }
+ }
+
+ fprintf(stderr,"Error: appropriate GSNAPL version not found\n");
+ free(new_argv);
+ return -1;
+}
+
diff --git a/src/iit-read-univ.c b/src/iit-read-univ.c
index f76e46c..3d0a167 100644
--- a/src/iit-read-univ.c
+++ b/src/iit-read-univ.c
@@ -1,9 +1,10 @@
-static char rcsid[] = "$Id: iit-read-univ.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: iit-read-univ.c 186727 2016-03-30 23:02:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "iit-read-univ.h"
+#include "parserange.h"
#ifdef WORDS_BIGENDIAN
#include "bigendian.h"
@@ -127,23 +128,23 @@ struct T {
UINT4 *typepointers;
char *typestrings;
- off_t labelorder_offset;
+ size_t labelorder_offset;
size_t labelorder_length; /* mmap length (mmap uses size_t, not off_t) */
char *labelorder_mmap;
- off_t labelpointers_offset;
+ size_t labelpointers_offset;
size_t labelpointers_length; /* mmap length (mmap uses size_t, not off_t) */
char *labelpointers_mmap;
- off_t label_offset;
+ size_t label_offset;
size_t label_length; /* mmap length (mmap uses size_t, not off_t) */
char *label_mmap;
- off_t annotpointers_offset;
+ size_t annotpointers_offset;
size_t annotpointers_length; /* mmap length (mmap uses size_t, not off_t) */
char *annotpointers_mmap;
- off_t annot_offset;
+ size_t annot_offset;
size_t annot_length; /* mmap length (mmap uses size_t, not off_t) */
char *annot_mmap;
@@ -160,7 +161,7 @@ struct T {
static void
-file_move_absolute (int fd, off_t offset, off_t objsize, Univcoord_T n) {
+file_move_absolute (int fd, size_t offset, size_t objsize, Univcoord_T n) {
off_t position = offset + n*objsize;
if (lseek(fd,position,SEEK_SET) < 0) {
@@ -248,6 +249,97 @@ Univ_IIT_circularp (bool *any_circular_p, T chromosome_iit) {
}
+bool *
+Univ_IIT_altlocp (Univcoord_T **alias_starts, Univcoord_T **alias_ends, T chromosome_iit, T altscaffold_iit) {
+ bool *altlocp, alloc_header_p;
+ char *chr, *primary_chr, *restofheader, *p;
+ int chri, nchromosomes, alti, primary_chrnum;
+ bool revcomp;
+ Univcoord_T genomicstart, chroffset;
+ Chrpos_T genomiclength, chrstart, chrend, chrlength;
+ UINT4 start;
+ int nprimary = 0, naltloc = 0;
+ int circular_typeint;
+ Univinterval_T interval;
+
+
+ nchromosomes = chromosome_iit->total_nintervals;
+ altlocp = (bool *) CALLOC(nchromosomes+1,sizeof(bool));
+ *alias_starts = (Univcoord_T *) CALLOC(nchromosomes+1,sizeof(Univcoord_T));
+ *alias_ends = (Univcoord_T *) CALLOC(nchromosomes+1,sizeof(Univcoord_T));
+
+ altlocp[0] = false; /* chrnum of 0 indicates translocation */
+ circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
+
+ /* Can go through all chromosomes in chromosome_iit, since it contains both primary and alternate loci */
+ for (chri = 0; chri < nchromosomes; chri++) {
+#ifdef WORDS_BIGENDIAN
+ /* chromosome_iit should be version 1 */
+ start = Bigendian_convert_uint(chromosome_iit->labelpointers[chri]);
+#else
+ start = chromosome_iit->labelpointers[chri];
+#endif
+ chr = &(chromosome_iit->labels[start]);
+
+ if ((alti = Univ_IIT_find_one(altscaffold_iit,chr)) >= 0) {
+ /* Don't need to assign result, since annot is never allocated */
+ Univ_IIT_annotation(&restofheader,altscaffold_iit,alti/*+1*/,&alloc_header_p);
+ p = restofheader;
+ while (isspace((int) *p)) {
+ p++;
+ }
+
+ if (naltloc > 10) {
+ /* Don't print */
+ } else if (naltloc == 10) {
+ fprintf(stderr,"More than 10 alternate loci. Will stop printing.\n");
+ } else {
+ fprintf(stderr,"Alternate locus %s maps to primary region %s\n",chr,p);
+ }
+
+ Parserange_universal_iit(&primary_chr,&revcomp,&genomicstart,&genomiclength,
+ &chrstart,&chrend,&chroffset,&chrlength,
+ p,chromosome_iit,/*contig_iit*/NULL);
+ /* fprintf(stderr," => %s %u..%u\n",primary_chr,genomicstart,genomicstart+genomiclength); */
+
+ if (circular_typeint < 0) {
+ altlocp[chri+1] = true;
+ (*alias_starts)[chri+1] = genomicstart;
+ (*alias_ends)[chri+1] = genomicstart + genomiclength;
+ naltloc++;
+
+ } else {
+ primary_chrnum = Univ_IIT_find_one(chromosome_iit,primary_chr);
+ interval = &(chromosome_iit->intervals[primary_chrnum-1]);
+ if (Univinterval_type(interval) != circular_typeint) {
+ altlocp[chri+1] = true;
+ (*alias_starts)[chri+1] = genomicstart;
+ (*alias_ends)[chri+1] = genomicstart + genomiclength;
+ naltloc++;
+
+ } else {
+ fprintf(stderr,"Alternate locus %s maps to region %s, which is circular and not allowed. Ignoring.\n",chr,p);
+ nprimary++;
+ }
+ }
+
+ if (alloc_header_p) {
+ FREE(restofheader);
+ }
+
+ } else {
+ /* printf("Chromosome %s is not an alt locus\n",chr); */
+ nprimary++;
+ }
+ }
+
+ fprintf(stderr,"Found %d alternate loci, and %d primary contigs (not mapping to another contig)\n",
+ naltloc,nprimary);
+
+ return altlocp;
+}
+
+
Univinterval_T
Univ_IIT_interval (T this, int index) {
assert(index <= this->total_nintervals);
@@ -949,8 +1041,8 @@ move_relative (FILE *fp, off_t offset) {
}
-static off_t
-read_tree_univ (off_t offset, off_t filesize, FILE *fp, char *filename, T new) {
+static size_t
+read_tree_univ (size_t offset, size_t filesize, FILE *fp, char *filename, T new) {
size_t items_read;
int i;
UINT4 uint4;
@@ -1054,8 +1146,8 @@ read_tree_univ (off_t offset, off_t filesize, FILE *fp, char *filename, T new) {
}
-static off_t
-read_intervals_univ (off_t offset, off_t filesize, FILE *fp, char *filename, T new) {
+static size_t
+read_intervals_univ (size_t offset, size_t filesize, FILE *fp, char *filename, T new) {
int i;
UINT4 uint4;
@@ -1116,8 +1208,8 @@ read_intervals_univ (off_t offset, off_t filesize, FILE *fp, char *filename, T n
static void
-read_words (off_t offset, off_t filesize, FILE *fp, T new) {
- off_t stringlen;
+read_words (size_t offset, size_t filesize, FILE *fp, T new) {
+ size_t stringlen;
UINT4 length;
#ifdef DEBUG
int i;
@@ -1142,8 +1234,8 @@ read_words (off_t offset, off_t filesize, FILE *fp, T new) {
}
debug(
printf("typestrings:\n");
- for (i = 0; i < stringlen; i++) {
- printf("%c",new->typestrings[i]);
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->typestrings[s]);
}
printf("\n");
);
@@ -1203,12 +1295,12 @@ read_words (off_t offset, off_t filesize, FILE *fp, T new) {
}
static void
-read_words_debug (off_t offset, off_t filesize, FILE *fp, T new) {
- off_t stringlen;
+read_words_debug (size_t offset, size_t filesize, FILE *fp, T new) {
+ size_t stringlen, s;
UINT4 length;
int i;
#if 0
- off_t last_offset;
+ size_t last_offset;
#endif
new->typepointers = (unsigned int *) CALLOC(new->ntypes+1,sizeof(unsigned int));
@@ -1227,8 +1319,8 @@ read_words_debug (off_t offset, off_t filesize, FILE *fp, T new) {
offset += sizeof(char)*FREAD_CHARS(new->typestrings,stringlen,fp);
}
printf("typestrings:\n");
- for (i = 0; i < stringlen; i++) {
- printf("%c",new->typestrings[i]);
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->typestrings[s]);
}
printf("\n");
@@ -1298,32 +1390,32 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
exit(9);
}
- new->labelorder_mmap = Access_mmap_offset(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
- sizeof(char),/*randomp*/true);
+ new->labelorder_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
+ /*randomp*/true);
debug(fprintf(stderr,"labelorder_mmap is %p\n",new->labelorder_mmap));
new->labelorder = (int *) &(new->labelorder_mmap[remainder]);
new->labelorder_length += (size_t) remainder;
- new->labelpointers_mmap = Access_mmap_offset(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
- sizeof(char),/*randomp*/true);
+ new->labelpointers_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
+ /*randomp*/true);
debug(fprintf(stderr,"labelpointers_mmap is %p\n",new->labelpointers_mmap));
new->labelpointers = (UINT4 *) &(new->labelpointers_mmap[remainder]);
new->labelpointers_length += (size_t) remainder;
- new->label_mmap = Access_mmap_offset(&remainder,new->fd,new->label_offset,new->label_length,
- sizeof(char),/*randomp*/true);
+ new->label_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->label_offset,new->label_length,
+ /*randomp*/true);
debug(fprintf(stderr,"labels_mmap is %p\n",new->label_mmap));
new->labels = (char *) &(new->label_mmap[remainder]);
new->label_length += (size_t) remainder;
- new->annotpointers_mmap = Access_mmap_offset(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
- sizeof(char),/*randomp*/true);
+ new->annotpointers_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
+ /*randomp*/true);
debug(fprintf(stderr,"annotpointers_mmap is %p\n",new->annotpointers_mmap));
new->annotpointers = (UINT4 *) &(new->annotpointers_mmap[remainder]);
new->annotpointers_length += (size_t) remainder;
- new->annot_mmap = Access_mmap_offset(&remainder,new->fd,new->annot_offset,new->annot_length,
- sizeof(char),/*randomp*/true);
+ new->annot_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->annot_offset,new->annot_length,
+ /*randomp*/true);
debug(fprintf(stderr,"annots_mmap is %p\n",new->annot_mmap));
new->annotations = (char *) &(new->annot_mmap[remainder]);
new->annot_length += (size_t) remainder;
@@ -1334,28 +1426,28 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
exit(9);
}
- new->labelorder_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
- sizeof(char),/*randomp*/true);
+ new->labelorder_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
+ /*randomp*/true);
new->labelorder = (int *) &(new->labelorder_mmap[remainder]);
new->labelorder_length += (size_t) remainder;
- new->labelpointers_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
- sizeof(char),/*randomp*/true);
+ new->labelpointers_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
+ /*randomp*/true);
new->labelpointers = (UINT4 *) &(new->labelpointers_mmap[remainder]);
new->labelpointers_length += (size_t) remainder;
- new->label_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->label_offset,new->label_length,
- sizeof(char),/*randomp*/true);
+ new->label_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->label_offset,new->label_length,
+ /*randomp*/true);
new->labels = (char *) &(new->label_mmap[remainder]);
new->label_length += (size_t) remainder;
- new->annotpointers_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
- sizeof(char),/*randomp*/true);
+ new->annotpointers_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
+ /*randomp*/true);
new->annotpointers = (UINT4 *) &(new->annotpointers_mmap[remainder]);
new->annotpointers_length += (size_t) remainder;
- new->annot_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->annot_offset,new->annot_length,
- sizeof(char),/*randomp*/true);
+ new->annot_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->annot_offset,new->annot_length,
+ /*randomp*/true);
new->annotations = (char *) &(new->annot_mmap[remainder]);
new->annot_length += (size_t) remainder;
}
@@ -1410,7 +1502,7 @@ Univ_IIT_read (char *filename, bool readonlyp, bool add_iit_p) {
T new;
FILE *fp;
char *newfile = NULL;
- off_t offset = 0, filesize;
+ size_t offset = 0, filesize;
/* printf("Reading IIT file %s\n",filename); */
if (add_iit_p == true) {
@@ -1537,7 +1629,7 @@ Univ_IIT_debug (char *filename) {
T new;
FILE *fp;
char *newfile = NULL;
- off_t offset = 0, filesize;
+ size_t offset = 0, filesize;
bool add_iit_p = false;
if (add_iit_p == true) {
@@ -1872,7 +1964,8 @@ int_compare (const void *a, const void *b) {
int *
Univ_IIT_get (int *nmatches, T this, Univcoord_T x, Univcoord_T y) {
- int *sorted, *matches = NULL, *uniq, neval, nuniq, i;
+ /* int *sorted; */
+ int *matches = NULL, *uniq, neval, nuniq, i;
int lambda, prev;
int min1, max1 = 0, min2, max2 = 0;
int nintervals;
diff --git a/src/iit-read-univ.h b/src/iit-read-univ.h
index 29e30ac..9ff244a 100644
--- a/src/iit-read-univ.h
+++ b/src/iit-read-univ.h
@@ -1,4 +1,4 @@
-/* $Id: iit-read-univ.h 157228 2015-01-22 18:49:11Z twu $ */
+/* $Id: iit-read-univ.h 186727 2016-03-30 23:02:10Z twu $ */
#ifndef IIT_READ_UNIV_INCLUDED
#define IIT_READ_UNIV_INCLUDED
@@ -30,6 +30,8 @@ extern Univcoord_T
Univ_IIT_genomelength (T chromosome_iit, bool with_circular_alias_p);
extern bool *
Univ_IIT_circularp (bool *any_circular_p, T chromosome_iit);
+extern bool *
+Univ_IIT_altlocp (Univcoord_T **alias_starts, Univcoord_T **alias_ends, T chromosome_iit, T altscaffold_iit);
extern Univinterval_T
Univ_IIT_interval (T this, int index);
extern Univcoord_T
diff --git a/src/iit-read.c b/src/iit-read.c
index 6194e60..6ee0e2f 100644
--- a/src/iit-read.c
+++ b/src/iit-read.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: iit-read.c 164702 2015-05-01 20:22:25Z twu $";
+static char rcsid[] = "$Id: iit-read.c 186665 2016-03-29 21:51:34Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -94,7 +94,7 @@ static char rcsid[] = "$Id: iit-read.c 164702 2015-05-01 20:22:25Z twu $";
#define T IIT_T
static void
-file_move_absolute (int fd, off_t offset, off_t objsize, Chrpos_T n) {
+file_move_absolute (int fd, size_t offset, size_t objsize, Chrpos_T n) {
off_t position = offset + n*objsize;
if (lseek(fd,position,SEEK_SET) < 0) {
@@ -780,7 +780,7 @@ IIT_dump_labels (FILE *fp, T this) {
void
-IIT_dump (T this, bool annotationonlyp, bool sortp) {
+IIT_dump (T this, bool sortp) {
int divno, i;
Interval_T interval;
char *divstring;
@@ -1256,7 +1256,8 @@ IIT_dump_counts (T this, bool alphabetizep) {
for (type = 0; type < this->ntypes; type++) {
typestring = IIT_typestring(this,type);
- chroms[type] = Chrom_from_string(typestring,/*mitochondrial_string*/NULL,/*order*/0U,/*circularp*/false);
+ chroms[type] = Chrom_from_string(typestring,/*mitochondrial_string*/NULL,/*order*/0U,/*circularp*/false,
+ /*alt_scaffold_start*/0,/*alt_scaffold_end*/0);
}
qsort(chroms,this->ntypes,sizeof(Chrom_T),Chrom_compare);
}
@@ -1370,7 +1371,10 @@ IIT_free (T *old) {
FREE((*old)->name);
}
- if ((*old)->access == MMAPPED) {
+ if ((*old)->access == LOADED) {
+ /* No need to munmap or free words */
+
+ } else if ((*old)->access == MMAPPED) {
#ifdef HAVE_MMAP
munmap((void *) (*old)->annot_mmap,(*old)->annot_length);
munmap((void *) (*old)->annotpointers_mmap,(*old)->annotpointers_length);
@@ -1423,42 +1427,54 @@ IIT_free (T *old) {
abort();
}
- if ((*old)->fieldstrings != NULL) {
- FREE((*old)->fieldstrings);
- }
- FREE((*old)->fieldpointers);
- FREE((*old)->typestrings);
- FREE((*old)->typepointers);
+ if ((*old)->access == LOADED) {
+ FREE((*old)->intervals);
+ FREE((*old)->nodes);
+ FREE((*old)->omegas);
+ FREE((*old)->sigmas);
+ if ((*old)->alphas != NULL) {
+ FREE((*old)->betas);
+ FREE((*old)->alphas);
+ }
- FREE((*old)->intervals[0]);
- FREE((*old)->intervals);
+ } else {
+ if ((*old)->fieldstrings != NULL) {
+ FREE((*old)->fieldstrings);
+ }
+ FREE((*old)->fieldpointers);
+ FREE((*old)->typestrings);
+ FREE((*old)->typepointers);
+
+ FREE((*old)->intervals[0]);
+ FREE((*old)->intervals);
+
+ for (divno = 0; divno < (*old)->ndivs; divno++) {
+ /* Note: we are depending on Mem_free() to check that these are non-NULL */
+ FREE((*old)->nodes[divno]);
+ FREE((*old)->omegas[divno]);
+ FREE((*old)->sigmas[divno]);
+ if ((*old)->alphas != NULL) {
+ FREE((*old)->betas[divno]);
+ FREE((*old)->alphas[divno]);
+ }
+ }
- for (divno = 0; divno < (*old)->ndivs; divno++) {
- /* Note: we are depending on Mem_free() to check that these are non-NULL */
- FREE((*old)->nodes[divno]);
- FREE((*old)->omegas[divno]);
- FREE((*old)->sigmas[divno]);
+ FREE((*old)->nodes);
+ FREE((*old)->omegas);
+ FREE((*old)->sigmas);
if ((*old)->alphas != NULL) {
- FREE((*old)->betas[divno]);
- FREE((*old)->alphas[divno]);
+ FREE((*old)->betas);
+ FREE((*old)->alphas);
}
- }
- FREE((*old)->nodes);
- FREE((*old)->omegas);
- FREE((*old)->sigmas);
- if ((*old)->alphas != NULL) {
- FREE((*old)->betas);
- FREE((*old)->alphas);
+ FREE((*old)->divstrings);
+ FREE((*old)->divpointers);
+ FREE((*old)->cum_nnodes);
+ FREE((*old)->nnodes);
+ FREE((*old)->cum_nintervals);
+ FREE((*old)->nintervals);
}
- FREE((*old)->divstrings);
- FREE((*old)->divpointers);
- FREE((*old)->cum_nnodes);
- FREE((*old)->nnodes);
- FREE((*old)->cum_nintervals);
- FREE((*old)->nintervals);
-
FREE(*old);
}
@@ -1487,18 +1503,18 @@ move_relative (FILE *fp, off_t offset) {
}
-static off_t
-skip_trees (off_t offset, off_t filesize, FILE *fp, char *filename,
+static size_t
+skip_trees (size_t offset, size_t filesize, FILE *fp, char *filename,
int skip_ndivs, int skip_nintervals, int skip_nnodes) {
- off_t skipsize;
+ size_t skipsize;
/* 4 is for alphas, betas, sigmas, and omegas */
skipsize = (skip_nintervals + skip_ndivs) * 4 * sizeof(int);
skipsize += skip_nnodes * sizeof(struct FNode_T);
if ((offset += skipsize) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after skip_trees %jd, filesize %jd). Did you generate it using iit_store?\n",
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after skip_trees %zu, filesize %zu). Did you generate it using iit_store?\n",
filename,offset,filesize);
exit(9);
} else {
@@ -1510,8 +1526,85 @@ skip_trees (off_t offset, off_t filesize, FILE *fp, char *filename,
-static off_t
-read_tree (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int divno) {
+static char *
+load_tree (char *memory, T new, int divno) {
+#ifdef DEBUG
+ int i;
+#endif
+
+ if (new->version < 2) {
+#if 0
+ /* Computing only if needed */
+ compute_flanking(new);
+#else
+ new->alphas[divno] = new->betas[divno] = (int *) NULL;
+#endif
+
+ } else {
+ new->alphas[divno] = (int *) memory;
+ memory += (new->nintervals[divno]+1) * sizeof(int);
+
+ new->betas[divno] = (int *) memory;
+ memory += (new->nintervals[divno]+1) * sizeof(int);
+ }
+
+ new->sigmas[divno] = (int *) memory;
+ memory += (new->nintervals[divno]+1) * sizeof(int);
+
+ new->omegas[divno] = (int *) memory;
+ memory += (new->nintervals[divno]+1) * sizeof(int);
+
+ if (new->nnodes[divno] == 0) {
+ new->nodes[divno] = (struct FNode_T *) NULL;
+ } else {
+#ifdef WORDS_BIGENDIAN
+ /* Not supported */
+ abort();
+#if 0
+ new->nodes[divno] = (struct FNode_T *) CALLOC(new->nnodes[divno],sizeof(struct FNode_T));
+ for (i = 0; i < new->nnodes[divno]; i++) {
+ Bigendian_fread_uint(&(new->nodes[divno][i].value),fp);
+ Bigendian_fread_int(&(new->nodes[divno][i].a),fp);
+ Bigendian_fread_int(&(new->nodes[divno][i].b),fp);
+ Bigendian_fread_int(&(new->nodes[divno][i].leftindex),fp);
+ Bigendian_fread_int(&(new->nodes[divno][i].rightindex),fp);
+ }
+#endif
+
+#else
+ if (sizeof(struct FNode_T) == sizeof(unsigned int)+sizeof(int)+sizeof(int)+sizeof(int)+sizeof(int)) {
+ new->nodes[divno] = (struct FNode_T *) memory;
+ memory += new->nnodes[divno] * sizeof(struct FNode_T);
+ } else {
+ /* Not supported */
+ abort();
+#if 0
+ for (i = 0; i < new->nnodes[divno]; i++) {
+ fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp);
+ fread(&(new->nodes[divno][i].a),sizeof(int),1,fp);
+ fread(&(new->nodes[divno][i].b),sizeof(int),1,fp);
+ fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp);
+ fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp);
+ }
+#endif
+ }
+#endif
+
+ debug(
+ for (i = 0; i < new->nnodes[divno]; i++) {
+ printf("Read node %d %d %d\n",new->nodes[divno][i].value,new->nodes[divno][i].a,new->nodes[divno][i].b);
+ }
+ );
+ }
+ debug(printf("\n"));
+
+ return memory;
+}
+
+
+
+static size_t
+read_tree (size_t offset, size_t filesize, FILE *fp, char *filename, T new, int divno) {
size_t items_read;
int i;
@@ -1525,21 +1618,21 @@ read_tree (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int di
} else {
if ((offset += sizeof(int)*(new->nintervals[divno]+1)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after alphas %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after alphas %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
} else {
new->alphas[divno] = (int *) CALLOC(new->nintervals[divno]+1,sizeof(int));
if ((items_read = FREAD_INTS(new->alphas[divno],new->nintervals[divno]+1,fp)) != (unsigned int) new->nintervals[divno] + 1) {
- fprintf(stderr,"IIT file %s appears to be truncated. items_read = %lld\n",
- filename,(long long int) items_read);
+ fprintf(stderr,"IIT file %s appears to be truncated. items_read = %zu\n",
+ filename,items_read);
exit(9);
}
}
if ((offset += sizeof(int)*(new->nintervals[divno]+1)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after betas %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after betas %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
} else {
new->betas[divno] = (int *) CALLOC(new->nintervals[divno]+1,sizeof(int));
@@ -1560,8 +1653,8 @@ read_tree (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int di
}
if ((offset += sizeof(int)*(new->nintervals[divno]+1)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after sigmas %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after sigmas %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
} else {
new->sigmas[divno] = (int *) CALLOC(new->nintervals[divno]+1,sizeof(int));
@@ -1581,8 +1674,8 @@ read_tree (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int di
}
if ((offset += sizeof(int)*(new->nintervals[divno]+1)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after omegas %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after omegas %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
} else {
new->omegas[divno] = (int *) CALLOC(new->nintervals[divno]+1,sizeof(int));
@@ -1630,8 +1723,8 @@ read_tree (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int di
}
#endif
if (offset > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nodes %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nodes %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
}
@@ -1650,11 +1743,11 @@ read_tree (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int di
}
-static off_t
-skip_intervals (int *skip_nintervals, off_t offset, off_t filesize, FILE *fp, char *filename, T new,
+static size_t
+skip_intervals (int *skip_nintervals, size_t offset, size_t filesize, FILE *fp, char *filename, T new,
int divstart, int divend) {
int divno;
- off_t skipsize = 0;
+ size_t skipsize = 0;
*skip_nintervals = 0;
for (divno = divstart; divno <= divend; divno++) {
@@ -1667,8 +1760,8 @@ skip_intervals (int *skip_nintervals, off_t offset, off_t filesize, FILE *fp, ch
}
if ((offset += skipsize) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after skip_intervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after skip_intervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
} else {
move_relative(fp,skipsize);
@@ -1678,8 +1771,52 @@ skip_intervals (int *skip_nintervals, off_t offset, off_t filesize, FILE *fp, ch
}
-static off_t
-read_intervals (off_t offset, off_t filesize, FILE *fp, char *filename, T new, int divno) {
+static char *
+load_intervals (char *memory, T new, int divno) {
+
+#ifdef WORDS_BIGENDIAN
+ /* Not supported */
+ abort();
+#if 0
+ for (i = 0; i < new->nintervals[divno]; i++) {
+ Bigendian_fread_uint(&(new->intervals[divno][i].low),fp);
+ Bigendian_fread_uint(&(new->intervals[divno][i].high),fp);
+ if (new->version >= 2) {
+ Bigendian_fread_int(&(new->intervals[divno][i].sign),fp);
+ } else {
+ new->intervals[divno][i].sign = +1;
+ }
+ Bigendian_fread_int(&(new->intervals[divno][i].type),fp);
+ }
+ if (new->version >= 2) {
+ offset += (sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int))*new->nintervals[divno];
+ } else {
+ offset += (sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int))*new->nintervals[divno];
+ }
+#endif
+
+#else
+ if (new->version >= 2 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)+sizeof(int)) {
+ new->intervals[divno] = (struct Interval_T *) memory;
+ memory += new->nintervals[divno] * sizeof(struct Interval_T);
+
+ } else if (new->version <= 1 && sizeof(struct Interval_T) == sizeof(unsigned int)+sizeof(unsigned int)+sizeof(int)) {
+ new->intervals[divno] = (struct Interval_T *) memory;
+ memory += new->nintervals[divno] * sizeof(struct Interval_T);
+
+ } else {
+ /* Not supported */
+ abort();
+
+ }
+#endif
+
+ return memory;
+}
+
+
+static size_t
+read_intervals (size_t offset, size_t filesize, FILE *fp, char *filename, T new, int divno) {
int i;
#ifdef WORDS_BIGENDIAN
@@ -1722,8 +1859,8 @@ read_intervals (off_t offset, off_t filesize, FILE *fp, char *filename, T new, i
}
#endif
if (offset > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after intervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after intervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
exit(9);
}
@@ -1731,9 +1868,152 @@ read_intervals (off_t offset, off_t filesize, FILE *fp, char *filename, T new, i
}
-static void
-read_words (off_t offset, off_t filesize, FILE *fp, T new) {
+static char *
+load_words (char *memory, T new) {
off_t stringlen;
+#ifdef DEBUG
+ int i;
+#endif
+
+ new->typepointers = (unsigned int *) memory;
+ memory += (new->ntypes+1) * sizeof(unsigned int);
+ debug(
+ printf("typepointers:");
+ for (i = 0; i < new->ntypes+1; i++) {
+ printf(" %u",new->typepointers[i]);
+ }
+ printf("\n");
+ );
+
+ /* Note: To keep ints aligned, would be better to make stringlen a
+ multiple of 4, and put a terminating '\0' as needed */
+ stringlen = new->typepointers[new->ntypes];
+ if (stringlen == 0) {
+ new->typestrings = (char *) NULL;
+ } else {
+ new->typestrings = (char *) memory;
+ memory += stringlen * sizeof(char);
+ }
+ debug(
+ printf("typestrings:\n");
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->typestrings[s]);
+ }
+ printf("\n");
+ );
+
+ if (new->version < 2) {
+ new->fieldpointers = (unsigned int *) CALLOC(new->nfields+1,sizeof(unsigned int));
+ new->fieldpointers[0] = '\0';
+ } else {
+ new->fieldpointers = (unsigned int *) memory;
+ memory += (new->nfields+1) * sizeof(unsigned int);
+ }
+
+ /* Note: To keep ints aligned, would be better to make stringlen a
+ multiple of 4, and put a terminating '\0' as needed */
+ stringlen = new->fieldpointers[new->nfields];
+ if (stringlen == 0) {
+ new->fieldstrings = (char *) NULL;
+ } else {
+ new->fieldstrings = (char *) memory;
+ memory += stringlen * sizeof(char);
+ }
+ debug(
+ printf("fieldstrings:\n");
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->fieldstrings[s]);
+ }
+ printf("\n");
+ );
+
+ if (new->valuep == true) {
+ debug(printf("Starting load of valueorder offset/length\n"));
+ /* new->valueorder_offset = offset; -- Needed only for mmap_annotations */
+ new->valueorder = (int *) memory;
+ new->valueorder_length = (size_t) (new->total_nintervals*sizeof(int));
+ memory += new->valueorder_length;
+
+ debug1(printf("Starting read of value offset/length\n"));
+ /* new->value_offset = offset; -- Needed only for mmap_annotations */
+ new->values = (double *) memory;
+ new->value_length = (size_t) (new->total_nintervals*sizeof(double));
+ memory += new->value_length;
+ }
+
+ debug(printf("Starting load of labelorder at %p\n",memory));
+ /* new->labelorder_offset = offset; -- Needed only for mmap_annotations */
+ new->labelorder = (int *) memory;
+ new->labelorder_length = (size_t) (new->total_nintervals*sizeof(int));
+ memory += new->labelorder_length;
+ debug(
+ printf("labelorder:\n");
+ for (i = 0; i < new->total_nintervals; i++) {
+ printf("%d ",new->labelorder[i]);
+ }
+ printf("\n");
+ );
+
+ debug(printf("Starting load of labelpointer offset/length\n"));
+ /* new->labelpointers_offset = offset; -- Needed only for mmap_annotations */
+#ifdef HAVE_64_BIT
+ if (new->label_pointers_8p == true) {
+ new->labelpointers8 = (UINT8 *) memory;
+ new->labelpointers_length = (size_t) ((new->total_nintervals+1)*sizeof(UINT8));
+ memory += new->total_nintervals * sizeof(UINT8);
+ new->label_length = (size_t) * (UINT8 *) memory;
+ memory += sizeof(UINT8);
+ } else {
+ new->labelpointers = (UINT4 *) memory;
+ new->labelpointers_length = (size_t) ((new->total_nintervals+1)*sizeof(UINT4));
+ memory += new->total_nintervals * sizeof(UINT4);
+ new->label_length = (size_t) * (UINT4 *) memory;
+ memory += sizeof(UINT4);
+ }
+#else
+ new->labelpointers = (UINT4 *) memory;
+ new->labelpointers_length = (size_t) ((new->total_nintervals+1)*sizeof(UINT4));
+ memory += new->total_nintervals * sizeof(UINT4);
+ new->label_length = (size_t) * (UINT4 *) memory;
+ memory += sizeof(UINT4);
+#endif
+
+ debug(printf("Starting load of label offset/length\n"));
+ /* new->label_offset = offset; -- Needed only for mmap_annotations */
+ new->labels = (char *) memory;
+ /* new->label_length computed above */
+ memory += new->label_length;
+
+ debug(printf("Starting load of annotpointers offset/length\n"));
+ /* new->annotpointers_offset = offset; -- Needed only for mmap_annotations */
+#ifdef HAVE_64_BIT
+ if (new->annot_pointers_8p == true) {
+ new->annotpointers8 = (UINT8 *) memory;
+ new->annotpointers_length = (size_t) ((new->total_nintervals+1)*sizeof(UINT8));
+ } else {
+ new->annotpointers = (UINT4 *) memory;
+ new->annotpointers_length = (size_t) ((new->total_nintervals+1)*sizeof(UINT4));
+ }
+#else
+ new->annotpointers = (UINT4 *) memory;
+ new->annotpointers_length = (size_t) ((new->total_nintervals+1)*sizeof(UINT4));
+#endif
+ memory += new->annotpointers_length;
+
+ debug(printf("Starting load of annotations at %p\n",memory));
+ /* new->annot_offset = offset; -- Needed only for mmap_annotations */
+ new->annotations = (char *) memory;
+ /* new->annot_length = filesize - new->annot_offset; -- Needed only for mmap_annotations or read_words */
+ /* fprintf(stderr,"annot_length: %zu\n",new->annot_length); */
+
+ return memory;
+}
+
+
+
+static void
+read_words (size_t offset, size_t filesize, FILE *fp, T new) {
+ size_t stringlen;
#ifdef HAVE_64_BIT
UINT8 length8;
#endif
@@ -1761,8 +2041,8 @@ read_words (off_t offset, off_t filesize, FILE *fp, T new) {
}
debug(
printf("typestrings:\n");
- for (i = 0; i < stringlen; i++) {
- printf("%c",new->typestrings[i]);
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->typestrings[s]);
}
printf("\n");
);
@@ -1782,8 +2062,8 @@ read_words (off_t offset, off_t filesize, FILE *fp, T new) {
}
debug(
printf("fieldstrings:\n");
- for (i = 0; i < stringlen; i++) {
- printf("%c",new->fieldstrings[i]);
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->fieldstrings[s]);
}
printf("\n");
);
@@ -1872,8 +2152,8 @@ read_words (off_t offset, off_t filesize, FILE *fp, T new) {
/* To do this check, we need to get stringlen for annotation similarly to that for labels */
last_offset = offset + sizeof(char)*stringlen;
if (last_offset != filesize) {
- fprintf(stderr,"Problem with last_offset (%lld) not equal to filesize = (%lld)\n",
- (long long int) last_offset,(long long int) filesize);
+ fprintf(stderr,"Problem with last_offset (%zu) not equal to filesize = (%zu)\n",
+ last_offset,filesize);
exit(9);
}
#endif
@@ -1882,15 +2162,15 @@ read_words (off_t offset, off_t filesize, FILE *fp, T new) {
}
static void
-read_words_debug (off_t offset, off_t filesize, FILE *fp, T new) {
- off_t stringlen;
+read_words_debug (size_t offset, size_t filesize, FILE *fp, T new) {
+ size_t stringlen, s;
#ifdef HAVE_64_BIT
UINT8 length8;
#endif
UINT4 length;
int i;
#if 0
- off_t last_offset;
+ size_t last_offset;
#endif
new->typepointers = (unsigned int *) CALLOC(new->ntypes+1,sizeof(unsigned int));
@@ -1909,8 +2189,8 @@ read_words_debug (off_t offset, off_t filesize, FILE *fp, T new) {
offset += sizeof(char)*FREAD_CHARS(new->typestrings,stringlen,fp);
}
printf("typestrings:\n");
- for (i = 0; i < stringlen; i++) {
- printf("%c",new->typestrings[i]);
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->typestrings[s]);
}
printf("\n");
@@ -1928,8 +2208,8 @@ read_words_debug (off_t offset, off_t filesize, FILE *fp, T new) {
offset += sizeof(char)*FREAD_CHARS(new->fieldstrings,stringlen,fp);
}
printf("fieldstrings:\n");
- for (i = 0; i < stringlen; i++) {
- printf("%c",new->fieldstrings[i]);
+ for (s = 0; s < stringlen; s++) {
+ printf("%c",new->fieldstrings[s]);
}
printf("\n");
@@ -2014,8 +2294,8 @@ read_words_debug (off_t offset, off_t filesize, FILE *fp, T new) {
/* To do this check, we need to get stringlen for annotation similarly to that for labels */
last_offset = offset + sizeof(char)*stringlen;
if (last_offset != filesize) {
- fprintf(stderr,"Problem with last_offset (%lld) not equal to filesize = (%lld)\n",
- (long long int) last_offset,(long long int) filesize);
+ fprintf(stderr,"Problem with last_offset (%zu) not equal to filesize = (%zu)\n",
+ last_offset,filesize);
exit(9);
}
#endif
@@ -2038,27 +2318,27 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
}
if (new->valuep == true) {
- new->valueorder_mmap = Access_mmap_offset(&remainder,new->fd,new->valueorder_offset,new->valueorder_length,
- sizeof(char),/*randomp*/true);
+ new->valueorder_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->valueorder_offset,new->valueorder_length,
+ /*randomp*/true);
debug(fprintf(stderr,"valueorder_mmap is %p\n",new->valueorder_mmap));
new->valueorder = (int *) &(new->valueorder_mmap[remainder]);
new->valueorder_length += (size_t) remainder;
- new->value_mmap = Access_mmap_offset(&remainder,new->fd,new->value_offset,new->value_length,
- sizeof(char),/*randomp*/true);
+ new->value_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->value_offset,new->value_length,
+ /*randomp*/true);
debug(fprintf(stderr,"values_mmap is %p\n",new->value_mmap));
new->values = (double *) &(new->value_mmap[remainder]);
new->value_length += (size_t) remainder;
}
- new->labelorder_mmap = Access_mmap_offset(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
- sizeof(char),/*randomp*/true);
+ new->labelorder_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
+ /*randomp*/true);
debug(fprintf(stderr,"labelorder_mmap is %p\n",new->labelorder_mmap));
new->labelorder = (int *) &(new->labelorder_mmap[remainder]);
new->labelorder_length += (size_t) remainder;
- new->labelpointers_mmap = Access_mmap_offset(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
- sizeof(char),/*randomp*/true);
+ new->labelpointers_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
+ /*randomp*/true);
debug(fprintf(stderr,"labelpointers_mmap is %p\n",new->labelpointers_mmap));
#ifdef HAVE_64_BIT
if (new->label_pointers_8p == true) {
@@ -2073,14 +2353,14 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
#endif
new->labelpointers_length += (size_t) remainder;
- new->label_mmap = Access_mmap_offset(&remainder,new->fd,new->label_offset,new->label_length,
- sizeof(char),/*randomp*/true);
+ new->label_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->label_offset,new->label_length,
+ /*randomp*/true);
debug(fprintf(stderr,"labels_mmap is %p\n",new->label_mmap));
new->labels = (char *) &(new->label_mmap[remainder]);
new->label_length += (size_t) remainder;
- new->annotpointers_mmap = Access_mmap_offset(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
- sizeof(char),/*randomp*/true);
+ new->annotpointers_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
+ /*randomp*/true);
debug(fprintf(stderr,"annotpointers_mmap is %p\n",new->annotpointers_mmap));
#ifdef HAVE_64_BIT
if (new->annot_pointers_8p == true) {
@@ -2095,8 +2375,8 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
#endif
new->annotpointers_length += (size_t) remainder;
- new->annot_mmap = Access_mmap_offset(&remainder,new->fd,new->annot_offset,new->annot_length,
- sizeof(char),/*randomp*/true);
+ new->annot_mmap = (char *) Access_mmap_offset(&remainder,new->fd,new->annot_offset,new->annot_length,
+ /*randomp*/true);
debug(fprintf(stderr,"annots_mmap is %p\n",new->annot_mmap));
new->annotations = (char *) &(new->annot_mmap[remainder]);
new->annot_length += (size_t) remainder;
@@ -2107,13 +2387,13 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
exit(9);
}
- new->labelorder_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
- sizeof(char),/*randomp*/true);
+ new->labelorder_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->labelorder_offset,new->labelorder_length,
+ /*randomp*/true);
new->labelorder = (int *) &(new->labelorder_mmap[remainder]);
new->labelorder_length += (size_t) remainder;
- new->labelpointers_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
- sizeof(char),/*randomp*/true);
+ new->labelpointers_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->labelpointers_offset,new->labelpointers_length,
+ /*randomp*/true);
#ifdef HAVE_64_BIT
if (new->label_pointers_8p == true) {
new->labelpointers8 = (UINT8 *) &(new->labelpointers_mmap[remainder]);
@@ -2127,13 +2407,13 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
#endif
new->labelpointers_length += (size_t) remainder;
- new->label_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->label_offset,new->label_length,
- sizeof(char),/*randomp*/true);
+ new->label_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->label_offset,new->label_length,
+ /*randomp*/true);
new->labels = (char *) &(new->label_mmap[remainder]);
new->label_length += (size_t) remainder;
- new->annotpointers_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
- sizeof(char),/*randomp*/true);
+ new->annotpointers_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->annotpointers_offset,new->annotpointers_length,
+ /*randomp*/true);
#ifdef HAVE_64_BIT
if (new->annot_pointers_8p == true) {
new->annotpointers8 = (UINT8 *) &(new->annotpointers_mmap[remainder]);
@@ -2147,8 +2427,8 @@ mmap_annotations (char *filename, T new, bool readonlyp) {
#endif
new->annotpointers_length += (size_t) remainder;
- new->annot_mmap = Access_mmap_offset_rw(&remainder,new->fd,new->annot_offset,new->annot_length,
- sizeof(char),/*randomp*/true);
+ new->annot_mmap = (char *) Access_mmap_offset_rw(&remainder,new->fd,new->annot_offset,new->annot_length,
+ /*randomp*/true);
new->annotations = (char *) &(new->annot_mmap[remainder]);
new->annot_length += (size_t) remainder;
}
@@ -2268,7 +2548,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
char *newfile = NULL;
FILE *fp;
int version;
- off_t offset, filesize, skipsize;
+ size_t offset, skipsize;
+ size_t filesize;
int total_nintervals, ntypes, nfields, divsort;
int label_pointer_size, annot_pointer_size;
@@ -2299,8 +2580,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fclose(fp);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after first byte %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after first byte %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
@@ -2315,8 +2596,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
version,IIT_LATEST_VERSION_NOVALUES,IIT_LATEST_VERSION_VALUES);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after version %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after version %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
@@ -2327,8 +2608,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
@@ -2336,8 +2617,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
@@ -2363,8 +2644,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
}
@@ -2380,8 +2661,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to have a negative number of types\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ntypes %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ntypes %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
debug(printf("ntypes: %d\n",ntypes));
@@ -2397,8 +2678,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to have a negative number of fields\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nfields %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nfields %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
}
@@ -2417,8 +2698,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to have a negative number of divs\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ndivs %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ndivs %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
debug(printf("ndivs: %d\n",ndivs));
@@ -2446,8 +2727,8 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
fprintf(stderr,"IIT file %s appears to have a negative value for divsort\n",filename);
return -1;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after divsort %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after divsort %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return -1;
}
debug(printf("divsort: %d\n",divsort));
@@ -2472,11 +2753,11 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
offset += sizeof(char)*FREAD_CHARS(divstrings,stringlen,fp);
debug(
printf("divstrings:\n");
- for (i = 0; i < stringlen; i++) {
- if (divstrings[i] == '\0') {
+ for (s = 0; s < stringlen; s++) {
+ if (divstrings[s] == '\0') {
printf("\n");
} else {
- printf("%c",divstrings[i]);
+ printf("%c",divstrings[s]);
}
}
printf("(end of divstrings)\n");
@@ -2510,12 +2791,263 @@ IIT_read_divint (char *filename, char *divstring, bool add_iit_p) {
T
+IIT_load (char *memory, char *name) {
+ T new;
+ off_t stringlen;
+ int divno;
+ int label_pointer_size, annot_pointer_size;
+#ifdef DEBUG
+ int i;
+ Interval_T interval;
+#endif
+
+ new = (T) MALLOC(sizeof(*new));
+
+ if (name == NULL) {
+ new->name = NULL;
+ } else {
+ new->name = (char *) CALLOC(strlen(name)+1,sizeof(char));
+ strcpy(new->name,name);
+ }
+
+ new->total_nintervals = * (int *) memory; memory += sizeof(int);
+
+ if (new->total_nintervals != 0) {
+ /* Need to use Univ_IIT_read instead */
+ fprintf(stderr,"Unexpected error. Using IIT_read code on a version 1 IIT\n");
+ abort();
+
+ } else {
+ /* New format to indicate version > 1 */
+ new->version = * (int *) memory; memory += sizeof(int);
+ if (new->version > IIT_LATEST_VERSION_NOVALUES && new->version > IIT_LATEST_VERSION_VALUES) {
+ fprintf(stderr,"This file is version %d, but this software can only read up to versions %d and %d\n",
+ new->version,IIT_LATEST_VERSION_NOVALUES,IIT_LATEST_VERSION_VALUES);
+ return NULL;
+ }
+
+ if (new->version == IIT_LATEST_VERSION_VALUES) {
+ /* If IIT_LATEST_VERSION_VALUES increases, need to revise this code to handle version 6 */
+ new->valuep = true;
+ } else {
+ new->valuep = false;
+ }
+
+ if (new->version <= 3) {
+ new->label_pointers_8p = false;
+ new->annot_pointers_8p = false;
+ } else if (new->version == 4) {
+ new->label_pointers_8p = true;
+ new->annot_pointers_8p = true;
+ } else {
+ /* Read new variables indicating sizes of label and annot pointers */
+ label_pointer_size = * (int *) memory; memory += sizeof(int);
+ annot_pointer_size = * (int *) memory; memory += sizeof(int);
+
+ if (label_pointer_size == 4) {
+ new->label_pointers_8p = false;
+ } else if (label_pointer_size == 8) {
+ new->label_pointers_8p = true;
+ } else {
+ fprintf(stderr,"IIT file has a problem with label_pointer_size being %d, expecting 4 or 8\n",
+ label_pointer_size);
+ }
+
+ if (annot_pointer_size == 4) {
+ new->annot_pointers_8p = false;
+ } else if (annot_pointer_size == 8) {
+ new->annot_pointers_8p = true;
+ } else {
+ fprintf(stderr,"IIT file has a problem with annot_pointer_size being %d, expecting 4 or 8\n",
+ annot_pointer_size);
+ }
+ }
+
+ /* Re-read total_nintervals */
+ new->total_nintervals = * (int *) memory; memory += sizeof(int);
+ }
+
+ debug(printf("version: %d\n",new->version));
+ debug(printf("total_nintervals: %d\n",new->total_nintervals));
+
+
+ new->ntypes = * (int *) memory; memory += sizeof(int);
+ if (new->ntypes < 0) {
+ fprintf(stderr,"IIT file appears to have a negative number of types\n");
+ return NULL;
+ }
+ debug(printf("ntypes: %d\n",new->ntypes));
+
+
+ if (new->version < 2) {
+ new->nfields = 0;
+ } else {
+ new->nfields = * (int *) memory; memory += sizeof(int);
+ if (new->nfields < 0) {
+ fprintf(stderr,"IIT file appears to have a negative number of fields\n");
+ return NULL;
+ }
+ }
+ debug(printf("nfields: %d\n",new->nfields));
+
+
+ if (new->version <= 2) {
+ /* Might not be supported */
+ new->ndivs = 1;
+
+ new->nintervals = (int *) CALLOC(new->ndivs,sizeof(int));
+ new->nintervals[0] = new->total_nintervals;
+ new->cum_nintervals = (int *) CALLOC(new->ndivs+1,sizeof(int));
+ new->cum_nintervals[0] = 0;
+ new->cum_nintervals[1] = new->total_nintervals;
+
+ new->nnodes = (int *) CALLOC(new->ndivs,sizeof(int));
+ new->nnodes[0] = * (int *) memory; memory += sizeof(int);
+ if (new->nnodes[0] < 0) {
+ fprintf(stderr,"IIT file appears to have a negative number of nodes\n");
+ return NULL;
+ }
+ new->cum_nnodes = (int *) CALLOC(new->ndivs+1,sizeof(int));
+ new->cum_nnodes[0] = 0;
+ new->cum_nnodes[1] = new->nnodes[0];
+
+ new->divsort = NO_SORT;
+
+ new->divpointers = (UINT4 *) CALLOC(new->ndivs+1,sizeof(UINT4));
+ new->divpointers[0] = 0;
+ new->divpointers[1] = 1;
+
+ new->divstrings = (char *) CALLOC(1,sizeof(char));
+ new->divstrings[0] = '\0';
+
+ } else {
+
+ new->ndivs = * (int *) memory; memory += sizeof(int);
+ if (new->ndivs < 0) {
+ fprintf(stderr,"IIT file appears to have a negative number of divs\n");
+ return NULL;
+ }
+ debug(printf("ndivs: %d\n",new->ndivs));
+
+ new->nintervals = (int *) memory;
+ memory += new->ndivs * sizeof(int);
+ debug(
+ printf("nintervals:");
+ for (i = 0; i < new->ndivs; i++) {
+ printf(" %d",new->nintervals[i]);
+ }
+ printf("\n");
+ );
+
+ new->cum_nintervals = (int *) memory;
+ memory += (new->ndivs+1) * sizeof(int);
+ debug(
+ printf("cum_nintervals:");
+ for (i = 0; i <= new->ndivs; i++) {
+ printf(" %d",new->cum_nintervals[i]);
+ }
+ printf("\n");
+ );
+
+ new->nnodes = (int *) memory;
+ memory += new->ndivs * sizeof(int);
+ debug(
+ printf("nnodes:");
+ for (i = 0; i < new->ndivs; i++) {
+ printf(" %d",new->nnodes[i]);
+ }
+ printf("\n");
+ );
+
+ new->cum_nnodes = (int *) memory;
+ memory += (new->ndivs+1) * sizeof(int);
+ debug(
+ printf("cum_nnodes:");
+ for (i = 0; i <= new->ndivs; i++) {
+ printf(" %d",new->cum_nnodes[i]);
+ }
+ printf("\n");
+ );
+
+ new->divsort = * (int *) memory; memory += sizeof(int);
+ if (new->divsort < 0) {
+ fprintf(stderr,"IIT file appears to have a negative value for divsort\n");
+ return NULL;
+ }
+ debug(printf("divsort: %d\n",new->divsort));
+
+ new->divpointers = (UINT4 *) memory;
+ memory += (new->ndivs+1) * sizeof(int);;
+ debug(
+ printf("divpointers:");
+ for (i = 0; i < new->ndivs+1; i++) {
+ printf(" %u",new->divpointers[i]);
+ }
+ printf("\n");
+ );
+
+ /* Note: To keep ints aligned, would be better to make stringlen a
+ multiple of 4, and put a terminating '\0' as needed */
+ stringlen = new->divpointers[new->ndivs];
+ if (stringlen == 0) {
+ new->divstrings = (char *) NULL;
+ } else {
+ new->divstrings = (char *) memory;
+ memory += stringlen * sizeof(char);
+ }
+ debug(
+ printf("divstrings:\n");
+ for (s = 0; s < stringlen; s++) {
+ if (new->divstrings[s] == '\0') {
+ printf("\n");
+ } else {
+ printf("%c",new->divstrings[s]);
+ }
+ }
+ printf("(end of divstrings)\n");
+ );
+ }
+
+ new->alphas = (int **) CALLOC(new->ndivs,sizeof(int *));
+ new->betas = (int **) CALLOC(new->ndivs,sizeof(int *));
+ new->sigmas = (int **) CALLOC(new->ndivs,sizeof(int *));
+ new->omegas = (int **) CALLOC(new->ndivs,sizeof(int *));
+ new->nodes = (struct FNode_T **) CALLOC(new->ndivs,sizeof(struct FNode_T *));
+
+ if (new->version == 1) {
+ abort();
+ }
+
+ new->intervals = (struct Interval_T **) CALLOC(new->ndivs,sizeof(struct Interval_T *));
+
+ /* Load all divs */
+ debug(printf("Loading all divs\n"));
+ for (divno = 0; divno < new->ndivs; divno++) {
+ debug(fprintf(stderr,"Starting load of div\n"));
+ memory = load_tree(memory,new,divno);
+ debug(fprintf(stderr,"Ending read of div\n"));
+ }
+
+ for (divno = 0; divno < new->ndivs; divno++) {
+ memory = load_intervals(memory,new,divno);
+ }
+
+ /* memory = */ load_words(memory,new);
+ new->access = LOADED;
+
+ return new;
+}
+
+
+
+T
IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *divstring,
- bool add_iit_p, bool labels_read_p) {
+ bool add_iit_p) {
T new;
FILE *fp;
char *newfile = NULL;
- off_t offset = 0, filesize, stringlen;
+ size_t offset = 0, stringlen;
+ size_t filesize;
int skip_nintervals, desired_divno, divno;
int label_pointer_size, annot_pointer_size;
#ifdef DEBUG
@@ -2523,22 +3055,26 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
Interval_T interval;
#endif
- /* printf("Reading IIT file %s\n",filename); */
- if (add_iit_p == true) {
+ if (add_iit_p == false) {
+ if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
+ return NULL;
+ }
+
+ } else {
+ /* Try adding .iit first */
newfile = (char *) CALLOC(strlen(filename)+strlen(".iit")+1,sizeof(char));
sprintf(newfile,"%s.iit",filename);
if ((fp = FOPEN_READ_BINARY(newfile)) != NULL) {
filename = newfile;
- } else if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
- /* fprintf(stderr,"Cannot open IIT file %s or %s\n",filename,newfile); */
+ } else {
FREE(newfile);
- return NULL;
+ if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
+ return NULL;
+ }
}
- } else if ((fp = FOPEN_READ_BINARY(filename)) == NULL) {
- /* fprintf(stderr,"Cannot open IIT file %s\n",filename); */
- return NULL;
}
+
new = (T) MALLOC(sizeof(*new));
filesize = Access_filesize(filename);
@@ -2555,8 +3091,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fclose(fp);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after first byte %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after first byte %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
@@ -2573,8 +3109,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
new->version,IIT_LATEST_VERSION_NOVALUES,IIT_LATEST_VERSION_VALUES);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after version %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after version %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
@@ -2597,8 +3133,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
@@ -2606,8 +3142,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
@@ -2635,8 +3171,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
}
@@ -2652,8 +3188,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to have a negative number of types\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ntypes %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ntypes %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
debug(printf("ntypes: %d\n",new->ntypes));
@@ -2669,8 +3205,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to have a negative number of fields\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nfields %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nfields %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
}
@@ -2694,8 +3230,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to have a negative number of nodes\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nnodes %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nnodes %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
new->cum_nnodes = (int *) CALLOC(new->ndivs+1,sizeof(int));
@@ -2720,8 +3256,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to have a negative number of divs\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ndivs %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ndivs %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
debug(printf("ndivs: %d\n",new->ndivs));
@@ -2773,8 +3309,8 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
fprintf(stderr,"IIT file %s appears to have a negative value for divsort\n",filename);
return NULL;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after divsort %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after divsort %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return NULL;
}
debug(printf("divsort: %d\n",new->divsort));
@@ -2798,11 +3334,11 @@ IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *d
}
debug(
printf("divstrings:\n");
- for (i = 0; i < stringlen; i++) {
- if (new->divstrings[i] == '\0') {
+ for (s = 0; s < stringlen; s++) {
+ if (new->divstrings[s] == '\0') {
printf("\n");
} else {
- printf("%c",new->divstrings[i]);
+ printf("%c",new->divstrings[s]);
}
}
printf("(end of divstrings)\n");
@@ -2931,7 +3467,8 @@ IIT_debug (char *filename) {
T new;
FILE *fp;
char *newfile = NULL;
- off_t offset = 0, filesize, stringlen;
+ size_t stringlen, s;
+ size_t offset = 0, filesize;
int skip_nintervals, desired_divno, divno, i;
int label_pointer_size, annot_pointer_size;
Divread_T divread = READ_ALL;
@@ -2967,8 +3504,8 @@ IIT_debug (char *filename) {
fclose(fp);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after first byte %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after first byte %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
@@ -2984,8 +3521,8 @@ IIT_debug (char *filename) {
new->version,IIT_LATEST_VERSION_NOVALUES,IIT_LATEST_VERSION_VALUES);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after version %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after version %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
@@ -3008,8 +3545,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
@@ -3017,8 +3554,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
@@ -3046,8 +3583,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to be truncated\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nintervals %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
}
@@ -3072,8 +3609,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to have a negative number of types\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ntypes %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ntypes %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
printf("ntypes: %d\n",new->ntypes);
@@ -3089,8 +3626,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to have a negative number of fields\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nfields %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nfields %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
}
@@ -3114,8 +3651,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to have a negative number of nodes\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nnodes %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after nnodes %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
new->cum_nnodes = (int *) CALLOC(new->ndivs+1,sizeof(int));
@@ -3140,8 +3677,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to have a negative number of divs\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ndivs %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after ndivs %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
printf("ndivs: %d\n",new->ndivs);
@@ -3185,8 +3722,8 @@ IIT_debug (char *filename) {
fprintf(stderr,"IIT file %s appears to have a negative value for divsort\n",filename);
return;
} else if ((offset += sizeof(int)) > filesize) {
- fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after divsort %lld, filesize %lld). Did you generate it using iit_store?\n",
- filename,(long long int) offset,(long long int) filesize);
+ fprintf(stderr,"IIT file %s has an invalid binary format -- offset is too large (offset after divsort %zu, filesize %zu). Did you generate it using iit_store?\n",
+ filename,offset,filesize);
return;
}
printf("divsort: %d\n",new->divsort);
@@ -3207,11 +3744,11 @@ IIT_debug (char *filename) {
offset += sizeof(char)*FREAD_CHARS(new->divstrings,stringlen,fp);
}
printf("divstrings:\n");
- for (i = 0; i < stringlen; i++) {
- if (new->divstrings[i] == '\0') {
+ for (s = 0; s < stringlen; s++) {
+ if (new->divstrings[s] == '\0') {
printf("\n");
} else {
- printf("%c",new->divstrings[i]);
+ printf("%c",new->divstrings[s]);
}
}
}
@@ -3403,33 +3940,8 @@ IIT_find (int *nmatches, T this, char *label) {
high = this->total_nintervals;
*nmatches = 0;
-#ifdef DEBUG
-#ifndef WORDS_BIGENDIAN
-#ifdef HAVE_64_BIT
- for (middle = low; middle < high; middle++) {
- printf("%d:%d:%s, ",middle,this->labelorder[middle],
- &(this->labels[this->labelpointers8[this->labelorder[middle]]]));
- }
- printf("\n");
-#endif
-#endif
-#endif
-
while (!foundp && low < high) {
middle = (low+high)/2;
-#ifdef DEBUG
-#ifndef WORDS_BIGENDIAN
-#ifdef HAVE_64_BIT
- printf("low %d:%d:%s. middle %d:%d:%s high %d:%d:%s\n",
- low,this->labelorder[low],
- &(this->labels[this->labelpointers8[this->labelorder[low]]]),
- middle,this->labelorder[middle],
- &(this->labels[this->labelpointers8[this->labelorder[middle]]]),
- high,this->labelorder[high],
- &(this->labels[this->labelpointers8[this->labelorder[high]]]));
-#endif
-#endif
-#endif
#ifdef WORDS_BIGENDIAN
#ifdef HAVE_64_BIT
@@ -3552,13 +4064,13 @@ IIT_find (int *nmatches, T this, char *label) {
j = 0;
for (recno = low; recno <= high; recno++) {
#ifdef WORDS_BIGENDIAN
-#ifdef DEBUG
+#if 0
printf("Pushing %d:%d\n",recno,Bigendian_convert_int(this->labelorder[recno]));
#endif
matches[j++] = Bigendian_convert_int(this->labelorder[recno])+1;
#else
-#ifdef DEBUG
+#if 0
printf("Pushing %d:%d\n",recno,this->labelorder[recno]);
#endif
matches[j++] = this->labelorder[recno]+1;
@@ -4049,6 +4561,7 @@ IIT_get (int *nmatches, T this, char *divstring, Chrpos_T x, Chrpos_T y, bool so
int nintervals;
divno = IIT_divint(this,divstring);
+
#if 1
/* Usually don't need to check, unless crossing between iits,
because divstring comes from same iit */
@@ -4058,6 +4571,7 @@ IIT_get (int *nmatches, T this, char *divstring, Chrpos_T x, Chrpos_T y, bool so
return (int *) NULL;
}
#endif
+
if ((nintervals = this->nintervals[divno]) == 0) {
*nmatches = 0;
return (int *) NULL;
@@ -4144,6 +4658,7 @@ IIT_get_signed (int *nmatches, T this, char *divstring, Chrpos_T x, Chrpos_T y,
int index;
divno = IIT_divint(this,divstring);
+
#if 1
/* Usually don't need to check, unless crossing between iits,
because divstring comes from same iit */
@@ -4153,6 +4668,7 @@ IIT_get_signed (int *nmatches, T this, char *divstring, Chrpos_T x, Chrpos_T y,
return (int *) NULL;
}
#endif
+
if ((nintervals = this->nintervals[divno]) == 0) {
*nmatches = 0;
return (int *) NULL;
@@ -5040,7 +5556,8 @@ IIT_get_one_safe (T this, Chrpos_T x, Chrpos_T y) {
int *
IIT_get_typed (int *ntypematches, T this, char *divstring, Chrpos_T x, Chrpos_T y, int type, bool sortp) {
int *sorted;
- int index, divno;
+ int index;
+ /* int divno; */
int *typematches = NULL, *matches, nmatches, i, j;
Interval_T interval;
@@ -5079,7 +5596,7 @@ IIT_get_typed (int *ntypematches, T this, char *divstring, Chrpos_T x, Chrpos_T
return sorted;
#endif
} else {
- divno = IIT_divint(this,divstring);
+ /* divno = IIT_divint(this,divstring); */
sorted = sort_matches_by_position(this,typematches,*ntypematches);
FREE(typematches);
return sorted;
@@ -5146,7 +5663,8 @@ int *
IIT_get_typed_signed (int *ntypematches, T this, char *divstring, Chrpos_T x, Chrpos_T y,
int type, int sign, bool sortp) {
int *sorted;
- int index, divno;
+ int index;
+ /* int divno; */
int *typematches = NULL, *matches, nmatches, i, j;
Interval_T interval;
@@ -5185,7 +5703,7 @@ IIT_get_typed_signed (int *ntypematches, T this, char *divstring, Chrpos_T x, Ch
return sorted;
#endif
} else {
- divno = IIT_divint(this,divstring);
+ /* divno = IIT_divint(this,divstring); */
sorted = sort_matches_by_position(this,typematches,*ntypematches);
FREE(typematches);
return sorted;
@@ -5253,7 +5771,8 @@ int *
IIT_get_multiple_typed (int *ntypematches, T this, char *divstring, Chrpos_T x, Chrpos_T y,
int *types, int ntypes, bool sortp) {
int *sorted;
- int index, divno;
+ int index;
+ /* int divno; */
int *typematches = NULL, *matches, nmatches, i, j, k;
Interval_T interval;
@@ -5300,7 +5819,7 @@ IIT_get_multiple_typed (int *ntypematches, T this, char *divstring, Chrpos_T x,
return sorted;
#endif
} else {
- divno = IIT_divint(this,divstring);
+ /* divno = IIT_divint(this,divstring); */
sorted = sort_matches_by_position(this,typematches,*ntypematches);
FREE(typematches);
return sorted;
@@ -5455,7 +5974,7 @@ IIT_get_exact_multiple_with_divno (int *nexactmatches, T this, int divno, Chrpos
/* Modified from IIT_find */
int *
-IIT_get_values_between (int *nmatches, T this, double lowval, double highval, bool sortp) {
+IIT_get_values_between (int *nmatches, T this, double lowval, double highval) {
int *matches = NULL, j;
double val;
int start, end;
@@ -5640,7 +6159,7 @@ IIT_get_values_between (int *nmatches, T this, double lowval, double highval, bo
int *
-IIT_get_values_below (int *nmatches, T this, double highval, bool sortp) {
+IIT_get_values_below (int *nmatches, T this, double highval) {
int *matches = NULL, j;
double val;
int start = 0, end;
@@ -5747,7 +6266,7 @@ IIT_get_values_below (int *nmatches, T this, double highval, bool sortp) {
int *
-IIT_get_values_above (int *nmatches, T this, double lowval, bool sortp) {
+IIT_get_values_above (int *nmatches, T this, double lowval) {
int *matches = NULL, j;
double val;
int start, end = this->total_nintervals - 1;
@@ -5922,7 +6441,7 @@ IIT_typelist (T this) {
/* Assume 0-based index */
static void
-print_header (Filestring_T fp, T this, int recno, char *chr, bool map_bothstrands_p,
+print_header (Filestring_T fp, T this, int recno, char *chr,
bool relativep, Chrpos_T left, bool print_comment_p) {
char *string, *restofheader, *p;
Interval_T interval;
@@ -5994,7 +6513,7 @@ print_header (Filestring_T fp, T this, int recno, char *chr, bool map_bothstrand
void
-IIT_print_header (Filestring_T fp, T this, int *matches, int nmatches, bool map_bothstrands_p,
+IIT_print_header (Filestring_T fp, T this, int *matches, int nmatches,
char *chr, bool reversep, bool relativep, Chrpos_T left,
bool print_comment_p) {
int recno, i;
@@ -6002,12 +6521,12 @@ IIT_print_header (Filestring_T fp, T this, int *matches, int nmatches, bool map_
if (reversep == true) {
for (i = nmatches-1; i >= 0; i--) {
recno = matches[i] - 1; /* Convert to 0-based */
- print_header(fp,this,recno,chr,map_bothstrands_p,relativep,left,print_comment_p);
+ print_header(fp,this,recno,chr,relativep,left,print_comment_p);
}
} else {
for (i = 0; i < nmatches; i++) {
recno = matches[i] - 1; /* Convert to 0-based */
- print_header(fp,this,recno,chr,map_bothstrands_p,relativep,left,print_comment_p);
+ print_header(fp,this,recno,chr,relativep,left,print_comment_p);
}
}
diff --git a/src/iit-read.h b/src/iit-read.h
index 208fc7b..6bb1dca 100644
--- a/src/iit-read.h
+++ b/src/iit-read.h
@@ -1,4 +1,4 @@
-/* $Id: iit-read.h 157225 2015-01-22 18:47:23Z twu $ */
+/* $Id: iit-read.h 184169 2016-02-12 19:35:45Z twu $ */
#ifndef IIT_READ_INCLUDED
#define IIT_READ_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -108,7 +108,7 @@ IIT_dump_fieldstrings (FILE *fp, T this);
extern void
IIT_dump_labels (FILE *fp, T this);
extern void
-IIT_dump (T this, bool annotationonlyp, bool sortp);
+IIT_dump (T this, bool sortp);
extern void
IIT_dump_simple (T this);
extern void
@@ -124,10 +124,15 @@ extern void
IIT_free (T *old);
extern int
IIT_read_divint (char *filename, char *divstring, bool add_iit_p);
+
+/* Same as IIT_read, but can handle a region of memory, instead of a file */
+extern T
+IIT_load (char *memory, char *name);
+
extern T
/* add_iit_p means to add the ".iit" suffix to the filename */
IIT_read (char *filename, char *name, bool readonlyp, Divread_T divread, char *divstring,
- bool add_iit_p, bool labels_read_p);
+ bool add_iit_p);
extern int *
IIT_find (int *nmatches, T this, char *label);
@@ -202,11 +207,11 @@ extern int *
IIT_get_exact_multiple_with_divno (int *nmatches, T this, int divno, Chrpos_T x, Chrpos_T y, int type);
extern int *
-IIT_get_values_between (int *nmatches, T this, double lowval, double highval, bool sortp);
+IIT_get_values_between (int *nmatches, T this, double lowval, double highval);
extern int *
-IIT_get_values_below (int *nmatches, T this, double highval, bool sortp);
+IIT_get_values_below (int *nmatches, T this, double highval);
extern int *
-IIT_get_values_above (int *nmatches, T this, double lowval, bool sortp);
+IIT_get_values_above (int *nmatches, T this, double lowval);
extern List_T
IIT_intervallist_typed (List_T *labellist, Uintlist_T *seglength_list, T this);
@@ -214,7 +219,7 @@ extern List_T
IIT_typelist (T this);
extern void
-IIT_print_header (Filestring_T fp, T this, int *matches, int nmatches, bool map_bothstrands_p,
+IIT_print_header (Filestring_T fp, T this, int *matches, int nmatches,
char *chr, bool reversep, bool relativep, Chrpos_T left, bool print_comment_p);
extern Overlap_T
diff --git a/src/iit-write.c b/src/iit-write.c
index 7fd1dd0..453e75a 100644
--- a/src/iit-write.c
+++ b/src/iit-write.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: iit-write.c 115892 2013-11-20 22:52:31Z twu $";
+static char rcsid[] = "$Id: iit-write.c 184463 2016-02-18 00:08:41Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -29,12 +29,22 @@ static char rcsid[] = "$Id: iit-write.c 115892 2013-11-20 22:52:31Z twu $";
#include "doublelist.h"
+/* Makes IIT files more efficient, because the integer arrays will be aligned */
+#define PAD_STRINGS 1
+
#ifdef DEBUG
#define debug(x) x
#else
#define debug(x)
#endif
+/* Padding */
+#ifdef DEBUG1
+#define debug1(x) x
+#else
+#define debug1(x)
+#endif
+
typedef struct Node_T *Node_T;
struct Node_T {
@@ -576,6 +586,7 @@ Node_create (T new, int divno, int *i, Node_T node) {
}
+#if 0
/* Stores in DFS order */
static void
Node_store (int *fnodei, struct FNode_T *fnodes, Node_T node) {
@@ -606,6 +617,7 @@ Node_store (int *fnodei, struct FNode_T *fnodes, Node_T node) {
}
return;
}
+#endif
static void
@@ -615,7 +627,7 @@ IIT_write_div_header (FILE *fp, int total_nintervals, int ntypes, int nfields, i
bool label_pointers_8p, bool annot_pointers_8p) {
int new_format_indicator = 0, label_pointer_size, annot_pointer_size;
int divno;
- UINT4 pointer = 0U;
+ UINT4 pointer = 0U, padded;
List_T p;
char *divstring;
@@ -667,18 +679,32 @@ IIT_write_div_header (FILE *fp, int total_nintervals, int ntypes, int nfields, i
if (version >= 3) {
/* Write div pointers */
pointer = 0U;
- FWRITE_UINT(pointer,fp);
for (p = divlist; p != NULL; p = List_next(p)) {
+ FWRITE_UINT(pointer,fp);
divstring = (char *) List_head(p);
pointer += (UINT4) strlen(divstring)+1U; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
}
+#ifdef PAD_STRINGS
+ /* Pad last pointer to next multiple of 4 */
+ padded = (pointer + 3) & ~3;
+ debug1(printf("divstrings: converting pointer %d to padded %d\n",pointer,padded));
+ FWRITE_UINT(padded,fp);
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
/* Write divs */
for (p = divlist; p != NULL; p = List_next(p)) {
divstring = (char *) List_head(p);
FWRITE_CHARS(divstring,strlen(divstring)+1,fp); /* Write '\0' */
}
+#ifdef PAD_STRINGS
+ /* Add padding */
+ while (pointer++ < padded) {
+ debug1(printf("divstrings: adding 0 as padding\n"));
+ fputc('\0',fp);
+ }
+#endif
}
return;
@@ -690,7 +716,7 @@ IIT_create_div_header (T new, int total_nintervals, int ntypes, int nfields, int
int *nintervals, int *nnodes, int *cum_nintervals, int *cum_nnodes,
List_T divlist, Sorttype_T divsort, int version) {
int divno;
- UINT4 pointer = 0U;
+ UINT4 pointer = 0U, padded;
List_T p;
char *divstring;
int stringlen, k;
@@ -726,12 +752,20 @@ IIT_create_div_header (T new, int total_nintervals, int ntypes, int nfields, int
new->divpointers = (UINT4 *) CALLOC(new->ndivs+1,sizeof(UINT4));
/* Create div pointers */
k = 0;
- new->divpointers[k++] = pointer = 0U;
+ pointer = 0U;
for (p = divlist; p != NULL; p = List_next(p)) {
+ new->divpointers[k++] = pointer;
divstring = (char *) List_head(p);
pointer += (UINT4) strlen(divstring)+1U; /* Add count for '\0' */
- new->divpointers[k++] = pointer;
}
+#ifdef PAD_STRINGS
+ /* Pad last pointer to next multiple of 4 */
+ padded = (pointer + 3) & ~3;
+ debug1(printf("divstrings: converting pointer %d to padded %d\n",pointer,padded));
+ new->divpointers[k++] = padded;
+#else
+ new->divpointers[k++] = pointer;
+#endif
stringlen = new->divpointers[new->ndivs];
new->divstrings = (char *) CALLOC(stringlen,sizeof(char));
@@ -743,6 +777,13 @@ IIT_create_div_header (T new, int total_nintervals, int ntypes, int nfields, int
k += strlen(divstring);
new->divstrings[k++] = '\0';
}
+#ifdef PAD_STRINGS
+ /* Add padding */
+ while (k < padded) {
+ debug1(printf("divstrings: adding 0 as padding\n"));
+ new->divstrings[k++] = '\0';
+ }
+#endif
return;
}
@@ -844,9 +885,9 @@ IIT_write_div_footer (FILE *fp, List_T divlist, List_T typelist, List_T fieldlis
Doublelist_T valuelist, v;
Interval_T interval;
#ifdef HAVE_64_BIT
- UINT8 pointer8 = 0LU;
+ UINT8 pointer8 = 0LU, padded8;
#endif
- UINT4 pointer = 0U;
+ UINT4 pointer = 0U, padded;
int *labelorder, *valueorder;
double value;
char *divstring, *typestring, *fieldstring, *label, *annot;
@@ -873,37 +914,69 @@ IIT_write_div_footer (FILE *fp, List_T divlist, List_T typelist, List_T fieldlis
/* Write type pointers */
pointer = 0U;
- FWRITE_UINT(pointer,fp);
for (p = typelist; p != NULL; p = List_next(p)) {
+ FWRITE_UINT(pointer,fp);
typestring = (char *) List_head(p);
if (typestring == NULL) {
abort(); /* Even type 0 has an empty string */
} else {
pointer += (UINT4) strlen(typestring)+1U; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
}
}
+#ifdef PAD_STRINGS
+ /* Pad last pointer to next multiple of 4 */
+ padded = (pointer + 3) & ~3;
+ debug1(printf("typestrings: converting pointer %d to padded %d\n",pointer,padded));
+ FWRITE_UINT(padded,fp);
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
+
/* Write types */
for (p = typelist; p != NULL; p = List_next(p)) {
typestring = (char *) List_head(p);
FWRITE_CHARS(typestring,strlen(typestring)+1,fp); /* Write '\0' */
}
+#ifdef PAD_STRINGS
+ /* Add padding */
+ while (pointer++ < padded) {
+ debug1(printf("typestrings: adding 0 as padding\n"));
+ fputc('\0',fp);
+ }
+#endif
+
/* Write field pointers */
pointer = 0U;
- FWRITE_UINT(pointer,fp);
for (p = fieldlist; p != NULL; p = List_next(p)) {
+ FWRITE_UINT(pointer,fp);
fieldstring = (char *) List_head(p);
pointer += (UINT4) strlen(fieldstring)+1U; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
}
+#ifdef PAD_STRINGS
+ /* Pad last pointer to next multiple of 4 */
+ padded = (pointer + 3) & ~3;
+ debug1(printf("fieldstrings: converting pointer %d to padded %d\n",pointer,padded));
+ FWRITE_UINT(padded,fp);
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
+
/* Write fields */
for (p = fieldlist; p != NULL; p = List_next(p)) {
fieldstring = (char *) List_head(p);
FWRITE_CHARS(fieldstring,strlen(fieldstring)+1,fp); /* Write '\0' */
}
+#ifdef PAD_STRINGS
+ /* Add padding */
+ while (pointer++ < padded) {
+ debug1(printf("fieldstrings: adding 0 as padding\n"));
+ fputc('\0',fp);
+ }
+#endif
+
/* Write valueorder (if values present) */
if (valuetable != NULL) {
@@ -931,36 +1004,68 @@ IIT_write_div_footer (FILE *fp, List_T divlist, List_T typelist, List_T fieldlis
#ifdef HAVE_64_BIT
if (label_pointers_8p == true) {
pointer8 = 0LU;
- FWRITE_UINT8(pointer8,fp);
} else {
pointer = 0U;
- FWRITE_UINT(pointer,fp);
}
#else
pointer = 0U;
- FWRITE_UINT(pointer,fp);
#endif
for (d = divlist; d != NULL; d = List_next(d)) {
divstring = (char *) List_head(d);
labellist = (List_T) Table_get(labeltable,(void *) divstring);
for (p = labellist; p != NULL; p = List_next(p)) {
+#ifdef HAVE_64_BIT
+ if (label_pointers_8p == true) {
+ FWRITE_UINT8(pointer8,fp);
+ } else {
+ FWRITE_UINT(pointer,fp);
+ }
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
+
label = (char *) List_head(p);
#ifdef HAVE_64_BIT
if (label_pointers_8p == true) {
pointer8 += (UINT8) strlen(label)+1LU; /* Add count for '\0' */
- FWRITE_UINT8(pointer8,fp);
} else {
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
}
#else
pointer += (UINT4) strlen(label)+1U; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
#endif
}
}
+#ifdef PAD_STRINGS
+ /* Pad last pointer to next multiple of 4 */
+#ifdef HAVE_64_BIT
+ if (label_pointers_8p == true) {
+ padded8 = (pointer8 + 3) & ~3;
+ FWRITE_UINT8(padded8,fp);
+ } else {
+ padded = (pointer + 3) & ~3;
+ debug1(printf("labels: converting pointer %d to padded %d\n",pointer,padded));
+ FWRITE_UINT(padded,fp);
+ }
+#else
+ padded = (pointer + 3) & ~3;
+ FWRITE_UINT(padded,fp);
+#endif
+#else
+#ifdef HAVE_64_BIT
+ if (label_pointers_8p == true) {
+ FWRITE_UINT8(pointer8,fp);
+ } else {
+ FWRITE_UINT(pointer,fp);
+ }
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
+#endif
+
+
/* Write labels */
for (d = divlist; d != NULL; d = List_next(d)) {
divstring = (char *) List_head(d);
@@ -970,41 +1075,94 @@ IIT_write_div_footer (FILE *fp, List_T divlist, List_T typelist, List_T fieldlis
FWRITE_CHARS(label,strlen(label)+1,fp); /* Write '\0' */
}
}
+#ifdef PAD_STRINGS
+ /* Add padding */
+#ifdef HAVE_64_BIT
+ if (label_pointers_8p == true) {
+ while (pointer8++ < padded8) {
+ fputc('\0',fp);
+ }
+ } else {
+ while (pointer++ < padded) {
+ debug1(printf("labels: adding 0 as padding\n"));
+ fputc('\0',fp);
+ }
+ }
+#else
+ while (pointer++ < padded) {
+ fputc('\0',fp);
+ }
+#endif
+#endif
+
+
/* Write annot pointers */
#ifdef HAVE_64_BIT
if (annot_pointers_8p == true) {
pointer8 = 0LU;
- FWRITE_UINT8(pointer8,fp);
} else {
pointer = 0U;
- FWRITE_UINT(pointer,fp);
}
#else
pointer = 0U;
- FWRITE_UINT(pointer,fp);
#endif
for (d = divlist; d != NULL; d = List_next(d)) {
divstring = (char *) List_head(d);
annotlist = (List_T) Table_get(annottable,(void *) divstring);
for (p = annotlist; p != NULL; p = List_next(p)) {
+#ifdef HAVE_64_BIT
+ if (annot_pointers_8p == true) {
+ FWRITE_UINT8(pointer8,fp);
+ } else {
+ FWRITE_UINT(pointer,fp);
+ }
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
+
annot = (char *) List_head(p);
#ifdef HAVE_64_BIT
if (annot_pointers_8p == true) {
pointer8 += (UINT8) strlen(annot)+1LU; /* Add count for '\0' */
- FWRITE_UINT8(pointer8,fp);
} else {
pointer += (UINT4) strlen(annot)+1; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
}
#else
pointer += (UINT4) strlen(annot)+1; /* Add count for '\0' */
- FWRITE_UINT(pointer,fp);
#endif
}
}
+#ifdef PAD_STRINGS
+ /* Pad last pointer to next multiple of 4 */
+#ifdef HAVE_64_BIT
+ if (annot_pointers_8p == true) {
+ padded8 = (pointer8 + 3) & ~3;
+ FWRITE_UINT8(padded8,fp);
+ } else {
+ padded = (pointer + 3) & ~3;
+ debug1(printf("annotations: converting pointer %d to padded %d\n",pointer,padded));
+ FWRITE_UINT(padded,fp);
+ }
+#else
+ padded = (pointer + 3) & ~3;
+ FWRITE_UINT(padded,fp);
+#endif
+#else
+#ifdef HAVE_64_BIT
+ if (annot_pointers_8p == true) {
+ FWRITE_UINT8(pointer8,fp);
+ } else {
+ FWRITE_UINT(pointer,fp);
+ }
+#else
+ FWRITE_UINT(pointer,fp);
+#endif
+#endif
+
+
/* Write annotations */
for (d = divlist; d != NULL; d = List_next(d)) {
divstring = (char *) List_head(d);
@@ -1014,6 +1172,26 @@ IIT_write_div_footer (FILE *fp, List_T divlist, List_T typelist, List_T fieldlis
FWRITE_CHARS(annot,strlen(annot)+1,fp); /* Write '\0' */
}
}
+#ifdef PAD_STRINGS
+ /* Add padding */
+#ifdef HAVE_64_BIT
+ if (annot_pointers_8p == true) {
+ while (pointer8++ < padded8) {
+ fputc('\0',fp);
+ }
+ } else {
+ while (pointer++ < padded) {
+ debug1(printf("annotations: adding 0 as padding\n"));
+ fputc('\0',fp);
+ }
+ }
+#else
+ while (pointer++ < padded) {
+ fputc('\0',fp);
+ }
+#endif
+#endif
+
return;
}
diff --git a/src/iit_dump.c b/src/iit_dump.c
index 109c4b5..6a5e249 100644
--- a/src/iit_dump.c
+++ b/src/iit_dump.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: iit_dump.c 99737 2013-06-27 19:33:03Z twu $";
+static char rcsid[] = "$Id: iit_dump.c 184165 2016-02-12 19:14:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -237,7 +237,7 @@ main (int argc, char *argv[]) {
return 0;
} else if ((iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"Unable to open or parse IIT file %s\n",iitfile);
exit(9);
}
@@ -259,7 +259,7 @@ main (int argc, char *argv[]) {
}
} else {
- IIT_dump(iit,annotationonlyp,sortp);
+ IIT_dump(iit,sortp);
}
IIT_free(&iit);
diff --git a/src/iit_get.c b/src/iit_get.c
index a37b468..39f24c1 100644
--- a/src/iit_get.c
+++ b/src/iit_get.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: iit_get.c 153955 2014-11-24 17:54:45Z twu $";
+static char rcsid[] = "$Id: iit_get.c 184172 2016-02-12 19:41:14Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -60,7 +60,7 @@ static bool zeroesp = false;
static bool statsp = false;
static bool force_label_p = false;
static bool force_coords_p = false;
-static bool overall_total_p = false;
+
static struct option long_options[] = {
/* Input options */
@@ -482,6 +482,7 @@ compute_totals_tally (long int *total, int *n, Chrpos_T coordstart, Chrpos_T coo
}
+#if 0
/* Need to store just the part of the query specified (e.g., 1..10) */
static double
compute_logtotal_tally (long int *total, int *n, Chrpos_T coordstart, Chrpos_T coordend,
@@ -529,6 +530,7 @@ compute_logtotal_tally (long int *total, int *n, Chrpos_T coordstart, Chrpos_T c
return logtotal;
}
+#endif
@@ -611,8 +613,7 @@ print_interval (Chrpos_T *lastcoord, long int total,
static void
-print_interval_univ (Univcoord_T coordstart, Univcoord_T coordend, int index,
- Univ_IIT_T chromosome_iit) {
+print_interval_univ (int index, Univ_IIT_T chromosome_iit) {
Univinterval_T interval;
char *label, *annotation, *restofheader;
bool allocp;
@@ -669,7 +670,7 @@ get_matches (int *nmatches, char **divstring, Univcoord_T *coordstart, Univcoord
if (*iit == NULL) {
/* Read no divs */
if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_NONE,/*divstring*/NULL,
- /*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
@@ -690,7 +691,7 @@ get_matches (int *nmatches, char **divstring, Univcoord_T *coordstart, Univcoord
} else {
if (*iit == NULL) {
if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,
- /*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
+ /*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
@@ -754,7 +755,6 @@ get_matches (int *nmatches, char **divstring, Univcoord_T *coordstart, Univcoord
static int *
get_matches_univ (int *nmatches, char **divstring, Univcoord_T *coordstart, Univcoord_T *coordend,
- int **leftflanks, int *nleftflanks, int **rightflanks, int *nrightflanks,
char *query, char *typestring, Univ_IIT_T *chromosome_iit, char *filename) {
int *matches;
bool revcomp;
@@ -776,7 +776,6 @@ get_matches_univ (int *nmatches, char **divstring, Univcoord_T *coordstart, Univ
exit(9);
}
}
- *nleftflanks = *nrightflanks = 0;
matches = Univ_IIT_find(&(*nmatches),*chromosome_iit,query);
} else {
@@ -797,7 +796,6 @@ get_matches_univ (int *nmatches, char **divstring, Univcoord_T *coordstart, Univ
if (nflanking > 0) {
fprintf(stderr,"Flanking not supported on chromosome IIT\n");
}
- *nleftflanks = *nrightflanks = 0;
} else if ((typeint = Univ_IIT_typeint(*chromosome_iit,typestring)) < 0) {
fprintf(stderr,"No such type as %s.\n",typestring);
@@ -807,10 +805,8 @@ get_matches_univ (int *nmatches, char **divstring, Univcoord_T *coordstart, Univ
if (nflanking > 0) {
fprintf(stderr,"Flanking not supported on chromosome IIT\n");
}
- *nleftflanks = *nrightflanks = 0;
#else
matches = (int *) NULL;
- *nleftflanks = *nrightflanks = 0;
*nmatches = 0;
#endif
@@ -818,7 +814,6 @@ get_matches_univ (int *nmatches, char **divstring, Univcoord_T *coordstart, Univ
/* Treat query as coordinates, with a typestring */
fprintf(stderr,"Ignoring types on chromosome IIT\n");
matches = Univ_IIT_get(&(*nmatches),*chromosome_iit,*coordstart,*coordend);
- *nleftflanks = *nrightflanks = 0;
}
}
@@ -839,8 +834,7 @@ get_matches_multiple_typed (int *nmatches, char **divstring, Univcoord_T *coords
abort();
}
- if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true,
- /*labels_read_p*/false)) == NULL) {
+ if ((*iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ONE,*divstring,/*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
@@ -1008,7 +1002,7 @@ main (int argc, char *argv[]) {
if (value_matches_p == true) {
if ((iit = IIT_read(filename,/*name*/NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,
- /*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
@@ -1033,20 +1027,19 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Cannot have lowval %f > highval %f\n",lowval,highval);
exit(9);
} else {
- value_matches = IIT_get_values_between(&n_value_matches,iit,lowval,highval,/*sortp*/false);
+ value_matches = IIT_get_values_between(&n_value_matches,iit,lowval,highval);
}
} else if (user_lowvalue_p == true) {
- value_matches = IIT_get_values_above(&n_value_matches,iit,lowval,/*sortp*/false);
+ value_matches = IIT_get_values_above(&n_value_matches,iit,lowval);
} else { /* user_highvalue_p == true */
- value_matches = IIT_get_values_below(&n_value_matches,iit,highval,/*sortp*/false);
+ value_matches = IIT_get_values_below(&n_value_matches,iit,highval);
}
}
if (0 && statsp == true && argc == 2) {
/* Want total over entire IIT */
- if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true,
- /*labels_read_p*/false)) == NULL) {
+ if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
@@ -1080,12 +1073,11 @@ main (int argc, char *argv[]) {
} else {
/* Try as 0:<iitfile> 1:<query> */
matches = get_matches_univ(&nmatches,&divstring,&univ_coordstart,&univ_coordend,
- &leftflanks,&nleftflanks,&rightflanks,&nrightflanks,
argv[2],/*typestring*/NULL,&chromosome_iit,filename);
for (i = 0; i < nmatches; i++) {
debug(printf("\nindex = %d\n",matches[i]));
- print_interval_univ(univ_coordstart,univ_coordend,matches[i],chromosome_iit);
+ print_interval_univ(matches[i],chromosome_iit);
}
}
@@ -1113,8 +1105,7 @@ main (int argc, char *argv[]) {
debug(printf("Running under argc 2\n"));
/* Expecting input from stdin */
- if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true,
- /*labels_read_p*/true)) == NULL) {
+ if ((iit = IIT_read(filename,NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
diff --git a/src/iit_store.c b/src/iit_store.c
index 028dcb8..d94fc27 100644
--- a/src/iit_store.c
+++ b/src/iit_store.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: iit_store.c 153955 2014-11-24 17:54:45Z twu $";
+static char rcsid[] = "$Id: iit_store.c 182437 2016-01-15 22:26:55Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1078,7 +1078,8 @@ main (int argc, char *argv[]) {
if (tempstring[0] == '\0') {
/* FREE(tempstring); -- Causes invalid read later in table_string_compare */
} else {
- chroms[i++] = Chrom_from_string(tempstring,mitochondrial_string,order++,/*circularp*/false);
+ chroms[i++] = Chrom_from_string(tempstring,mitochondrial_string,order++,
+ /*circularp*/false,/*alt_scaffold_start*/0,/*alt_scaffold_end*/0);
}
}
}
diff --git a/src/inbuffer.c b/src/inbuffer.c
index e3c2f85..93ee3cf 100644
--- a/src/inbuffer.c
+++ b/src/inbuffer.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: inbuffer.c 175728 2015-09-30 15:08:16Z twu $";
+static char rcsid[] = "$Id: inbuffer.c 179288 2015-11-20 00:45:00Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -343,7 +343,7 @@ fill_buffer_master (T this) {
int nextchar_end;
bool donep;
#if 0
- int nchars1 = 0, nchars2 = 0; /* Doesn't need to be saved as a field in Inbuffer_T. */
+ int nchars1, nchars2; /* Doesn't need to be saved as a field in Inbuffer_T. */
#endif
/* Need to receive nextchar_end because of the difference between
@@ -519,7 +519,7 @@ fill_buffer_slave (T this) {
int offset_start_1, offset_end_1, offset_start_2, offset_end_2;
int nextchar_end;
#if 0
- int nchars1 = 0, nchars2 = 0; /* Doesn't need to be saved as a field in Inbuffer_T. */
+ int nchars1, nchars2; /* Doesn't need to be saved as a field in Inbuffer_T. */
#endif
/* Need to receive nextchar_end because of the difference between
diff --git a/src/indel.c b/src/indel.c
index 7127a47..10ae2a9 100644
--- a/src/indel.c
+++ b/src/indel.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: indel.c 167164 2015-06-09 20:54:17Z twu $";
+static char rcsid[] = "$Id: indel.c 184486 2016-02-18 03:21:44Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -37,8 +37,7 @@ int
Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j,
Univcoord_T left, int indels, Compress_T query_compress,
int querystart, int queryend, int querylength,
- int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
int best_indel_pos = -1, indel_pos;
#ifdef DEBUG2
int i;
@@ -46,7 +45,7 @@ Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j
#endif
int nmismatches_left, nmismatches_right;
int best_sum, sum, nmismatches_lefti, nmismatches_righti, lefti, righti;
- int nmismatches1, nmismatches2;
+
#ifdef HAVE_ALLOCA
int *mismatch_positions_left = (int *) ALLOCA(querylength * sizeof(int));
@@ -75,7 +74,7 @@ Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j
debug2(printf("max_mismatches_allowed is %d\n",max_mismatches_allowed));
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,left,/*pos5*/querystart,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on left at:",nmismatches_left);
@@ -90,7 +89,7 @@ Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j
debug2(printf("max_mismatches_allowed is %d\n",max_mismatches_allowed));
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,left-indels,/*pos5*/querystart,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on right at:",nmismatches_right);
@@ -117,7 +116,8 @@ Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j
sum,righti,lefti+1,mismatch_positions_right[righti]-indels+1));
if (sum <= best_sum) {
indel_pos = mismatch_positions_right[righti] - indels + 1;
- if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches) {
+ if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches &&
+ /* Require more matches on both ends than indel length */ indel_pos >= indels && indel_pos + indels <= querylength - indels) {
best_indel_pos = indel_pos;
nmismatches_righti = righti;
nmismatches_lefti = lefti + 1;
@@ -143,7 +143,8 @@ Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j
sum,lefti,righti+1,mismatch_positions_left[lefti]));
if (sum < best_sum) {
indel_pos = mismatch_positions_left[lefti];
- if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches) {
+ if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches &&
+ /* Require more matches on both ends than insertion length */ indel_pos >= indels && indel_pos + indels <= querylength - indels) {
best_indel_pos = indel_pos;
nmismatches_righti = righti + 1;
nmismatches_lefti = lefti;
@@ -153,7 +154,8 @@ Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j
} else if (sum == best_sum) {
indel_pos = mismatch_positions_left[lefti];
if (indel_pos < best_indel_pos) {
- if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches) {
+ if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches &&
+ /* Require more matches on both ends than insertion length */ indel_pos >= indels && indel_pos + indels <= querylength - indels) {
best_indel_pos = indel_pos;
nmismatches_righti = righti + 1;
nmismatches_lefti = lefti;
@@ -192,8 +194,7 @@ int
Indel_resolve_middle_deletion (int *best_nmismatches_i, int *best_nmismatches_j,
Univcoord_T left, int indels, Compress_T query_compress,
int querystart, int queryend, int querylength,
- int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
int best_indel_pos = -1, indel_pos;
#ifdef DEBUG2
int i;
@@ -229,7 +230,7 @@ Indel_resolve_middle_deletion (int *best_nmismatches_i, int *best_nmismatches_j,
/* No need to check chromosome bounds */
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,left,/*pos5*/querystart,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on left at:",nmismatches_left);
@@ -242,7 +243,7 @@ Indel_resolve_middle_deletion (int *best_nmismatches_i, int *best_nmismatches_j,
/* No need to check chromosome bounds */
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,left-indels,/*pos5*/querystart,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on right at:",nmismatches_right);
@@ -344,7 +345,7 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
Univcoord_T chrhigh, Chrpos_T chrlength,
int indels, Compress_T query_compress,
int querylength, int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p, bool sarrayp) {
+ bool plusp, int genestrand, bool sarrayp) {
#ifdef DEBUG2
int i;
char *gbuffer;
@@ -379,7 +380,7 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
/* No need to check chromosome bounds */
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,left+indels,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on left at:",nmismatches_left);
@@ -393,7 +394,7 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
/* No need to check chromosome bounds */
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on right at:",nmismatches_right);
@@ -420,7 +421,8 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
sum,righti,lefti+1,mismatch_positions_right[righti]-indels+1));
if (sum <= best_sum) {
indel_pos = mismatch_positions_right[righti] - indels + 1;
- if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches) {
+ if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches &&
+ /* Require more matches on both ends than insertion length */ indel_pos >= indels && indel_pos + indels <= querylength - indels) {
best_indel_pos = indel_pos;
nmismatches_righti = righti;
nmismatches_lefti = lefti + 1;
@@ -446,7 +448,8 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
sum,lefti,righti+1,mismatch_positions_left[lefti]));
if (sum < best_sum) {
indel_pos = mismatch_positions_left[lefti];
- if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches) {
+ if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches &&
+ /* Require more matches on both ends than insertion length */ indel_pos >= indels && indel_pos + indels <= querylength - indels) {
best_indel_pos = indel_pos;
nmismatches_righti = righti + 1;
nmismatches_lefti = lefti;
@@ -456,7 +459,8 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
} else if (sum == best_sum) {
indel_pos = mismatch_positions_left[lefti];
if (indel_pos < best_indel_pos) {
- if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches) {
+ if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matches &&
+ /* Require more matches on both ends than insertion length */ indel_pos >= indels && indel_pos + indels <= querylength - indels) {
best_indel_pos = indel_pos;
nmismatches_righti = righti + 1;
nmismatches_lefti = lefti;
@@ -480,10 +484,10 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
nmismatches2 = nmismatches_lefti;
}
+ /* genomiclength = querylength-indels; */
if ((hit = Stage3end_new_insertion(&(*found_score),indels,query_indel_pos,
- nmismatches1,nmismatches2,
- /*left*/left+indels,/*genomiclength*/querylength-indels,
- query_compress,querylength,plusp,genestrand,first_read_p,
+ nmismatches1,nmismatches2,/*left*/left+indels,
+ query_compress,querylength,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,
indel_penalty_middle,sarrayp)) != NULL) {
debug2(printf("successful insertion with %d=%d+%d mismatches and indel_pos at %d\n",
@@ -507,7 +511,7 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
Univcoord_T chrhigh, Chrpos_T chrlength,
int indels, Compress_T query_compress, int querylength,
int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p, bool sarrayp) {
+ bool plusp, int genestrand, bool sarrayp) {
#ifdef DEBUG2
int i;
char *gbuffer;
@@ -543,7 +547,7 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
/* No need to check chromosome bounds */
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on left at:",nmismatches_left);
@@ -556,7 +560,7 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
/* No need to check chromosome bounds */
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,left-indels,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2(
printf("%d mismatches on right at:",nmismatches_right);
@@ -643,10 +647,10 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
nmismatches2 = nmismatches_lefti;
}
+ /* genomiclength = querylength-indels; */
if ((hit = Stage3end_new_deletion(&(*found_score),-indels,query_indel_pos,
- nmismatches1,nmismatches2,
- left,/*genomiclength*/querylength-indels,
- query_compress,querylength,plusp,genestrand,first_read_p,
+ nmismatches1,nmismatches2,left,
+ query_compress,querylength,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,
indel_penalty_middle,sarrayp)) != NULL) {
debug2(printf("successful middle deletion with %d=%d+%d mismatches and indel_pos at %d and nindels %d\n",
diff --git a/src/indel.h b/src/indel.h
index 18b0213..055c5b7 100644
--- a/src/indel.h
+++ b/src/indel.h
@@ -1,4 +1,4 @@
-/* $Id: indel.h 166641 2015-05-29 21:13:04Z twu $ */
+/* $Id: indel.h 184464 2016-02-18 00:09:13Z twu $ */
#ifndef INDEL_INCLUDED
#define INDEL_INCLUDED
@@ -16,15 +16,13 @@ extern int
Indel_resolve_middle_insertion (int *best_nmismatches_i, int *best_nmismatches_j,
Univcoord_T left, int indels, Compress_T query_compress,
int querystart, int queryend, int querylength,
- int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p);
+ int max_mismatches_allowed, bool plusp, int genestrand);
extern int
Indel_resolve_middle_deletion (int *best_nmismatches_i, int *best_nmismatches_j,
Univcoord_T left, int indels, Compress_T query_compress,
int querystart, int queryend, int querylength,
- int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p);
+ int max_mismatches_allowed, bool plusp, int genestrand);
extern List_T
@@ -33,7 +31,7 @@ Indel_solve_middle_insertion (bool *foundp, int *found_score, int *nhits, List_T
Univcoord_T chrhigh, Chrpos_T chrlength,
int indels, Compress_T query_compress,
int querylength, int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p, bool sarrayp);
+ bool plusp, int genestrand, bool sarrayp);
extern List_T
Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T hits,
@@ -41,7 +39,7 @@ Indel_solve_middle_deletion (bool *foundp, int *found_score, int *nhits, List_T
Univcoord_T chrhigh, Chrpos_T chrlength,
int indels, Compress_T query_compress, int querylength,
int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p, bool sarrayp);
+ bool plusp, int genestrand, bool sarrayp);
#endif
diff --git a/src/indexdb-write.c b/src/indexdb-write.c
index a96ee88..faf0eb3 100644
--- a/src/indexdb-write.c
+++ b/src/indexdb-write.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: indexdb-write.c 165969 2015-05-20 00:18:07Z twu $";
+static char rcsid[] = "$Id: indexdb-write.c 184465 2016-02-18 00:09:34Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -64,6 +64,8 @@ static char rcsid[] = "$Id: indexdb-write.c 165969 2015-05-20 00:18:07Z twu $";
#include "bitpack64-read.h"
#include "bitpack64-write.h"
+#include "bitpack64-access.h"
+#include "bitpack64-incr.h"
#define MAX_BITPACK_BLOCKSIZE 64
@@ -99,11 +101,7 @@ static char rcsid[] = "$Id: indexdb-write.c 165969 2015-05-20 00:18:07Z twu $";
static Oligospace_T
power (int base, int exponent) {
-#ifdef OLIGOSPACE_NOT_LONG
- Oligospace_T result = 1U;
-#else
- Oligospace_T result = 1UL;
-#endif
+ Oligospace_T result = 1;
int i;
for (i = 0; i < exponent; i++) {
@@ -117,7 +115,6 @@ power (int base, int exponent) {
static void
check_bitpack (char *offsetsmetafile, char *offsetsstrmfile,
Oligospace_T oligospace, Blocksize_T blocksize) {
- int shmid;
UINT4 *offsetsmeta, *offsetsstrm, *info;
int offsetsmeta_fd, offsetsstrm_fd;
size_t offsetsmeta_len, offsetsstrm_len;
@@ -129,15 +126,15 @@ check_bitpack (char *offsetsmetafile, char *offsetsstrmfile,
#endif
#ifdef HAVE_MMAP
- offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,sizeof(UINT4),/*randomp*/false);
- offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,sizeof(UINT4),/*randomp*/false);
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
#else
- offsetsmeta = (UINT4 *) Access_allocate(&shmid,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4),/*sharedp*/false);
- offsetsstrm = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4),/*sharedp*/false);
+ offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
#endif
for (oligo = 0; oligo < oligospace; oligo += blocksize) {
- info = &(offsetsmeta[oligo/blocksize * METAINFO_SIZE]);
+ info = &(offsetsmeta[oligo/BLOCKSIZE * METAINFO_SIZE]);
blockptr = &(offsetsstrm[info[0]]);
packsize = (info[2] - info[0])/2;
if (packsize > 32) {
@@ -163,11 +160,13 @@ check_bitpack (char *offsetsmetafile, char *offsetsstrmfile,
#endif
+#if 0
+/* Old method */
+
#ifndef PMAP
static void
check_offsets_from_bitpack (char *offsetsmetafile, char *offsetsstrmfile, Positionsptr_T *offsets,
Oligospace_T oligospace, Blocksize_T blocksize) {
- int shmid;
UINT4 *offsetsmeta;
UINT4 *offsetsstrm;
Positionsptr_T offsets_decoded[MAX_BITPACK_BLOCKSIZE+1];
@@ -175,30 +174,27 @@ check_offsets_from_bitpack (char *offsetsmetafile, char *offsetsstrmfile, Positi
size_t offsetsmeta_len, offsetsstrm_len;
Oligospace_T oligoi, i;
#ifndef HAVE_MMAP
+ int shmid;
+ key_t key;
double seconds;
#endif
#ifdef HAVE_MMAP
- offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,sizeof(UINT4),/*randomp*/false);
- offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,sizeof(UINT4),/*randomp*/false);
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
#else
- offsetsmeta = (UINT4 *) Access_allocate(&shmid,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4),/*sharedp*/false);
- offsetsstrm = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4),/*sharedp*/false);
+ offsetsmeta = (UINT4 *) Access_allocate_private(&shmid,&key,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&shmid,&key,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
#endif
for (oligoi = 0UL; oligoi < oligospace; oligoi += blocksize) {
Bitpack64_block_offsets(offsets_decoded,oligoi,offsetsmeta,offsetsstrm);
for (i = 0; i <= blocksize; i++) {
if (offsets_decoded[i] != offsets[oligoi+i]) {
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Problem with bitpack at oligo %u+%u = %u: %u != %u. Please inform twu at gene.com\n",
- oligoi,i,oligoi+i,offsets_decoded[i],offsets[oligoi+i]);
-#else
fprintf(stderr,"Problem with bitpack at oligo %llu+%llu = %llu: %llu != %llu. Please inform twu at gene.com\n",
(unsigned long long) oligoi,(unsigned long long) i,
(unsigned long long) oligoi+i,(unsigned long long) offsets_decoded[i],(unsigned long long) offsets[oligoi+i]);
-#endif
exit(9);
}
}
@@ -217,13 +213,16 @@ check_offsets_from_bitpack (char *offsetsmetafile, char *offsetsstrmfile, Positi
return;
}
#endif
+#endif
+#if 0
+/* Old method */
+
#ifndef PMAP
static void
check_offsets_from_bitpack_huge (char *offsetspagesfile, char *offsetsmetafile, char *offsetsstrmfile,
Hugepositionsptr_T *offsets, Oligospace_T oligospace, Blocksize_T blocksize) {
- int shmid;
UINT4 *offsetspages;
UINT4 *offsetsmeta;
UINT4 *offsetsstrm;
@@ -234,13 +233,13 @@ check_offsets_from_bitpack_huge (char *offsetspagesfile, char *offsetsmetafile,
double seconds;
- offsetspages = (UINT4 *) Access_allocate(&shmid,&offsetspages_len,&seconds,offsetspagesfile,sizeof(UINT4),/*sharedp*/false);
+ offsetspages = (UINT4 *) Access_allocate_private(&offsetspages_len,&seconds,offsetspagesfile,sizeof(UINT4));
#ifdef HAVE_MMAP
- offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,sizeof(UINT4),/*randomp*/false);
- offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,sizeof(UINT4),/*randomp*/false);
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
#else
- offsetsmeta = (UINT4 *) Access_allocate(&shmid,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4),/*sharedp*/false);
- offsetsstrm = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4),/*sharedp*/false);
+ offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
#endif
for (oligoi = 0UL; oligoi < oligospace; oligoi += blocksize) {
@@ -271,6 +270,7 @@ check_offsets_from_bitpack_huge (char *offsetspagesfile, char *offsetsmetafile,
return;
}
#endif
+#endif
@@ -293,7 +293,7 @@ Indexdb_count_offsets (FILE *sequence_fp, Univ_IIT_T chromosome_iit,
char *comma;
#ifdef PMAP
int frame = -1, between_counter[3], in_counter[3];
- Storedoligomer_T low = 0U;
+ Shortoligomer_T low = 0U;
#else
int between_counter = 0, in_counter = 0;
#endif
@@ -349,7 +349,9 @@ Indexdb_count_offsets (FILE *sequence_fp, Univ_IIT_T chromosome_iit,
fprintf(stderr,"\n");
}
+/* Don't need 64-bit distinction, because we need oligomers only for PMAP */
#ifdef PMAP
+ /* Need to compute low, so we can determine if we have a stop codon */
switch (uppercaseCode[c]) {
case 'A': low = (low << 2); break;
case 'C': low = (low << 2) | 1U; break;
@@ -409,6 +411,7 @@ Indexdb_count_offsets (FILE *sequence_fp, Univ_IIT_T chromosome_iit,
}
in_counter[frame] -= 1;
}
+
#else
if (in_counter == index1part) {
if (
@@ -427,12 +430,13 @@ Indexdb_count_offsets (FILE *sequence_fp, Univ_IIT_T chromosome_iit,
chrpos++; /* Needs to go here, before we reset chrpos to 0 */
if (position >= next_chrbound) {
-#ifdef PMAP
- low = 0U;
- in_counter[0] = in_counter[1] = in_counter[2] = 0;
-#else
+#ifndef PMAP
in_counter = 0;
+#else
+ /* high = */ low = /* carry = */ 0U;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
#endif
+
chrpos = 0U;
chrnum++;
while (chrnum <= nchrs && (next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint)) < position) {
@@ -447,6 +451,7 @@ Indexdb_count_offsets (FILE *sequence_fp, Univ_IIT_T chromosome_iit,
#endif
+#define BLOCKSIZE 64
void
Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Univ_IIT_T chromosome_iit,
@@ -455,36 +460,40 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
#else
Width_T index1part,
#endif
- Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
- int compression_types) {
+ Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p) {
char *uppercaseCode;
char *pointersfile, *offsetsfile;
char *filesuffix;
- FILE *offsets_fp;
/* If offsets[oligospace] > 2^32, then will will want to allocate and write 8-mers for offsets file */
- Positionsptr_T *offsets;
+ char *packsizes;
+ UINT4 **bitpacks;
char *comma;
int c, nchrs, chrnum;
- Oligospace_T oligospace, oligoi;
+ Oligospace_T oligospace, bmerspace;
Univcoord_T position = 0, next_chrbound;
Chrpos_T chrpos = 0U;
+#ifdef HAVE_64_BIT
+ Oligospace_T oligo = 0ULL;
+#else
+ Shortoligomer_T high = 0U, low = 0U, carry;
+#endif
+ Oligospace_T bmer;
+
#ifdef PMAP
+ int alphabet_size;
int frame = -1, between_counter[3], in_counter[3];
- Storedoligomer_T high = 0U, low = 0U, carry;
- Storedoligomer_T aaindex;
+ Shortoligomer_T aaindex;
int index1part_nt = 3*index1part_aa;
- int alphabet_size;
#else
- int between_counter = 0, in_counter = 0;
- Storedoligomer_T oligo = 0U, masked, mask;
+ Oligospace_T masked, mask;
+ int between_counter, in_counter;
#endif
#ifdef DEBUG1
char *aa;
#endif
- int blocksize;
int circular_typeint;
if (mask_lowercase_p == false) {
@@ -498,42 +507,35 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
oligospace = power(alphabet_size,index1part_aa);
between_counter[0] = between_counter[1] = between_counter[2] = 0;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Allocating %u*%d bytes for offsets\n",oligospace+1U,(int) sizeof(Positionsptr_T));
+
#else
- fprintf(stderr,"Allocating %llu*%d bytes for offsets\n",(unsigned long long) oligospace+1UL,(int) sizeof(Positionsptr_T));
-#endif
- offsets = (Positionsptr_T *) CALLOC_NO_EXCEPTION(oligospace+1,sizeof(Positionsptr_T));
- if (offsets == NULL) {
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Unable to allocate %u bytes of memory, needed to build offsets with %d-mers\n",oligospace+1U,index1part_aa);
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
#else
- fprintf(stderr,"Unable to allocate %llu bytes of memory, needed to build offsets with %d-mers\n",
- (unsigned long long) oligospace+1UL,index1part_aa);
+ mask = ~(~0U << 2*index1part);
#endif
- fprintf(stderr,"Either find a computer with more RAM, or lower your value for the k-mer size\n");
- exit(9);
- }
-#else
- mask = ~(~0UL << 2*index1part);
oligospace = power(4,index1part);
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Allocating %u*%d bytes for offsets\n",oligospace+1U,(int) sizeof(Positionsptr_T));
-#else
- fprintf(stderr,"Allocating %llu*%d bytes for offsets\n",oligospace+1UL,(int) sizeof(Positionsptr_T));
+ between_counter = in_counter = 0;
#endif
- offsets = (Positionsptr_T *) CALLOC_NO_EXCEPTION(oligospace+1,sizeof(Positionsptr_T));
- if (offsets == NULL) {
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Unable to allocate %u bytes of memory, needed to build offsets with %d-mers\n",oligospace+1U,index1part);
+
+ bmerspace = oligospace/BLOCKSIZE;
+ fprintf(stderr,"Allocating %llu*%d bytes for packsizes\n",bmerspace,(int) sizeof(char));
+ packsizes = (char *) CALLOC_NO_EXCEPTION(bmerspace,sizeof(char));
+ fprintf(stderr,"Allocating %llu*%d bytes for bitpacks\n",bmerspace,(int) sizeof(UINT4 *));
+ bitpacks = (UINT4 **) CALLOC_NO_EXCEPTION(bmerspace,sizeof(UINT4 *));
+
+ if (packsizes == NULL || bitpacks == NULL) {
+#ifdef PMAP
+ fprintf(stderr,"Unable to allocate %llu+%llu bytes of memory, needed to build offsets with %d-mers\n",
+ bmerspace*sizeof(char),bmerspace*sizeof(UINT4 *),index1part_aa);
#else
- fprintf(stderr,"Unable to allocate %llu bytes of memory, needed to build offsets with %d-mers\n",
- (unsigned long long) oligospace+1UL,index1part);
+ fprintf(stderr,"Unable to allocate %llu+%llu bytes of memory, needed to build offsets with %d-mers\n",
+ bmerspace*sizeof(char),bmerspace*sizeof(UINT4 *),index1part);
#endif
fprintf(stderr,"Either find a computer with more RAM, or lower your value for the k-mer size\n");
exit(9);
}
-#endif
+
/* Handle reference strain */
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
@@ -542,7 +544,6 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint);
while ((c = Compress_get_char(sequence_fp,position,genome_lc_p)) != EOF) {
-
#ifdef PMAP
if (++frame == 3) {
frame = 0;
@@ -574,7 +575,35 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
fprintf(stderr,"\n");
}
+#ifdef HAVE_64_BIT
+ switch (uppercaseCode[c]) {
+ case 'A': oligo = (oligo << 2); break;
+ case 'C': oligo = (oligo << 2) | 1U; break;
+ case 'G': oligo = (oligo << 2) | 2U; break;
+ case 'T': oligo = (oligo << 2) | 3U; break;
+ case 'X': case 'N':
+ oligo = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
+ default:
+ if (genome_lc_p == true) {
+ oligo = 0U;
#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ } else {
+ fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
+ abort();
+ }
+ }
+
+#else
carry = (low >> 30);
switch (uppercaseCode[c]) {
case 'A': low = (low << 2); break;
@@ -583,33 +612,26 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
case 'T': low = (low << 2) | 3U; break;
case 'X': case 'N':
high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
break;
default:
if (genome_lc_p == true) {
high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
} else {
fprintf(stderr,"Bad character %c at position %u\n",c,position);
abort();
}
}
high = (high << 2) | carry;
-#else
- switch (uppercaseCode[c]) {
- case 'A': oligo = (oligo << 2); break;
- case 'C': oligo = (oligo << 2) | 1U; break;
- case 'G': oligo = (oligo << 2) | 2U; break;
- case 'T': oligo = (oligo << 2) | 3U; break;
- case 'X': case 'N': oligo = 0U; in_counter = 0; break;
- default:
- if (genome_lc_p == true) {
- oligo = 0U; in_counter = 0;
- } else {
- fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
- abort();
- }
- }
#endif
#ifdef PMAP
@@ -618,39 +640,50 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
if (in_counter[frame] > 0) {
if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ debug(printf("Resetting in_counter for frame %d to 0\n",frame));
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_fwd(low) == AA_STOP) {
debug(printf("Resetting in_counter for frame %d to 0\n",frame));
in_counter[frame] = 0;
}
+#endif
} else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ debug(printf("Resetting in_counter for frame %d to 0\n",frame));
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_rev(low) == AA_STOP) {
debug(printf("Resetting in_counter for frame %d to 0\n",frame));
in_counter[frame] = 0;
}
+#endif
}
}
if (in_counter[frame] == index1part_aa + 1) {
if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
-#ifdef OLIGOSPACE_NOT_LONG
- oligoi = (Oligospace_T) aaindex + 1U;
-#else
- oligoi = (Oligospace_T) aaindex + 1UL;
-#endif
- offsets[oligoi] += 1;
- debug1(
- aa = aaindex_aa(aaindex);
- if (watsonp == true) {
- printf("Storing %s (%u) at %u\n",aa,aaindex,position-index1part_nt+1U);
- } else {
- printf("Storing %s (%u) at %u\n",aa,aaindex,position);
- }
- FREE(aa);
- );
+#endif
+ bmer = aaindex/BLOCKSIZE;
+ if (Bitpack64_access_filledp(aaindex,(int) packsizes[bmer],bitpacks[bmer]) == true) {
+ bitpacks[bmer] = Bitpack64_realloc_one((int) packsizes[bmer],bitpacks[bmer]);
+ packsizes[bmer] += 2;
+ }
+ Bitpack64_incr_bitpack(aaindex,(int) packsizes[bmer],bitpacks[bmer]);
+
between_counter[frame] = 0;
}
in_counter[frame] -= 1;
}
+
#else
if (in_counter == index1part) {
if (
@@ -661,14 +694,13 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
#endif
) {
masked = oligo & mask;
-#ifdef OLIGOSPACE_NOT_LONG
- oligoi = (Oligospace_T) masked + 1U;
-#else
- oligoi = (Oligospace_T) masked + 1UL;
-#endif
- offsets[oligoi] += 1;
- debug(printf("Found oligo %06X. Incremented offsets for %llu to be %llu\n",
- masked,(unsigned long long) oligoi,(unsigned long long) offsets[oligoi]));
+ bmer = masked/BLOCKSIZE;
+ if (Bitpack64_access_filledp(masked,(int) packsizes[bmer],bitpacks[bmer]) == true) {
+ bitpacks[bmer] = Bitpack64_realloc_one((int) packsizes[bmer],bitpacks[bmer]);
+ packsizes[bmer] += 2;
+ }
+ Bitpack64_incr_bitpack(masked,(int) packsizes[bmer],bitpacks[bmer]);
+
between_counter = 0;
}
in_counter--;
@@ -677,12 +709,17 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
chrpos++; /* Needs to go here, before we reset chrpos to 0 */
if (position >= next_chrbound) {
-#ifdef PMAP
- high = low = carry = 0U;
+#ifndef PMAP
+ oligo = 0;
+ in_counter = 0;
+#elif defined(HAVE_64_BIT)
+ oligo = 0ULL;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
#else
- oligo = 0U; in_counter = 0;
+ high = low = carry = 0U;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
#endif
+
chrpos = 0U;
chrnum++;
while (chrnum <= nchrs && (next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint)) < position) {
@@ -693,27 +730,6 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
}
-#ifdef ADDSENTINEL
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
- offsets[oligoi] = offsets[oligoi] + offsets[oligoi-1] + 1U;
- debug(if (offsets[oligoi] != offsets[oligoi-1]) {
- printf("Offset for %06X: %u\n",oligoi,offsets[oligoi]);
- });
- }
-#else
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
- offsets[oligoi] = offsets[oligoi] + offsets[oligoi-1];
- debug(if (offsets[oligoi] != offsets[oligoi-1]) {
- printf("Offset for %06X: %u\n",oligoi,offsets[oligoi]);
- });
- }
-#endif
-
- /*
- fprintf(stderr,"Offset for A...A is %u to %u\n",offsets[0],offsets[1]);
- fprintf(stderr,"Offset for T...T is %u to %u\n",offsets[oligospace-1],offsets[oligospace]);
- */
-
#ifdef PMAP
if (watsonp == true) {
filesuffix = FWD_FILESUFFIX;
@@ -724,91 +740,50 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
filesuffix = IDX_FILESUFFIX;
#endif
- if (compression_types == NO_COMPRESSION) {
- /* New convention. Previously this was called offsetsstrm. Will
- need to create a symbolic link for backward compatibility */
- offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
- strlen(".")+strlen(filesuffix)+
- /*for kmer*/2+/*for interval char*/1+
- strlen("offsets")+1,sizeof(char));
-#ifdef PMAP
- sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
- destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets");
-#else
- sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
- destdir,fileroot,filesuffix,index1part,interval_char,"offsets");
-#endif
-
- if ((offsets_fp = FOPEN_WRITE_BINARY(offsetsfile)) == NULL) {
- fprintf(stderr,"Can't write to file %s\n",offsetsfile);
- exit(9);
- } else {
- fprintf(stderr,"Writing %llu offsets to file with total of %llu k-mers...",
- (unsigned long long) oligospace+1,(unsigned long long) offsets[oligospace]);
- FWRITE_UINTS(offsets,oligospace+1,offsets_fp);
- fprintf(stderr,"done\n");
- }
- fclose(offsets_fp);
- FREE(offsetsfile);
-
- } else {
- if (compression_types & BITPACK64_COMPRESSION) {
- pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
- strlen(".")+strlen(filesuffix)+
- /*for kmer*/2+/*for interval char*/1+
- strlen("offsets64meta")+1,sizeof(char));
+ pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
+ strlen(".")+strlen(filesuffix)+
+ /*for kmer*/2+/*for interval char*/1+
+ strlen("offsets64meta")+1,sizeof(char));
#ifdef PMAP
- sprintf(pointersfile,"%s/%s.%s.%s%d%c%s",
- destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64meta");
+ sprintf(pointersfile,"%s/%s.%s.%s%d%c%s",
+ destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64meta");
#else
- sprintf(pointersfile,"%s/%s.%s%02d%c%s",
- destdir,fileroot,filesuffix,index1part,interval_char,"offsets64meta");
+ sprintf(pointersfile,"%s/%s.%s%02d%c%s",
+ destdir,fileroot,filesuffix,index1part,interval_char,"offsets64meta");
#endif
- offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
- strlen(".")+strlen(filesuffix)+
- /*for kmer*/2+/*for interval char*/1+
- strlen("offsets64strm")+1,sizeof(char));
+ offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
+ strlen(".")+strlen(filesuffix)+
+ /*for kmer*/2+/*for interval char*/1+
+ strlen("offsets64strm")+1,sizeof(char));
#ifdef PMAP
- sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
- destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64strm");
+ sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
+ destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64strm");
#else
- sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
- destdir,fileroot,filesuffix,index1part,interval_char,"offsets64strm");
+ sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
+ destdir,fileroot,filesuffix,index1part,interval_char,"offsets64strm");
#endif
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Writing %u offsets compressed via bitpack64 to file with total of %u k-mers...",oligospace+1U,offsets[oligospace]);
-#else
- fprintf(stderr,"Writing %llu offsets compressed via bitpack64 to file with total of %llu k-mers...",
- (unsigned long long) oligospace+1UL,(unsigned long long) offsets[oligospace]);
-#endif
+ fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL);
+ Bitpack64_write_differential_bitpacks(pointersfile,offsetsfile,packsizes,bitpacks,oligospace);
+ fprintf(stderr,"done\n");
- Bitpack64_write_differential(pointersfile,offsetsfile,offsets,oligospace);
-#ifdef PMAP
- /* 20-mers do not coincide with 64-element blocks */
-#else
- if (offsets[oligospace] == 0) {
- /* Don't check bitpack, which will crash on an empty file */
- } else {
- fprintf(stderr,"Checking bitpack...");
- check_offsets_from_bitpack(pointersfile,offsetsfile,offsets,oligospace,/*blocksize*/64);
- }
- fprintf(stderr,"done\n");
-#endif
+ FREE(offsetsfile);
+ FREE(pointersfile);
- FREE(offsetsfile);
- FREE(pointersfile);
- }
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
}
-
- FREE(offsets);
+ FREE(bitpacks);
+ FREE(packsizes);
return;
}
+
#ifdef HAVE_64_BIT
+
void
Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp, Univ_IIT_T chromosome_iit,
#ifdef PMAP
@@ -816,35 +791,40 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
#else
Width_T index1part,
#endif
- Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
- int compression_types) {
+ Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p) {
char *uppercaseCode;
char *pagesfile, *pointersfile, *offsetsfile;
char *filesuffix;
/* If offsets[oligospace] > 2^32, then we allocate and write 8-mers for offsets file */
- Hugepositionsptr_T *offsets;
+ char *packsizes;
+ UINT4 **bitpacks;
char *comma;
int c, nchrs, chrnum;
- Oligospace_T oligospace, oligoi;
+ Oligospace_T oligospace, bmerspace;
Univcoord_T position = 0, next_chrbound;
Chrpos_T chrpos = 0U;
+#ifdef HAVE_64_BIT
+ Oligospace_T oligo = 0ULL;
+#else
+ Shortoligomer_T high = 0U, low = 0U, carry;
+#endif
+ Oligospace_T bmer;
+
#ifdef PMAP
int alphabet_size;
int frame = -1, between_counter[3], in_counter[3];
- Storedoligomer_T high = 0U, low = 0U, carry;
- Storedoligomer_T aaindex;
+ Oligospace_T aaindex;
int index1part_nt = 3*index1part_aa;
#else
- int between_counter = 0, in_counter = 0;
- Storedoligomer_T oligo = 0U, masked, mask;
+ Oligospace_T masked, mask;
+ int between_counter, in_counter;
#endif
#ifdef DEBUG1
char *aa;
#endif
- int blocksize;
int circular_typeint;
if (mask_lowercase_p == false) {
@@ -858,43 +838,36 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
oligospace = power(alphabet_size,index1part_aa);
between_counter[0] = between_counter[1] = between_counter[2] = 0;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Allocating %u*%d bytes for offsets\n",oligospace+1U,(int) sizeof(Hugepositionsptr_T));
+
#else
- fprintf(stderr,"Allocating %llu*%d bytes for offsets\n",
- (unsigned long long) oligospace+1UL,(int) sizeof(Hugepositionsptr_T));
-#endif
- offsets = (Hugepositionsptr_T *) CALLOC_NO_EXCEPTION(oligospace+1,sizeof(Hugepositionsptr_T));
- if (offsets == NULL) {
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Unable to allocate %u bytes of memory, needed to build offsets with %d-mers\n",oligospace+1U,index1part_aa);
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
#else
- fprintf(stderr,"Unable to allocate %llu bytes of memory, needed to build offsets with %d-mers\n",
- (unsigned long long) oligospace+1UL,index1part_aa);
+ mask = ~(~0U << 2*index1part);
#endif
- fprintf(stderr,"Either find a computer with more RAM, or lower your value for the k-mer size\n");
- exit(9);
- }
-#else
- mask = ~(~0UL << 2*index1part);
oligospace = power(4,index1part);
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Allocating %u*%d bytes for offsets\n",oligospace+1U,(int) sizeof(Hugepositionsptr_T));
-#else
- fprintf(stderr,"Allocating %llu*%d bytes for offsets\n",(unsigned long long) oligospace+1UL,(int) sizeof(Hugepositionsptr_T));
+ between_counter = in_counter = 0;
#endif
- offsets = (Hugepositionsptr_T *) CALLOC_NO_EXCEPTION(oligospace+1,sizeof(Hugepositionsptr_T));
- if (offsets == NULL) {
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Unable to allocate %u bytes of memory, needed to build offsets with %d-mers\n",oligospace+1U,index1part);
+
+ bmerspace = oligospace/BLOCKSIZE;
+
+ fprintf(stderr,"Allocating %llu*%d bytes for packsizes\n",bmerspace,(int) sizeof(char));
+ packsizes = (char *) CALLOC_NO_EXCEPTION(bmerspace,sizeof(char));
+ fprintf(stderr,"Allocating %llu*%d bytes for bitpacks\n",bmerspace,(int) sizeof(UINT4 *));
+ bitpacks = (UINT4 **) CALLOC_NO_EXCEPTION(bmerspace,sizeof(UINT4 *));
+
+ if (packsizes == NULL || bitpacks == NULL) {
+#ifdef PMAP
+ fprintf(stderr,"Unable to allocate %llu+%llu bytes of memory, needed to build offsets with %d-mers\n",
+ bmerspace*sizeof(char),bmerspace*sizeof(UINT4 *),index1part_aa);
#else
- fprintf(stderr,"Unable to allocate %llu bytes of memory, needed to build offsets with %d-mers\n",
- (unsigned long long) oligospace+1UL,index1part);
+ fprintf(stderr,"Unable to allocate %llu+%llu bytes of memory, needed to build offsets with %d-mers\n",
+ bmerspace*sizeof(char),bmerspace*sizeof(UINT4 *),index1part);
#endif
fprintf(stderr,"Either find a computer with more RAM, or lower your value for the k-mer size\n");
exit(9);
}
-#endif
+
/* Handle reference strain */
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
@@ -903,6 +876,7 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint);
while ((c = Compress_get_char(sequence_fp,position,genome_lc_p)) != EOF) {
+
#ifdef PMAP
if (++frame == 3) {
frame = 0;
@@ -934,7 +908,35 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
fprintf(stderr,"\n");
}
+#ifdef HAVE_64_BIT
+ switch (uppercaseCode[c]) {
+ case 'A': oligo = (oligo << 2); break;
+ case 'C': oligo = (oligo << 2) | 1U; break;
+ case 'G': oligo = (oligo << 2) | 2U; break;
+ case 'T': oligo = (oligo << 2) | 3U; break;
+ case 'X': case 'N':
+ oligo = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
+ default:
+ if (genome_lc_p == true) {
+ oligo = 0U;
#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ } else {
+ fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
+ abort();
+ }
+ }
+
+#else
carry = (low >> 30);
switch (uppercaseCode[c]) {
case 'A': low = (low << 2); break;
@@ -943,33 +945,26 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
case 'T': low = (low << 2) | 3U; break;
case 'X': case 'N':
high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
break;
default:
if (genome_lc_p == true) {
high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
} else {
fprintf(stderr,"Bad character %c at position %u\n",c,position);
abort();
}
}
high = (high << 2) | carry;
-#else
- switch (uppercaseCode[c]) {
- case 'A': oligo = (oligo << 2); break;
- case 'C': oligo = (oligo << 2) | 1U; break;
- case 'G': oligo = (oligo << 2) | 2U; break;
- case 'T': oligo = (oligo << 2) | 3U; break;
- case 'X': case 'N': oligo = 0U; in_counter = 0; break;
- default:
- if (genome_lc_p == true) {
- oligo = 0U; in_counter = 0;
- } else {
- fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
- abort();
- }
- }
#endif
#ifdef PMAP
@@ -978,39 +973,50 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
if (in_counter[frame] > 0) {
if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ debug(printf("Resetting in_counter for frame %d to 0\n",frame));
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_fwd(low) == AA_STOP) {
debug(printf("Resetting in_counter for frame %d to 0\n",frame));
in_counter[frame] = 0;
}
+#endif
} else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ debug(printf("Resetting in_counter for frame %d to 0\n",frame));
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_rev(low) == AA_STOP) {
debug(printf("Resetting in_counter for frame %d to 0\n",frame));
in_counter[frame] = 0;
}
+#endif
}
}
if (in_counter[frame] == index1part_aa + 1) {
if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
-#ifdef OLIGOSPACE_NOT_LONG
- oligoi = (Oligospace_T) aaindex + 1U;
-#else
- oligoi = (Oligospace_T) aaindex + 1UL;
-#endif
- offsets[oligoi] += 1;
- debug1(
- aa = aaindex_aa(aaindex);
- if (watsonp == true) {
- printf("Storing %s (%u) at %u\n",aa,aaindex,position-index1part_nt+1U);
- } else {
- printf("Storing %s (%u) at %u\n",aa,aaindex,position);
- }
- FREE(aa);
- );
+#endif
+ bmer = aaindex/BLOCKSIZE;
+ if (Bitpack64_access_filledp(aaindex,(int) packsizes[bmer],bitpacks[bmer]) == true) {
+ bitpacks[bmer] = Bitpack64_realloc_one((int) packsizes[bmer],bitpacks[bmer]);
+ packsizes[bmer] += 2;
+ }
+ Bitpack64_incr_bitpack(aaindex,(int) packsizes[bmer],bitpacks[bmer]);
+
between_counter[frame] = 0;
}
in_counter[frame] -= 1;
}
+
#else
if (in_counter == index1part) {
if (
@@ -1021,14 +1027,13 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
#endif
) {
masked = oligo & mask;
-#ifdef OLIGOSPACE_NOT_LONG
- oligoi = (Oligospace_T) masked + 1U;
-#else
- oligoi = (Oligospace_T) masked + 1UL;
-#endif
- offsets[oligoi] += 1;
- debug(printf("Found oligo %06X. Incremented offsets for %llu to be %llu\n",
- masked,(unsigned long long) oligoi,(unsigned long long) offsets[oligoi]));
+ bmer = masked/BLOCKSIZE;
+ if (Bitpack64_access_filledp(masked,(int) packsizes[bmer],bitpacks[bmer]) == true) {
+ bitpacks[bmer] = Bitpack64_realloc_one((int) packsizes[bmer],bitpacks[bmer]);
+ packsizes[bmer] += 2;
+ }
+ Bitpack64_incr_bitpack(masked,(int) packsizes[bmer],bitpacks[bmer]);
+
between_counter = 0;
}
in_counter--;
@@ -1037,12 +1042,17 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
chrpos++; /* Needs to go here, before we reset chrpos to 0 */
if (position >= next_chrbound) {
-#ifdef PMAP
- high = low = carry = 0U;
+#ifndef PMAP
+ oligo = 0;
+ in_counter = 0;
+#elif defined(HAVE_64_BIT)
+ oligo = 0ULL;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
#else
- oligo = 0U; in_counter = 0;
+ high = low = carry = 0U;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
#endif
+
chrpos = 0U;
chrnum++;
while (chrnum <= nchrs && (next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint)) < position) {
@@ -1053,27 +1063,6 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
}
-#ifdef ADDSENTINEL
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
- offsets[oligoi] = offsets[oligoi] + offsets[oligoi-1] + 1U;
- debug(if (offsets[oligoi] != offsets[oligoi-1]) {
- printf("Offset for %06X: %u\n",oligoi,offsets[oligoi]);
- });
- }
-#else
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
- offsets[oligoi] = offsets[oligoi] + offsets[oligoi-1];
- debug(if (offsets[oligoi] != offsets[oligoi-1]) {
- printf("Offset for %06X: %u\n",oligoi,offsets[oligoi]);
- });
- }
-#endif
-
- /*
- fprintf(stderr,"Offset for A...A is %u to %u\n",offsets[0],offsets[1]);
- fprintf(stderr,"Offset for T...T is %u to %u\n",offsets[oligospace-1],offsets[oligospace]);
- */
-
#ifdef PMAP
if (watsonp == true) {
filesuffix = FWD_FILESUFFIX;
@@ -1084,84 +1073,223 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
filesuffix = IDX_FILESUFFIX;
#endif
- if (compression_types == NO_COMPRESSION) {
- fprintf(stderr,"Not supporting non-compression on huge genomes\n");
- abort();
+ pagesfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
+ strlen(".")+strlen(filesuffix)+
+ /*for kmer*/2+/*for interval char*/1+
+ strlen("offsets64pages")+1,sizeof(char));
+#ifdef PMAP
+ sprintf(pagesfile,"%s/%s.%s.%s%d%c%s",
+ destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64pages");
+#else
+ sprintf(pagesfile,"%s/%s.%s%02d%c%s",
+ destdir,fileroot,filesuffix,index1part,interval_char,"offsets64pages");
+#endif
- } else {
- if (compression_types & BITPACK64_COMPRESSION) {
+ pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
+ strlen(".")+strlen(filesuffix)+
+ /*for kmer*/2+/*for interval char*/1+
+ strlen("offsets64meta")+1,sizeof(char));
#ifdef PMAP
- /* blocksize = power(alphabet_size,index1part_aa - offsetsstrm_basesize); */
+ sprintf(pointersfile,"%s/%s.%s.%s%d%c%s",
+ destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64meta");
#else
- blocksize = 64; /* power(4,index1part - offsetsstrm_basesize); */
+ sprintf(pointersfile,"%s/%s.%s%02d%c%s",
+ destdir,fileroot,filesuffix,index1part,interval_char,"offsets64meta");
#endif
- pagesfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
- strlen(".")+strlen(filesuffix)+
- /*for kmer*/2+/*for interval char*/1+
- strlen("offsets64pages")+1,sizeof(char));
+
+ offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
+ strlen(".")+strlen(filesuffix)+
+ /*for kmer*/2+/*for interval char*/1+
+ strlen("offsets64strm")+1,sizeof(char));
#ifdef PMAP
- sprintf(pagesfile,"%s/%s.%s.%s%d%c%s",
- destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64pages");
+ sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
+ destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64strm");
#else
- sprintf(pagesfile,"%s/%s.%s%02d%c%s",
- destdir,fileroot,filesuffix,index1part,interval_char,"offsets64pages");
+ sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
+ destdir,fileroot,filesuffix,index1part,interval_char,"offsets64strm");
#endif
- pointersfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
- strlen(".")+strlen(filesuffix)+
- /*for kmer*/2+/*for interval char*/1+
- strlen("offsets64meta")+1,sizeof(char));
+ fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL);
+ Bitpack64_write_differential_huge_bitpacks(pagesfile,pointersfile,offsetsfile,packsizes,bitpacks,oligospace);
+
+ FREE(offsetsfile);
+ FREE(pointersfile);
+ FREE(pagesfile);
+
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
+ }
+ FREE(bitpacks);
+ FREE(packsizes);
+
+ return;
+}
+#endif
+
+
+UINT4 *
+Indexdb_bitpack_counter (UINT4 **counterstrm, UINT4 *offsetsmeta, UINT4 *offsetsstrm,
#ifdef PMAP
- sprintf(pointersfile,"%s/%s.%s.%s%d%c%s",
- destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64meta");
+ int alphabet_size, Width_T index1part_aa
#else
- sprintf(pointersfile,"%s/%s.%s%02d%c%s",
- destdir,fileroot,filesuffix,index1part,interval_char,"offsets64meta");
+ Width_T index1part
#endif
-
- offsetsfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
- strlen(".")+strlen(filesuffix)+
- /*for kmer*/2+/*for interval char*/1+
- strlen("offsets64strm")+1,sizeof(char));
+ ) {
+ UINT4 *countermeta;
+ UINT4 nvectors;
+ UINT4 *offsets = NULL, diff, maxdiff, k;
+ Oligospace_T oligospace, oligoi;
+ Blocksize_T blocksize, packsize, firstbit, i;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
+
+
#ifdef PMAP
- sprintf(offsetsfile,"%s/%s.%s.%s%d%c%s",
- destdir,fileroot,Alphabet_string(alphabet),filesuffix,index1part_aa,interval_char,"offsets64strm");
+ oligospace = power(alphabet_size,index1part_aa);
#else
- sprintf(offsetsfile,"%s/%s.%s%02d%c%s",
- destdir,fileroot,filesuffix,index1part,interval_char,"offsets64strm");
+ oligospace = power(4,index1part);
#endif
+ blocksize = 64;
+ offsets = (UINT4 *) MALLOC((blocksize + 1) * sizeof(UINT4));
-#ifdef OLIGOSPACE_NOT_LONG
- fprintf(stderr,"Writing %u offsets compressed via bitpack to file with total of %u k-mers...",oligospace+1U,offsets[oligospace]);
+
+ countermeta = (UINT4 *) MALLOC((oligospace/BLOCKSIZE + 1) * sizeof(UINT4));
+
+ fprintf(stderr,"Expanding offsetsstrm into counters...");
+#if defined(LARGE_GENOMES)
+ fprintf(stderr,"Cannot do expand offsets on large genomes\n");
+ exit(9);
#else
- fprintf(stderr,"Writing %llu offsets compressed via bitpack to file with total of %llu k-mers...",
- (unsigned long long) oligospace+1UL,(unsigned long long) offsets[oligospace]);
-#endif
+ k = 0;
+ nvectors = 0;
+ for (oligoi = 0ULL; oligoi < oligospace; oligoi += blocksize) {
+ countermeta[k++] = nvectors;
- Bitpack64_write_differential_huge(pagesfile,pointersfile,offsetsfile,offsets,oligospace);
-#ifndef PMAP
- if (offsets[oligospace] == 0) {
- /* Don't check bitpack, which will crash on an empty file */
- } else {
- fprintf(stderr,"Checking bitpack...");
- check_offsets_from_bitpack_huge(pagesfile,pointersfile,offsetsfile,offsets,oligospace,/*blocksize*/64);
+ Bitpack64_block_offsets(offsets,oligoi,offsetsmeta,offsetsstrm);
+
+ maxdiff = 0;
+ for (i = 1; i <= blocksize; i++) {
+ if ((diff = offsets[i] - offsets[i-1]) > maxdiff) {
+ maxdiff = diff;
}
- fprintf(stderr,"done\n");
-#endif
+ }
- FREE(offsetsfile);
- FREE(pointersfile);
- FREE(pagesfile);
+ if (maxdiff == 0) {
+ packsize = 0;
+ } else {
+#ifdef HAVE_BUILTIN_CLZ
+ firstbit = __builtin_clz(maxdiff);
+ packsize = 32 - firstbit;
+#elif defined(HAVE_ASM_BSR)
+ asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff));
+ packsize = msb + 1;
+#else
+ firstbit = ((maxdiff >> 16) ? clz_table[maxdiff >> 16] : 16 + clz_table[maxdiff]);
+ packsize = 32 - firstbit;
+#endif
}
+
+ packsize = (packsize + 1) & ~1; /* Converts packsizes to the next multiple of 2 */
+ /* nvectors += (packsize * blocksize)/128; */
+ nvectors += packsize / 2; /* For blocksize of 64 => *64/128 */
}
-
+#endif
+ countermeta[k] = nvectors;
+ fprintf(stderr,"done\n");
+
+ fprintf(stderr,"Allocating %u bytes for counterstrm\n",nvectors * 16);
+ *counterstrm = (UINT4 *) CALLOC(nvectors * 4,sizeof(UINT4)); /* 4 words per 128-bit vector */
+
FREE(offsets);
+ return countermeta;
+}
- return;
+
+#ifdef HAVE_64_BIT
+UINT4 *
+Indexdb_bitpack_counter_huge (UINT4 **counterstrm, UINT4 *offsetspages, UINT4 *offsetsmeta, UINT4 *offsetsstrm,
+#ifdef PMAP
+ int alphabet_size, Width_T index1part_aa
+#else
+ Width_T index1part
+#endif
+ ) {
+ UINT4 *countermeta;
+ UINT4 nvectors;
+ UINT8 *offsets = NULL;
+ UINT4 diff, maxdiff, k;
+ Oligospace_T oligospace, oligoi;
+ /* Oligospace_T bmerspace; */
+ /* UINT4 *pageptr; */
+ /* int npages; */
+ Blocksize_T packsize, firstbit, i;
+#ifdef HAVE_BUILTIN_CLZ
+#elif defined(HAVE_ASM_BSR)
+ int msb;
+#endif
+
+
+#ifdef PMAP
+ oligospace = power(alphabet_size,index1part_aa);
+#else
+ oligospace = power(4,index1part);
+#endif
+ /* bmerspace = oligospace/BLOCKSIZE; */
+ offsets = (UINT8 *) MALLOC((BLOCKSIZE + 1) * sizeof(UINT8));
+
+
+ countermeta = (UINT4 *) MALLOC((oligospace/BLOCKSIZE + 1) * sizeof(UINT4));
+
+ fprintf(stderr,"Expanding offsetsstrm into counters...");
+ k = 0;
+ nvectors = 0;
+ for (oligoi = 0ULL; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ countermeta[k++] = nvectors;
+
+ Bitpack64_block_offsets_huge(offsets,oligoi,offsetspages,offsetsmeta,offsetsstrm);
+
+ maxdiff = 0;
+ for (i = 1; i <= BLOCKSIZE; i++) {
+ if ((diff = (UINT4) (offsets[i] - offsets[i-1])) > maxdiff) {
+ maxdiff = diff;
+ }
+ }
+
+ if (maxdiff == 0) {
+ packsize = 0;
+ } else {
+#ifdef HAVE_BUILTIN_CLZ
+ firstbit = __builtin_clz(maxdiff);
+ packsize = 32 - firstbit;
+#elif defined(HAVE_ASM_BSR)
+ asm("bsr %1,%0" : "=r"(msb) : "r"(maxdiff));
+ packsize = msb + 1;
+#else
+ firstbit = ((maxdiff >> 16) ? clz_table[maxdiff >> 16] : 16 + clz_table[maxdiff]);
+ packsize = 32 - firstbit;
+#endif
+ }
+
+ packsize = (packsize + 1) & ~1; /* Converts packsizes to the next multiple of 2 */
+ /* nvectors += (packsize * blocksize)/128; */
+ nvectors += packsize / 2; /* For blocksize of 64 => *64/128 */
+ }
+
+ countermeta[k] = nvectors;
+ fprintf(stderr,"done\n");
+
+ fprintf(stderr,"Allocating %u bytes for counterstrm\n",nvectors * 16);
+ *counterstrm = (UINT4 *) CALLOC(nvectors * 4,sizeof(UINT4)); /* 4 words per 128-bit vector */
+
+ FREE(offsets);
+ return countermeta;
}
#endif
+
#if 0
static bool
need_to_sort_p (Univcoord_T *positions, int length) {
@@ -1181,29 +1309,35 @@ need_to_sort_p (Univcoord_T *positions, int length) {
#endif
+#if 0
static void
positions_move_absolute_1 (int positions_fd, Positionsptr_T ptr) {
- off_t offset = ptr*((off_t) sizeof(unsigned char));
+ off_t offset = ptr*sizeof(unsigned char);
if (lseek(positions_fd,offset,SEEK_SET) < 0) {
- fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(unsigned char),offset);
+ fprintf(stderr,"Attempted to do lseek on offset %zu*%zu=%zu\n",
+ (size_t) ptr,sizeof(unsigned char),(size_t) offset);
perror("Error in indexdb.c, positions_move_absolute_1");
exit(9);
}
return;
}
+#endif
+#if 0
static void
positions_move_absolute_4 (int positions_fd, Positionsptr_T ptr) {
- off_t offset = ptr*((off_t) sizeof(UINT4));
+ off_t offset = ptr*sizeof(UINT4);
if (lseek(positions_fd,offset,SEEK_SET) < 0) {
- fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT4),offset);
+ fprintf(stderr,"Attempted to do lseek on offset %zu*%zu=%zu\n",
+ (size_t) ptr,sizeof(UINT4),(size_t) offset);
perror("Error in indexdb.c, positions_move_absolute_4");
exit(9);
}
return;
}
+#endif
#if 0
/* Replaced by positions_move_absolute_1 and positions_move_absolute_4 */
@@ -1212,7 +1346,8 @@ positions_move_absolute_8 (int positions_fd, Positionsptr_T ptr) {
off_t offset = ptr*((off_t) sizeof(UINT8));
if (lseek(positions_fd,offset,SEEK_SET) < 0) {
- fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",ptr,(int) sizeof(UINT8),offset);
+ fprintf(stderr,"Attempted to do lseek on offset %zu*%zu=%zu\n",
+ (size_t) ptr,sizeof(UINT8),(size_t) offset);
perror("Error in indexdb.c, positions_move_absolute_8");
exit(9);
}
@@ -1221,6 +1356,9 @@ positions_move_absolute_8 (int positions_fd, Positionsptr_T ptr) {
#endif
+#if 0
+/* Old method */
+
/* Works directly in file, so we don't need to allocate memory */
static void
compute_positions_in_file (int positions_high_fd, int positions_low_fd, Positionsptr_T *offsets,
@@ -1242,11 +1380,11 @@ compute_positions_in_file (int positions_high_fd, int positions_low_fd, Position
#ifdef PMAP
int frame = -1, between_counter[3], in_counter[3];
Storedoligomer_T high = 0U, low = 0U, carry;
- Oligospace_T aaindex;
+ Storedoligomer_T aaindex;
Width_T index1part_nt = 3*index1part_aa;
#else
+ Oligospace_T oligo = 0U, masked, mask;
int between_counter = 0, in_counter = 0;
- Storedoligomer_T oligo = 0U, masked, mask;
#endif
int circular_typeint;
@@ -1264,7 +1402,11 @@ compute_positions_in_file (int positions_high_fd, int positions_low_fd, Position
#ifdef PMAP
/* oligospace = power(alphabet_size,index1part_aa); */
#else
- mask = ~(~0UL << 2*index1part);
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
+#else
+ mask = ~(~0U << 2*index1part);
+#endif
/* oligospace = power(4,index1part); */
#endif
@@ -1453,6 +1595,11 @@ compute_positions_in_file (int positions_high_fd, int positions_low_fd, Position
return;
}
+#endif
+
+
+#if 0
+/* Old method */
/* Requires sufficient memory to hold all positions */
static void
@@ -1471,23 +1618,26 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
char *comma;
int c, nchrs, chrnum;
UINT8 adjposition8;
+ Positionsptr_T offset;
+
+#ifdef HAVE_64_BIT
+ Oligospace_T oligo = 0ULL;
+#else
+ Shortoligomer_T high = 0U, low = 0U, carry;
+#endif
+
#ifdef PMAP
int frame = -1, between_counter[3], in_counter[3];
- Storedoligomer_T high = 0U, low = 0U, carry;
- Storedoligomer_T aaindex;
+ Oligospace_T aaindex;
Width_T index1part_nt = 3*index1part_aa;
debug1(char *aa);
#else
- int between_counter = 0, in_counter = 0;
- Storedoligomer_T oligo = 0U, masked, mask;
+ Oligospace_T masked, mask;
+ int between_counter, in_counter;
debug1(char *nt);
#endif
- int circular_typeint;
-#ifdef ADDSENTINEL
- Oligospace_T oligospace, oligoi;
- oligospace = power(4,index1part);
-#endif
+ int circular_typeint;
if (mask_lowercase_p == false) {
uppercaseCode = UPPERCASE_U2T; /* We are reading DNA sequence */
@@ -1498,9 +1648,16 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
#ifdef PMAP
between_counter[0] = between_counter[1] = between_counter[2] = 0;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+
+#else
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
#else
- mask = ~(~0UL << 2*index1part);
+ mask = ~(~0U << 2*index1part);
#endif
+ between_counter = in_counter = 0;
+#endif
+
/* Handle reference strain */
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
@@ -1540,95 +1697,394 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
fprintf(stderr,"\n");
}
+#ifdef HAVE_64_BIT
+ switch (uppercaseCode[c]) {
+ case 'A': oligo = (oligo << 2); break;
+ case 'C': oligo = (oligo << 2) | 1U; break;
+ case 'G': oligo = (oligo << 2) | 2U; break;
+ case 'T': oligo = (oligo << 2) | 3U; break;
+ case 'X': case 'N':
+ oligo = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
+ default:
+ if (genome_lc_p == true) {
+ oligo = 0U;
#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ } else {
+ fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
+ abort();
+ }
+ }
+
+#else
carry = (low >> 30);
switch (uppercaseCode[c]) {
case 'A': low = (low << 2); break;
case 'C': low = (low << 2) | 1U; break;
case 'G': low = (low << 2) | 2U; break;
case 'T': low = (low << 2) | 3U; break;
- case 'X': case 'N':
- high = low = carry = 0U;
+ case 'X': case 'N':
+ high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
break;
default:
if (genome_lc_p == true) {
high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
} else {
fprintf(stderr,"Bad character %c at position %u\n",c,position);
abort();
}
}
high = (high << 2) | carry;
+#endif
+#ifdef PMAP
debug(printf("frame=%d char=%c bc=%d ic=%d high=%08X low=%08X\n",
frame,c,between_counter[frame],in_counter[frame],high,low));
+
+ if (in_counter[frame] > 0) {
+ if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
+ if (Alphabet_get_codon_fwd(low) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#endif
+ } else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
#else
+ if (Alphabet_get_codon_rev(low) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#endif
+ }
+ }
+ if (in_counter[frame] == index1part_aa + 1) {
+ if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
+ aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
+#endif
+ offset = Bitpack64_read_one(aaindex,offsetsmeta,offsetsstrm) + Bitpack64_incr(aaindex,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ if (watsonp == true) {
+ adjposition8 = position - index1part_nt + 1;
+ positions8_high[offset] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
+ debug1(adjposition = position-index1part_nt+1UL);
+ } else {
+ positions8_high[offset] = (unsigned char) (position >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (position & POSITIONS8_LOW_MASK);
+ debug1(adjposition = position);
+ }
+ } else {
+ if (watsonp == true) {
+ positions4[offset] = (UINT4) (position - index1part_nt + 1);
+ debug1(adjposition = position - index1part_nt + 1);
+ } else {
+ positions4[offset] = (UINT4) position;
+ debug1(adjposition = position);
+ }
+ }
+
+ between_counter[frame] = 0;
+ }
+ in_counter[frame] -= 1;
+ }
+
+#else
+ if (in_counter == index1part) {
+ if (
+#ifdef NONMODULAR
+ between_counter >= index1interval
+#else
+ (chrpos-index1part+1U) % index1interval == 0
+#endif
+ ) {
+ masked = oligo & mask;
+ offset = Bitpack64_read_one(masked,offsetsmeta,offsetsstrm) + Bitpack64_incr(masked,countermeta,counterstrm);
+ if (coord_values_8p == true) {
+ adjposition8 = position - index1part + 1;
+ positions8_high[offset] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
+ } else {
+ positions4[offset] = (UINT4) (position - index1part + 1);
+ }
+ debug1(nt = shortoligo_nt(masked,index1part);
+ printf("Storing %s at %llu, chrpos %u\n",nt,(unsigned long long) (position-index1part+1U),chrpos-index1part+1U);
+ FREE(nt));
+
+ between_counter = 0;
+ }
+ in_counter--;
+ }
+#endif
+
+ chrpos++; /* Needs to go here, before we reset chrpos to 0 */
+ if (position >= next_chrbound) {
+ debug1(printf("Skipping because position %u is at chrbound\n",position));
+#ifndef PMAP
+ oligo = 0;
+ in_counter = 0;
+#elif defined(HAVE_64_BIT)
+ oligo = 0ULL;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ high = low = carry = 0U;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#endif
+
+ chrpos = 0U;
+ chrnum++;
+ while (chrnum <= nchrs && (next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint)) < position) {
+ chrnum++;
+ }
+ }
+ position++;
+ }
+
+ return;
+}
+#endif
+
+
+/* Requires sufficient memory to hold all positions */
+static void
+compute_positions (UINT4 *positions4, unsigned char *positions8_high, UINT4 *positions8_low,
+ UINT4 *offsetsmeta, UINT4 *offsetsstrm, UINT4 *countermeta, UINT4 *counterstrm,
+ FILE *sequence_fp, Univ_IIT_T chromosome_iit,
+#ifdef PMAP
+ Width_T index1part_aa, bool watsonp,
+#else
+ Width_T index1part,
+#endif
+ Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
+ bool coord_values_8p) {
+ char *uppercaseCode;
+ Univcoord_T position = 0, next_chrbound;
+ Chrpos_T chrpos = 0U;
+ char *comma;
+ int c, nchrs, chrnum;
+ UINT8 adjposition8;
+ Positionsptr_T offset;
+
+#ifdef HAVE_64_BIT
+ Oligospace_T oligo = 0ULL;
+#else
+ Shortoligomer_T high = 0U, low = 0U, carry;
+#endif
+
+#ifdef PMAP
+ int frame = -1, between_counter[3], in_counter[3];
+ Oligospace_T aaindex;
+ Width_T index1part_nt = 3*index1part_aa;
+ debug1(char *aa);
+#else
+ Oligospace_T masked, mask;
+ int between_counter = 0, in_counter = 0;
+ debug1(char *nt);
+#endif
+
+ int circular_typeint;
+
+ if (mask_lowercase_p == false) {
+ uppercaseCode = UPPERCASE_U2T; /* We are reading DNA sequence */
+ } else {
+ uppercaseCode = NO_UPPERCASE;
+ }
+
+#ifdef PMAP
+ between_counter[0] = between_counter[1] = between_counter[2] = 0;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
+#else
+ mask = ~(~0U << 2*index1part);
+#endif
+#endif
+
+
+ /* Handle reference strain */
+ circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
+ chrnum = 1;
+ nchrs = Univ_IIT_total_nintervals(chromosome_iit);
+ next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint);
+
+ while ((c = Compress_get_char(sequence_fp,position,genome_lc_p)) != EOF) {
+#ifdef PMAP
+ if (++frame == 3) {
+ frame = 0;
+ }
+ between_counter[frame] += 1;
+ in_counter[frame] += 1;
+#else
+ between_counter++;
+ in_counter++;
+#endif
+
+ if (position % MONITOR_INTERVAL == 0) {
+ comma = Genomicpos_commafmt(position);
+#ifdef PMAP
+ fprintf(stderr,"Indexing positions of oligomers in genome %s (%d aa every %d aa), position %s",
+ fileroot,index1part_aa,index1interval,comma);
+#else
+ fprintf(stderr,"Indexing positions of oligomers in genome %s (%d bp every %d bp), position %s",
+ fileroot,index1part,index1interval,comma);
+#endif
+ FREE(comma);
+#ifdef PMAP
+ if (watsonp == true) {
+ fprintf(stderr," (fwd)");
+ } else {
+ fprintf(stderr," (rev)");
+ }
+#endif
+ fprintf(stderr,"\n");
+ }
+
+#ifdef HAVE_64_BIT
switch (uppercaseCode[c]) {
case 'A': oligo = (oligo << 2); break;
case 'C': oligo = (oligo << 2) | 1U; break;
case 'G': oligo = (oligo << 2) | 2U; break;
case 'T': oligo = (oligo << 2) | 3U; break;
- case 'X': case 'N': oligo = 0U; in_counter = 0; break;
+ case 'X': case 'N':
+ oligo = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
default:
if (genome_lc_p == true) {
- oligo = 0U; in_counter = 0;
+ oligo = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ } else {
+ fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
+ abort();
+ }
+ }
+
+#else
+ carry = (low >> 30);
+ switch (uppercaseCode[c]) {
+ case 'A': low = (low << 2); break;
+ case 'C': low = (low << 2) | 1U; break;
+ case 'G': low = (low << 2) | 2U; break;
+ case 'T': low = (low << 2) | 3U; break;
+ case 'X': case 'N':
+ high = low = carry = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
+ default:
+ if (genome_lc_p == true) {
+ high = low = carry = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
} else {
- fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
+ fprintf(stderr,"Bad character %c at position %u\n",c,position);
abort();
}
}
-
- debug(printf("char=%c bc=%d ic=%d oligo=%08X\n",
- c,between_counter,in_counter,oligo));
+ high = (high << 2) | carry;
#endif
-
#ifdef PMAP
if (in_counter[frame] > 0) {
if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_fwd(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
} else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_rev(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
}
}
if (in_counter[frame] == index1part_aa + 1) {
if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
+#endif
+ offset = Bitpack64_read_one(aaindex,offsetsmeta,offsetsstrm) + Bitpack64_incr(aaindex,countermeta,counterstrm);
if (coord_values_8p == true) {
if (watsonp == true) {
adjposition8 = position - index1part_nt + 1;
- positions8_high[offsets[aaindex]/*++*/] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[aaindex]++] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
+ positions8_high[offset] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
debug1(adjposition = position-index1part_nt+1UL);
} else {
- positions8_high[offsets[aaindex]/*++*/] = (unsigned char) (position >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[aaindex]++] = (UINT4) (position & POSITIONS8_LOW_MASK);
+ positions8_high[offset] = (unsigned char) (position >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (position & POSITIONS8_LOW_MASK);
debug1(adjposition = position);
}
} else {
if (watsonp == true) {
- positions4[offsets[aaindex]++] = (UINT4) (position - index1part_nt + 1);
+ positions4[offset] = (UINT4) (position - index1part_nt + 1);
debug1(adjposition = position - index1part_nt + 1);
} else {
- positions4[offsets[aaindex]++] = (UINT4) position;
+ positions4[offset] = (UINT4) position;
debug1(adjposition = position);
}
}
- debug1(
- aa = aaindex_aa(aaindex);
- printf("Storing %s (%u) at %u\n",aa,aaindex,adjposition);
- FREE(aa);
- );
+
between_counter[frame] = 0;
}
in_counter[frame] -= 1;
}
+
#else
if (in_counter == index1part) {
if (
@@ -1639,23 +2095,15 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
#endif
) {
masked = oligo & mask;
-#if 0
- if (offsets[masked] >= totalcounts) {
- fprintf(stderr,"masked = %u, offsets[masked] = %u >= totalcounts %u\n",
- masked,offsets[masked],totalcounts);
- exit(9);
- }
-#endif
+ offset = Bitpack64_read_one(masked,offsetsmeta,offsetsstrm) + Bitpack64_incr(masked,countermeta,counterstrm);
if (coord_values_8p == true) {
adjposition8 = position - index1part + 1;
- positions8_high[offsets[masked]/*++*/] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[masked]++] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
+ positions8_high[offset] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
} else {
- positions4[offsets[masked]++] = (UINT4) (position - index1part + 1);
+ positions4[offset] = (UINT4) (position - index1part + 1);
}
- debug1(nt = shortoligo_nt(masked,index1part);
- printf("Storing %s at %llu, chrpos %u\n",nt,(unsigned long long) (position-index1part+1U),chrpos-index1part+1U);
- FREE(nt));
+
between_counter = 0;
}
in_counter--;
@@ -1665,12 +2113,17 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
chrpos++; /* Needs to go here, before we reset chrpos to 0 */
if (position >= next_chrbound) {
debug1(printf("Skipping because position %u is at chrbound\n",position));
-#ifdef PMAP
- high = low = carry = 0U;
+#ifndef PMAP
+ oligo = 0;
+ in_counter = 0;
+#elif defined(HAVE_64_BIT)
+ oligo = 0ULL;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
#else
- oligo = 0U; in_counter = 0;
+ high = low = carry = 0U;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
#endif
+
chrpos = 0U;
chrnum++;
while (chrnum <= nchrs && (next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint)) < position) {
@@ -1680,24 +2133,6 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
position++;
}
-#ifdef ADDSENTINEL
- if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- positions8_high[offsets[oligoi]] = (unsigned char) (-1UL >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[oligoi]] = (UINT4) (-1UL & POSITIONS8_LOW_MASK);
- }
- } else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- positions4[offsets[oligoi]] = (UINT4) -1U;
- }
- }
- /*
- fprintf(stderr,"Put a sentinel at %u\n",offsets[0]);
- fprintf(stderr,"Put a sentinel at %u\n",offsets[oligospace-2]);
- fprintf(stderr,"Put a sentinel at %u\n",offsets[oligospace-1]);
- */
-#endif
-
return;
}
@@ -1707,38 +2142,44 @@ compute_positions_in_memory (UINT4 *positions4, unsigned char *positions8_high,
/* Main difference is that we use Hugepositionsptr_T * for offsets.
Also, huge genome implies large genome, so need only positions8. */
static void
-compute_positions_in_memory_huge (UINT4 *positions4, unsigned char *positions8_high, UINT4 *positions8_low,
- Hugepositionsptr_T *offsets, FILE *sequence_fp, Univ_IIT_T chromosome_iit,
+compute_positions_huge (UINT4 *positions4, unsigned char *positions8_high, UINT4 *positions8_low,
+ UINT4 *offsetspages, UINT4 *offsetsmeta, UINT4 *offsetsstrm,
+ UINT4 *countermeta, UINT4 *counterstrm,
+ FILE *sequence_fp, Univ_IIT_T chromosome_iit,
#ifdef PMAP
- Width_T index1part_aa, bool watsonp,
+ Width_T index1part_aa, bool watsonp,
#else
- Width_T index1part,
+ Width_T index1part,
#endif
- Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
- bool coord_values_8p) {
+ Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
+ bool coord_values_8p) {
char *uppercaseCode;
Univcoord_T position = 0, next_chrbound;
Chrpos_T chrpos = 0U;
char *comma;
int c, nchrs, chrnum;
UINT8 adjposition8;
+ Hugepositionsptr_T offset;
+
+#ifdef HAVE_64_BIT
+ Oligospace_T oligo = 0ULL;
+#else
+ Shortoligomer_T high = 0U, low = 0U, carry;
+#endif
+
#ifdef PMAP
int frame = -1, between_counter[3], in_counter[3];
- Storedoligomer_T high = 0U, low = 0U, carry;
- Storedoligomer_T aaindex;
+ Oligospace_T aaindex;
Width_T index1part_nt = 3*index1part_aa;
debug1(char *aa);
#else
+ Oligospace_T masked, mask;
int between_counter = 0, in_counter = 0;
- Storedoligomer_T oligo = 0U, masked, mask;
debug1(char *nt);
#endif
+
int circular_typeint;
-#ifdef ADDSENTINEL
- Oligospace_T oligospace, oligoi;
- oligospace = power(4,index1part);
-#endif
if (mask_lowercase_p == false) {
uppercaseCode = UPPERCASE_U2T; /* We are reading DNA sequence */
@@ -1750,8 +2191,13 @@ compute_positions_in_memory_huge (UINT4 *positions4, unsigned char *positions8_h
between_counter[0] = between_counter[1] = between_counter[2] = 0;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
#else
- mask = ~(~0UL << 2*index1part);
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
+#else
+ mask = ~(~0U << 2*index1part);
#endif
+#endif
+
/* Handle reference strain */
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
@@ -1791,95 +2237,124 @@ compute_positions_in_memory_huge (UINT4 *positions4, unsigned char *positions8_h
fprintf(stderr,"\n");
}
-#ifdef PMAP
- carry = (low >> 30);
+#ifdef HAVE_64_BIT
switch (uppercaseCode[c]) {
- case 'A': low = (low << 2); break;
- case 'C': low = (low << 2) | 1U; break;
- case 'G': low = (low << 2) | 2U; break;
- case 'T': low = (low << 2) | 3U; break;
+ case 'A': oligo = (oligo << 2); break;
+ case 'C': oligo = (oligo << 2) | 1U; break;
+ case 'G': oligo = (oligo << 2) | 2U; break;
+ case 'T': oligo = (oligo << 2) | 3U; break;
case 'X': case 'N':
- high = low = carry = 0U;
+ oligo = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
break;
default:
if (genome_lc_p == true) {
- high = low = carry = 0U;
- in_counter[0] = in_counter[1] = in_counter[2] = 0;
+ oligo = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
} else {
- fprintf(stderr,"Bad character %c at position %u\n",c,position);
+ fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
abort();
}
}
- high = (high << 2) | carry;
- debug(printf("frame=%d char=%c bc=%d ic=%d high=%08X low=%08X\n",
- frame,c,between_counter[frame],in_counter[frame],high,low));
#else
+ carry = (low >> 30);
switch (uppercaseCode[c]) {
- case 'A': oligo = (oligo << 2); break;
- case 'C': oligo = (oligo << 2) | 1U; break;
- case 'G': oligo = (oligo << 2) | 2U; break;
- case 'T': oligo = (oligo << 2) | 3U; break;
- case 'X': case 'N': oligo = 0U; in_counter = 0; break;
+ case 'A': low = (low << 2); break;
+ case 'C': low = (low << 2) | 1U; break;
+ case 'G': low = (low << 2) | 2U; break;
+ case 'T': low = (low << 2) | 3U; break;
+ case 'X': case 'N':
+ high = low = carry = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
default:
if (genome_lc_p == true) {
- oligo = 0U; in_counter = 0;
+ high = low = carry = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
} else {
- fprintf(stderr,"Bad character %c at position %llu\n",c,(unsigned long long) position);
+ fprintf(stderr,"Bad character %c at position %u\n",c,position);
abort();
}
}
-
- debug(printf("char=%c bc=%d ic=%d oligo=%08X\n",
- c,between_counter,in_counter,oligo));
+ high = (high << 2) | carry;
#endif
-
#ifdef PMAP
if (in_counter[frame] > 0) {
if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_fwd(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
} else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_rev(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
}
}
if (in_counter[frame] == index1part_aa + 1) {
if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
+#endif
+ offset = Bitpack64_read_one_huge(aaindex,offsetspages,offsetsmeta,offsetsstrm) +
+ Bitpack64_incr(aaindex,countermeta,counterstrm);
if (coord_values_8p == true) {
if (watsonp == true) {
adjposition8 = position - index1part_nt + 1;
- positions8_high[offsets[aaindex]/*++*/] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[aaindex]++] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
+ positions8_high[offset] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
debug1(adjposition = position-index1part_nt+1);
} else {
- positions8_high[offsets[aaindex]/*++*/] = (unsigned char) (position >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[aaindex]++] = (UINT4) (position & POSITIONS8_LOW_MASK);
+ positions8_high[offset] = (unsigned char) (position >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (position & POSITIONS8_LOW_MASK);
debug1(adjposition = position);
}
} else {
if (watsonp == true) {
- positions4[offsets[aaindex]++] = (UINT4) (position-index1part_nt+1U);
+ positions4[offset] = (UINT4) (position-index1part_nt+1U);
debug1(adjposition = position-index1part_nt+1U);
} else {
- positions4[offsets[aaindex]++] = (UINT4) position;
+ positions4[offset] = (UINT4) position;
debug1(adjposition = position);
}
}
- debug1(
- aa = aaindex_aa(aaindex);
- printf("Storing %s (%u) at %u\n",aa,aaindex,adjposition);
- FREE(aa);
- );
+
between_counter[frame] = 0;
}
in_counter[frame] -= 1;
}
+
#else
if (in_counter == index1part) {
if (
@@ -1890,23 +2365,16 @@ compute_positions_in_memory_huge (UINT4 *positions4, unsigned char *positions8_h
#endif
) {
masked = oligo & mask;
-#if 0
- if (offsets[masked] >= totalcounts) {
- fprintf(stderr,"masked = %u, offsets[masked] = %u >= totalcounts %u\n",
- masked,offsets[masked],totalcounts);
- exit(9);
- }
-#endif
+ offset = Bitpack64_read_one_huge(masked,offsetspages,offsetsmeta,offsetsstrm) +
+ Bitpack64_incr(masked,countermeta,counterstrm);
if (coord_values_8p == true) {
adjposition8 = position - index1part + 1;
- positions8_high[offsets[masked]/*++*/] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[masked]++] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
+ positions8_high[offset] = (unsigned char) (adjposition8 >> POSITIONS8_HIGH_SHIFT);
+ positions8_low[offset] = (UINT4) (adjposition8 & POSITIONS8_LOW_MASK);
} else {
- positions4[offsets[masked]++] = (UINT4) (position - index1part + 1);
+ positions4[offset] = (UINT4) (position - index1part + 1);
}
- debug1(nt = shortoligo_nt(masked,index1part);
- printf("Storing %s at %llu, chrpos %u\n",nt,(unsigned long long) (position-index1part+1U),chrpos-index1part+1U);
- FREE(nt));
+
between_counter = 0;
}
in_counter--;
@@ -1916,12 +2384,17 @@ compute_positions_in_memory_huge (UINT4 *positions4, unsigned char *positions8_h
chrpos++; /* Needs to go here, before we reset chrpos to 0 */
if (position >= next_chrbound) {
debug1(printf("Skipping because position %u is at chrbound\n",position));
-#ifdef PMAP
- high = low = carry = 0U;
+#ifndef PMAP
+ oligo = 0;
+ in_counter = 0;
+#elif defined(HAVE_64_BIT)
+ oligo = 0ULL;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
#else
- oligo = 0U; in_counter = 0;
+ high = low = carry = 0U;
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
#endif
+
chrpos = 0U;
chrnum++;
while (chrnum <= nchrs && (next_chrbound = Univ_IIT_next_chrbound(chromosome_iit,chrnum,circular_typeint)) < position) {
@@ -1931,34 +2404,15 @@ compute_positions_in_memory_huge (UINT4 *positions4, unsigned char *positions8_h
position++;
}
-#ifdef ADDSENTINEL
- if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- positions8_high[offsets[oligoi]] = (unsigned char) (-1UL >> POSITIONS8_HIGH_SHIFT);
- positions8_low[offsets[oligoi]] = (UINT4) (-1UL & POSITIONS8_LOW_MASK);
- }
- } else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- positions4[offsets[oligoi]] = (UINT4) -1U;
- }
- }
- /*
- fprintf(stderr,"Put a sentinel at %u\n",offsets[0]);
- fprintf(stderr,"Put a sentinel at %u\n",offsets[oligospace-2]);
- fprintf(stderr,"Put a sentinel at %u\n",offsets[oligospace-1]);
- */
-#endif
-
return;
}
#endif
-
#define WRITE_CHUNK 1000000
void
-Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char *pointersfile, char *offsetsfile,
+Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char *offsetsmetafile, char *offsetsstrmfile,
FILE *sequence_fp, Univ_IIT_T chromosome_iit,
#ifdef PMAP
Alphabet_T alphabet, int index1part_aa, bool watsonp,
@@ -1966,49 +2420,50 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
int index1part,
#endif
int index1interval, Univcoord_T genomelength, bool genome_lc_p, bool writefilep,
- char *fileroot, bool mask_lowercase_p, int compression_type,
- bool coord_values_8p) {
- int shmid;
+ char *fileroot, bool mask_lowercase_p, bool coord_values_8p) {
FILE *positions_high_fp, *positions_low_fp; /* For building positions in memory */
- int positions_high_fd, positions_low_fd; /* For building positions in file */
- Positionsptr_T *offsets = NULL, totalcounts, count;
+ /* int positions_high_fd, positions_low_fd; */ /* For building positions in file */
+ int offsetsmeta_fd, offsetsstrm_fd;
+ size_t offsetsmeta_len, offsetsstrm_len;
+ UINT4 *offsetsmeta, *offsetsstrm, *countermeta, *counterstrm;
+ Oligospace_T oligospace;
+ Positionsptr_T totalcounts, count;
UINT4 *positions4;
unsigned char *positions8_high;
UINT4 *positions8_low;
- Oligospace_T oligospace;
- off_t filesize;
- size_t offsetsstrm_len;
- double seconds;
+ size_t filesize;
#ifdef PMAP
int alphabet_size;
- int offsetsstrm_fd;
#endif
+#ifdef HAVE_MMAP
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
+#else
+ offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
+#endif
#ifdef PMAP
alphabet_size = Alphabet_get_size(alphabet);
- if (compression_type == BITPACK64_COMPRESSION) {
- offsets = Indexdb_offsets_from_bitpack(pointersfile,offsetsfile,alphabet_size,index1part_aa);
- } else {
- offsets = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsfile,sizeof(UINT4),/*sharedp*/false);
- }
oligospace = power(alphabet_size,index1part_aa);
#else
- if (compression_type == BITPACK64_COMPRESSION) {
- offsets = Indexdb_offsets_from_bitpack(pointersfile,offsetsfile,index1part);
- } else {
- offsets = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsfile,sizeof(UINT4),/*sharedp*/false);
- }
oligospace = power(4,index1part);
#endif
- totalcounts = offsets[oligospace];
+
+ totalcounts = Bitpack64_read_one(oligospace,offsetsmeta,offsetsstrm);
if (totalcounts == 0) {
- if (genomelength > index1part) {
+ if (
+#ifdef PMAP
+ genomelength > (Univcoord_T) (index1part_aa * 3)
+#else
+ genomelength > (Univcoord_T) index1part
+#endif
+ ) {
fprintf(stderr,"Something is wrong with the offsets file. Total counts is zero.\n");
exit(9);
} else {
- FREE(offsets);
#if 0
if ((positions_high_fp = FOPEN_WRITE_BINARY(positionsfile_high)) == NULL) {
fprintf(stderr,"Can't open file %s\n",positionsfile_high);
@@ -2020,12 +2475,27 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
fclose(positions_high_fp);
fclose(positions_low_fp);
#endif
+#ifdef HAVE_MMAP
+ munmap((void *) offsetsstrm,offsetsstrm_len);
+ munmap((void *) offsetsmeta,offsetsmeta_len);
+#else
+ FREE(offsetsstrm);
+ FREE(offsetsmeta);
+#endif
return;
}
+ } else {
+#ifdef PMAP
+ countermeta = Indexdb_bitpack_counter(&counterstrm,offsetsmeta,offsetsstrm,alphabet_size,index1part_aa);
+#else
+ countermeta = Indexdb_bitpack_counter(&counterstrm,offsetsmeta,offsetsstrm,index1part);
+#endif
}
if (writefilep == true) {
- fprintf(stderr,"User requested build of positions in file\n");
+ fprintf(stderr,"User requested build of positions in file. Not supported\n");
+ abort();
+#if 0
positions_high_fd = Access_fileio_rw(positionsfile_high);
positions_low_fd = Access_fileio_rw(positionsfile_low);
#ifdef PMAP
@@ -2039,13 +2509,16 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
#endif
close(positions_high_fd);
close(positions_low_fd);
+#endif
} else if (coord_values_8p == true) {
fprintf(stderr,"Trying to allocate %u*(%d+%d) bytes of memory for positions...",totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT4));
positions8_high = (unsigned char *) CALLOC_NO_EXCEPTION(totalcounts,sizeof(unsigned char));
positions8_low = (UINT4 *) CALLOC_NO_EXCEPTION(totalcounts,sizeof(UINT4));
if (positions8_high == NULL || positions8_low == NULL) {
- fprintf(stderr,"failed. Building positions in file.\n");
+ fprintf(stderr,"failed. Building positions in file. Not supported\n");
+ abort();
+#if 0
positions_high_fd = Access_fileio_rw(positionsfile_high);
positions_low_fd = Access_fileio_rw(positionsfile_low);
#ifdef PMAP
@@ -2060,15 +2533,16 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
close(positions_high_fd);
close(positions_low_fd);
- if ((filesize = Access_filesize(positionsfile_high)) != totalcounts * (off_t) sizeof(unsigned char)) {
+ if ((filesize = Access_filesize(positionsfile_high)) != (size_t) (totalcounts * sizeof(unsigned char))) {
fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
abort();
- } else if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ } else if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
abort();
}
+#endif
} else {
fprintf(stderr,"succeeded. Building positions in memory.\n");
@@ -2080,15 +2554,17 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
exit(9);
}
#ifdef PMAP
- compute_positions_in_memory(/*positions4*/NULL,positions8_high,positions8_low,offsets,
- sequence_fp,chromosome_iit,index1part_aa,watsonp,
- index1interval,genome_lc_p,fileroot,
- mask_lowercase_p,/*coord_values_8p*/true);
+ compute_positions(/*positions4*/NULL,positions8_high,positions8_low,
+ offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,index1part_aa,watsonp,
+ index1interval,genome_lc_p,fileroot,
+ mask_lowercase_p,/*coord_values_8p*/true);
#else
- compute_positions_in_memory(/*positions4*/NULL,positions8_high,positions8_low,offsets,
- sequence_fp,chromosome_iit,index1part,
- index1interval,genome_lc_p,fileroot,
- mask_lowercase_p,/*coord_values_8p*/true);
+ compute_positions(/*positions4*/NULL,positions8_high,positions8_low,
+ offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,index1part,
+ index1interval,genome_lc_p,fileroot,
+ mask_lowercase_p,/*coord_values_8p*/true);
#endif
fprintf(stderr,"Writing %u genomic positions to files %s and %s ...\n",
totalcounts,positionsfile_high,positionsfile_low);
@@ -2098,7 +2574,7 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
fclose(positions_high_fp);
fclose(positions_low_fp);
- if ((filesize = Access_filesize(positionsfile_high)) != totalcounts * (off_t) sizeof(unsigned char)) {
+ if ((filesize = Access_filesize(positionsfile_high)) != (size_t) (totalcounts * sizeof(unsigned char))) {
fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n",
positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
if ((positions_high_fp = FOPEN_WRITE_BINARY(positionsfile_high)) == NULL) {
@@ -2113,14 +2589,14 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
}
fclose(positions_high_fp);
- if ((filesize = Access_filesize(positionsfile_high)) != totalcounts * (off_t) sizeof(unsigned char)) {
+ if ((filesize = Access_filesize(positionsfile_high)) != (size_t) (totalcounts * sizeof(unsigned char))) {
fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
abort();
}
}
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n",
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
if ((positions_low_fp = FOPEN_WRITE_BINARY(positionsfile_low)) == NULL) {
@@ -2135,7 +2611,7 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
}
fclose(positions_low_fp);
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
abort();
@@ -2150,7 +2626,9 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
fprintf(stderr,"Trying to allocate %u*%d bytes of memory for positions...",totalcounts,(int) sizeof(UINT4));
positions4 = (UINT4 *) CALLOC_NO_EXCEPTION(totalcounts,sizeof(UINT4));
if (positions4 == NULL) {
- fprintf(stderr,"failed. Building positions in file.\n");
+ fprintf(stderr,"failed. Building positions in file. Not supported.\n");
+ abort();
+#if 0
positions_low_fd = Access_fileio_rw(positionsfile_low);
#ifdef PMAP
compute_positions_in_file(/*positions_high_fd*/0,positions_low_fd,offsets,sequence_fp,chromosome_iit,
@@ -2163,11 +2641,12 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
#endif
close(positions_low_fd);
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error after file-based build: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
abort();
}
+#endif
} else {
fprintf(stderr,"succeeded. Building positions in memory.\n");
@@ -2176,23 +2655,25 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
exit(9);
}
#ifdef PMAP
- compute_positions_in_memory(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,
- offsets,sequence_fp,chromosome_iit,
- index1part_aa,watsonp,index1interval,genome_lc_p,fileroot,
- mask_lowercase_p,/*coord_values_8p*/false);
+ compute_positions(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,
+ offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,
+ index1part_aa,watsonp,index1interval,genome_lc_p,fileroot,
+ mask_lowercase_p,/*coord_values_8p*/false);
#else
- compute_positions_in_memory(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,
- offsets,sequence_fp,chromosome_iit,
- index1part,index1interval,genome_lc_p,fileroot,
- mask_lowercase_p,/*coord_values_8p*/false);
+ compute_positions(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,
+ offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,
+ index1part,index1interval,genome_lc_p,fileroot,
+ mask_lowercase_p,/*coord_values_8p*/false);
#endif
fprintf(stderr,"Writing %u genomic positions to file %s ...\n",
totalcounts,positionsfile_low);
FWRITE_UINTS(positions4,totalcounts,positions_low_fp);
-
fclose(positions_low_fp);
+ fprintf(stderr,"done\n");
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n",
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
if ((positions_low_fp = FOPEN_WRITE_BINARY(positionsfile_low)) == NULL) {
@@ -2207,7 +2688,7 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
}
fclose(positions_low_fp);
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
positionsfile_low,totalcounts*sizeof(UINT4),filesize);
abort();
@@ -2218,16 +2699,26 @@ Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char
}
}
- FREE(offsets);
+ FREE(counterstrm);
+ FREE(countermeta);
+
+#ifdef HAVE_MMAP
+ munmap((void *) offsetsstrm,offsetsstrm_len);
+ munmap((void *) offsetsmeta,offsetsmeta_len);
+#else
+ FREE(offsetsstrm);
+ FREE(offsetsmeta);
+#endif
return;
}
+
#ifdef HAVE_64_BIT
void
Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
- char *pagesfile, char *pointersfile, char *offsetsfile,
+ char *offsetspagesfile, char *offsetsmetafile, char *offsetsstrmfile,
FILE *sequence_fp, Univ_IIT_T chromosome_iit,
#ifdef PMAP
Alphabet_T alphabet, int index1part_aa, bool watsonp,
@@ -2235,39 +2726,57 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
int index1part,
#endif
int index1interval, Univcoord_T genomelength, bool genome_lc_p, bool writefilep,
- char *fileroot, bool mask_lowercase_p, int compression_type,
- bool coord_values_8p) {
+ char *fileroot, bool mask_lowercase_p, bool coord_values_8p) {
FILE *positions_high_fp, *positions_low_fp; /* For building positions in memory */
- Hugepositionsptr_T *offsets = NULL, totalcounts, count;
+ int offsetspages_fd, offsetsmeta_fd, offsetsstrm_fd;
+ size_t offsetspages_len, offsetsmeta_len, offsetsstrm_len;
+ UINT4 *offsetspages, *offsetsmeta, *offsetsstrm, *countermeta, *counterstrm;
+ Oligospace_T oligospace;
+ Hugepositionsptr_T totalcounts;
UINT4 *positions4;
unsigned char *positions8_high;
UINT4 *positions8_low;
- Oligospace_T oligospace;
- off_t filesize;
+ size_t filesize;
#ifdef PMAP
int alphabet_size;
#endif
+ UINT4 count;
+
+
+#ifdef HAVE_MMAP
+ offsetspages = (UINT4 *) Access_mmap(&offsetspages_fd,&offsetspages_len,offsetspagesfile,/*randomp*/false);
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
+#else
+ offsetspages = (UINT4 *) Access_allocate_private(&offsetspages_len,&seconds,offsetspagesfile,sizeof(UINT4));
+ offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
+#endif
+ fprintf(stderr,"offsetspages has len %zu\n",offsetspages_len);
+ fprintf(stderr,"offsetsmeta has len %zu\n",offsetsmeta_len);
+ fprintf(stderr,"offsetsstrm has len %zu\n",offsetsstrm_len);
#ifdef PMAP
alphabet_size = Alphabet_get_size(alphabet);
oligospace = power(alphabet_size,index1part_aa);
#else
- if (compression_type == BITPACK64_COMPRESSION) {
- offsets = Indexdb_offsets_from_bitpack_huge(pagesfile,pointersfile,offsetsfile,index1part);
- } else {
- fprintf(stderr,"Not supporting non-compression on huge genomes\n");
- return;
- }
+ oligospace = power(4,index1part);
oligospace = power(4,index1part);
#endif
- totalcounts = offsets[oligospace];
+
+ totalcounts = Bitpack64_read_one_huge(oligospace,offsetspages,offsetsmeta,offsetsstrm);
if (totalcounts == 0) {
- if (genomelength > index1part) {
+ if (
+#ifdef PMAP
+ genomelength > (Univcoord_T) (index1part_aa * 3)
+#else
+ genomelength > (Univcoord_T) index1part
+#endif
+ ) {
fprintf(stderr,"Something is wrong with the offsets file. Total counts is zero.\n");
exit(9);
} else {
- FREE(offsets);
#if 0
if ((positions_high_fp = FOPEN_WRITE_BINARY(positionsfile_high)) == NULL) {
fprintf(stderr,"Can't open file %s\n",positionsfile_high);
@@ -2279,21 +2788,37 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
fclose(positions_high_fp);
fclose(positions_low_fp);
#endif
+#ifdef HAVE_MMAP
+ munmap((void *) offsetsstrm,offsetsstrm_len);
+ munmap((void *) offsetsmeta,offsetsmeta_len);
+ munmap((void *) offsetspages,offsetspages_len);
+#else
+ FREE(offsetsstrm);
+ FREE(offsetsmeta);
+ FREE(offsetspages);
+#endif
return;
}
+
+ } else {
+#ifdef PMAP
+ countermeta = Indexdb_bitpack_counter_huge(&counterstrm,offsetspages,offsetsmeta,offsetsstrm,alphabet_size,index1part_aa);
+#else
+ countermeta = Indexdb_bitpack_counter_huge(&counterstrm,offsetspages,offsetsmeta,offsetsstrm,index1part);
+#endif
}
if (writefilep == true) {
- fprintf(stderr,"User requested build of positions in file, but not supported.\n");
+ fprintf(stderr,"User requested build of positions in file. Not supported\n");
abort();
} else if (coord_values_8p == true) {
fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...",
- (unsigned long long) totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8));
+ totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8));
positions8_high = (unsigned char *) CALLOC_NO_EXCEPTION(totalcounts,sizeof(unsigned char));
positions8_low = (UINT4 *) CALLOC_NO_EXCEPTION(totalcounts,sizeof(UINT4));
if (positions8_high == NULL || positions8_low == NULL) {
- fprintf(stderr,"failed. Not able to proceed.\n");
+ fprintf(stderr,"failed. Building positions in file. Not supported\n");
abort();
} else {
@@ -2306,14 +2831,16 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
exit(9);
}
#ifdef PMAP
- compute_positions_in_memory_huge(/*positions4*/NULL,positions8_high,positions8_low,offsets,
- sequence_fp,chromosome_iit,index1part_aa,watsonp,
- index1interval,genome_lc_p,fileroot,
- mask_lowercase_p,/*coord_values_8p*/true);
+ compute_positions_huge(/*positions4*/NULL,positions8_high,positions8_low,
+ offsetspages,offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,index1part_aa,watsonp,
+ index1interval,genome_lc_p,fileroot,
+ mask_lowercase_p,/*coord_values_8p*/true);
#else
- compute_positions_in_memory_huge(/*positions4*/NULL,positions8_high,positions8_low,offsets,
- sequence_fp,chromosome_iit,index1part,index1interval,
- genome_lc_p,fileroot,mask_lowercase_p,/*coord_values_8p*/true);
+ compute_positions_huge(/*positions4*/NULL,positions8_high,positions8_low,
+ offsetspages,offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,index1part,index1interval,
+ genome_lc_p,fileroot,mask_lowercase_p,/*coord_values_8p*/true);
#endif
fprintf(stderr,"Writing %llu genomic positions to files %s and %s...\n",
(unsigned long long) totalcounts,positionsfile_high,positionsfile_low);
@@ -2323,9 +2850,9 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
fclose(positions_high_fp);
fclose(positions_low_fp);
- if ((filesize = Access_filesize(positionsfile_high)) != totalcounts * (off_t) sizeof(unsigned char)) {
+ if ((filesize = Access_filesize(positionsfile_high)) != (size_t) (totalcounts * sizeof(unsigned char))) {
fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n",
- positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
+ positionsfile_high,(size_t) (totalcounts*sizeof(unsigned char)),filesize);
if ((positions_high_fp = FOPEN_WRITE_BINARY(positionsfile_high)) == NULL) {
fprintf(stderr,"Can't open file %s\n",positionsfile_high);
exit(9);
@@ -2338,16 +2865,16 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
}
fclose(positions_high_fp);
- if ((filesize = Access_filesize(positionsfile_high)) != totalcounts * (off_t) sizeof(unsigned char)) {
+ if ((filesize = Access_filesize(positionsfile_high)) != (size_t) (totalcounts * sizeof(unsigned char))) {
fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
- positionsfile_high,totalcounts*sizeof(unsigned char),filesize);
+ positionsfile_high,(size_t) (totalcounts*sizeof(unsigned char)),filesize);
abort();
}
}
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n",
- positionsfile_low,totalcounts*sizeof(UINT4),filesize);
+ positionsfile_low,(size_t) (totalcounts*sizeof(UINT4)),filesize);
if ((positions_low_fp = FOPEN_WRITE_BINARY(positionsfile_low)) == NULL) {
fprintf(stderr,"Can't open file %s\n",positionsfile_low);
exit(9);
@@ -2360,9 +2887,9 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
}
fclose(positions_low_fp);
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
- positionsfile_low,totalcounts*sizeof(UINT4),filesize);
+ positionsfile_low,(size_t) (totalcounts*sizeof(UINT4)),filesize);
abort();
}
}
@@ -2376,7 +2903,7 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
fprintf(stderr,"Please report this bug to twu at gene.com\n");
abort();
- fprintf(stderr,"Trying to allocate %llu*%d bytes of memory for positions...",(unsigned long long) totalcounts,(int) sizeof(UINT4));
+ fprintf(stderr,"Trying to allocate %llu*%d bytes of memory for positions...",totalcounts,(int) sizeof(UINT4));
positions4 = (UINT4 *) CALLOC_NO_EXCEPTION(totalcounts,sizeof(UINT4));
if (positions4 == NULL) {
fprintf(stderr,"failed. Not able to proceed.\n");
@@ -2389,23 +2916,25 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
exit(9);
}
#ifdef PMAP
- compute_positions_in_memory_huge(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,offsets,
- sequence_fp,chromosome_iit,index1part_aa,watsonp,index1interval,
- genome_lc_p,fileroot,mask_lowercase_p,/*coord_values_8p*/false);
+ compute_positions_huge(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,
+ offsetspages,offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,index1part_aa,watsonp,index1interval,
+ genome_lc_p,fileroot,mask_lowercase_p,/*coord_values_8p*/false);
#else
- compute_positions_in_memory_huge(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,offsets,
- sequence_fp,chromosome_iit,index1part,index1interval,
- genome_lc_p,fileroot,mask_lowercase_p,/*coord_values_8p*/false);
+ compute_positions_huge(positions4,/*positions8_high*/NULL,/*positions8_low*/NULL,
+ offsetspages,offsetsmeta,offsetsstrm,countermeta,counterstrm,
+ sequence_fp,chromosome_iit,index1part,index1interval,
+ genome_lc_p,fileroot,mask_lowercase_p,/*coord_values_8p*/false);
#endif
fprintf(stderr,"Writing %llu genomic positions to file %s ...\n",
(unsigned long long) totalcounts,positionsfile_low);
FWRITE_UINTS(positions4,totalcounts,positions_low_fp);
-
fclose(positions_low_fp);
+ fprintf(stderr,"done\n");
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error: expected file size for %s is %zu, but observed only %zu. Trying now to write with smaller chunks.\n",
- positionsfile_low,totalcounts*sizeof(UINT4),filesize);
+ positionsfile_low,(size_t) (totalcounts*sizeof(UINT4)),filesize);
if ((positions_low_fp = FOPEN_WRITE_BINARY(positionsfile_low)) == NULL) {
fprintf(stderr,"Can't open file %s\n",positionsfile_low);
exit(9);
@@ -2418,9 +2947,9 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
}
fclose(positions_low_fp);
- if ((filesize = Access_filesize(positionsfile_low)) != totalcounts * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(positionsfile_low)) != (size_t) (totalcounts * sizeof(UINT4))) {
fprintf(stderr,"Error persists: expected file size for %s is %zu, but observed only %zu. Please notify twu at gene.com of this error.\n",
- positionsfile_low,totalcounts*sizeof(UINT4),filesize);
+ positionsfile_low,(size_t) (totalcounts*sizeof(UINT4)),filesize);
abort();
}
}
@@ -2429,7 +2958,18 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
}
}
- FREE(offsets);
+ FREE(counterstrm);
+ FREE(countermeta);
+
+#ifdef HAVE_MMAP
+ munmap((void *) offsetsstrm,offsetsstrm_len);
+ munmap((void *) offsetsmeta,offsetsmeta_len);
+ munmap((void *) offsetspages,offsetspages_len);
+#else
+ FREE(offsetsstrm);
+ FREE(offsetsmeta);
+ FREE(offsetspages);
+#endif
return;
}
diff --git a/src/indexdb-write.h b/src/indexdb-write.h
index 40105ee..6760a41 100644
--- a/src/indexdb-write.h
+++ b/src/indexdb-write.h
@@ -1,4 +1,4 @@
-/* $Id: indexdb-write.h 165969 2015-05-20 00:18:07Z twu $ */
+/* $Id: indexdb-write.h 180699 2015-12-10 19:10:10Z twu $ */
#ifndef INDEXDB_WRITE_INCLUDED
#define INDEXDB_WRITE_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -40,8 +40,8 @@ Indexdb_write_offsets (char *destdir, char interval_char, FILE *sequence_fp, Uni
#else
Width_T index1part,
#endif
- Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
- int compression_types);
+ Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p);
+
#ifdef HAVE_64_BIT
extern void
Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp, Univ_IIT_T chromosome_iit,
@@ -50,23 +50,41 @@ Indexdb_write_offsets_huge (char *destdir, char interval_char, FILE *sequence_fp
#else
Width_T index1part,
#endif
- Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p,
- int compression_types);
+ Width_T index1interval, bool genome_lc_p, char *fileroot, bool mask_lowercase_p);
+#endif
+
+
+extern UINT4 *
+Indexdb_bitpack_counter (UINT4 **counterstrm, UINT4 *offsetsmeta, UINT4 *offsetsstrm,
+#ifdef PMAP
+ int alphabet_size, Width_T index1part_aa
+#else
+ Width_T index1part
+#endif
+ );
+
+#ifdef HAVE_64_BIT
+extern UINT4 *
+Indexdb_bitpack_counter_huge (UINT4 **counterstrm, UINT4 *offsetspages, UINT4 *offsetsmeta, UINT4 *offsetsstrm,
+#ifdef PMAP
+ int alphabet_size, Width_T index1part_aa
+#else
+ Width_T index1part
+#endif
+ );
#endif
extern void
-Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char *pointersfile, char *offsetsfile,
+Indexdb_write_positions (char *positionsfile_high, char *positionsfile_low, char *offsetsmetafile, char *offsetsstrmfile,
FILE *sequence_fp, Univ_IIT_T chromosome_iit,
#ifdef PMAP
- Alphabet_T alphabet, Width_T index1part_aa, bool watsonp,
+ Alphabet_T alphabet, int index1part_aa, bool watsonp,
#else
- Width_T index1part,
+ int index1part,
#endif
- Width_T index1interval, Univcoord_T genomelength, bool genome_lc_p, bool writefilep,
- char *fileroot, bool mask_lowercase_p, int compression_type,
- bool coord_values_8p);
-
+ int index1interval, Univcoord_T genomelength, bool genome_lc_p, bool writefilep,
+ char *fileroot, bool mask_lowercase_p, bool coord_values_8p);
#ifdef HAVE_64_BIT
extern void
@@ -78,9 +96,9 @@ Indexdb_write_positions_huge (char *positionsfile_high, char *positionsfile_low,
int index1part,
#endif
int index1interval, Univcoord_T genomelength, bool genome_lc_p, bool writefilep,
- char *fileroot, bool mask_lowercase_p, int compression_type,
- bool coord_values_8p);
-#endif
+ char *fileroot, bool mask_lowercase_p, bool coord_values_8p);
#endif
+
+#endif
diff --git a/src/indexdb.c b/src/indexdb.c
index ec4b674..ea3b70d 100644
--- a/src/indexdb.c
+++ b/src/indexdb.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: indexdb.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: indexdb.c 184480 2016-02-18 00:58:00Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -112,7 +112,7 @@ Indexdb_setup (Width_T index1part_aa_in) {
#else
#define poly_A 0U
-static Storedoligomer_T poly_T; /* Was LOW12MER 0x00FFFFFF */
+static Oligospace_T poly_T; /* Was LOW12MER 0x00FFFFFF */
#if (defined(DEBUG) || defined(DEBUG0))
static Width_T index1part;
@@ -124,7 +124,12 @@ Indexdb_setup (Width_T index1part_in) {
index1part = index1part_in;
#endif
- poly_T = ~(~0UL << 2*index1part_in);
+#ifdef HAVE_64_BIT
+ poly_T = ~(~0ULL << 2*index1part_in);
+#else
+ poly_T = ~(~0U << 2*index1part_in);
+#endif
+
return;
}
#endif
@@ -133,54 +138,53 @@ Indexdb_setup (Width_T index1part_in) {
#define T Indexdb_T
+#ifdef LARGE_GENOMES
void
Indexdb_free (T *old) {
if (*old) {
- if ((*old)->positions_access == ALLOCATED_PRIVATE) {
-#ifdef LARGE_GENOMES
+
+ if ((*old)->positions_high_access == ALLOCATED_PRIVATE) {
FREE((*old)->positions_high);
- FREE((*old)->positions_low);
-#else
- FREE((*old)->positions);
-#endif
- } else if ((*old)->positions_access == ALLOCATED_SHARED) {
-#ifdef LARGE_GENOMES
- Access_deallocate((*old)->positions_high,(*old)->positions_high_shmid);
- Access_deallocate((*old)->positions_low,(*old)->positions_low_shmid);
-#else
- Access_deallocate((*old)->positions,(*old)->positions_shmid);
-#endif
+ } else if ((*old)->positions_high_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->positions_high,(*old)->positions_high_shmid,(*old)->positions_high_key);
#ifdef HAVE_MMAP
- } else if ((*old)->positions_access == MMAPPED) {
-#ifdef LARGE_GENOMES
+ } else if ((*old)->positions_high_access == MMAPPED) {
munmap((void *) (*old)->positions_high,(*old)->positions_high_len);
close((*old)->positions_high_fd);
+#endif
+ } else {
+ close((*old)->positions_high_fd);
+ }
+
+ if ((*old)->positions_low_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->positions_low);
+
+ } else if ((*old)->positions_low_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->positions_low,(*old)->positions_low_shmid,(*old)->positions_low_key);
+
+#ifdef HAVE_MMAP
+ } else if ((*old)->positions_low_access == MMAPPED) {
munmap((void *) (*old)->positions_low,(*old)->positions_low_len);
close((*old)->positions_low_fd);
-#else
- munmap((void *) (*old)->positions,(*old)->positions_len);
- close((*old)->positions_fd);
-#endif
#endif
- } else if ((*old)->positions_access == FILEIO) {
+ } else {
+ close((*old)->positions_low_fd);
+ }
+
#ifdef HAVE_PTHREAD
+ if ((*old)->positions_high_access == FILEIO || (*old)->positions_low_access == FILEIO) {
pthread_mutex_destroy(&(*old)->positions_read_mutex);
-#endif
-#ifdef LARGE_GENOMES
- close((*old)->positions_high_fd);
- close((*old)->positions_low_fd);
-#else
- close((*old)->positions_fd);
-#endif
}
+#endif
+
if ((*old)->offsetsstrm_access == ALLOCATED_PRIVATE) {
FREE((*old)->offsetsstrm);
} else if ((*old)->offsetsstrm_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->offsetsstrm,(*old)->offsetsstrm_shmid);
+ Access_deallocate((*old)->offsetsstrm,(*old)->offsetsstrm_shmid,(*old)->offsetsstrm_key);
#ifdef HAVE_MMAP
} else if ((*old)->offsetsstrm_access == MMAPPED) {
@@ -192,28 +196,85 @@ Indexdb_free (T *old) {
if ((*old)->offsetsmeta_access == ALLOCATED_PRIVATE) {
FREE((*old)->offsetsmeta);
} else if ((*old)->offsetsmeta_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->offsetsmeta,(*old)->offsetsmeta_shmid);
- } else {
- /* Always ALLOCATED */
- abort();
+ Access_deallocate((*old)->offsetsmeta,(*old)->offsetsmeta_shmid,(*old)->offsetsmeta_key);
+#ifdef HAVE_MMAP
+ } else if ((*old)->offsetsmeta_access == MMAPPED) {
+ munmap((void *) (*old)->offsetsmeta,(*old)->offsetsmeta_len);
+ close((*old)->offsetsmeta_fd);
+#endif
}
-#ifdef LARGE_GENOMES
if ((*old)->offsetspages_access == ALLOCATED_PRIVATE) {
FREE((*old)->offsetspages);
} else if ((*old)->offsetspages_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->offsetspages,(*old)->offsetspages_shmid);
- } else {
- /* Always ALLOCATED */
- abort();
+ Access_deallocate((*old)->offsetspages,(*old)->offsetspages_shmid,(*old)->offsetspages_key);
+#ifdef HAVE_MMAP
+ } else if ((*old)->offsetspages_access == MMAPPED) {
+ munmap((void *) (*old)->offsetspages,(*old)->offsetspages_len);
+ close((*old)->offsetspages_fd);
+#endif
}
+
+ FREE(*old);
+ }
+ return;
+}
+
+#else
+
+void
+Indexdb_free (T *old) {
+ if (*old) {
+
+ if ((*old)->positions_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->positions);
+
+ } else if ((*old)->positions_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->positions,(*old)->positions_shmid,(*old)->positions_key);
+
+#ifdef HAVE_MMAP
+ } else if ((*old)->positions_access == MMAPPED) {
+ munmap((void *) (*old)->positions,(*old)->positions_len);
+ close((*old)->positions_fd);
+#endif
+ } else if ((*old)->positions_access == FILEIO) {
+#ifdef HAVE_PTHREAD
+ pthread_mutex_destroy(&(*old)->positions_read_mutex);
#endif
+ close((*old)->positions_fd);
+ }
+
+ if ((*old)->offsetsstrm_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->offsetsstrm);
+
+ } else if ((*old)->offsetsstrm_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->offsetsstrm,(*old)->offsetsstrm_shmid,(*old)->offsetsstrm_key);
+
+#ifdef HAVE_MMAP
+ } else if ((*old)->offsetsstrm_access == MMAPPED) {
+ munmap((void *) (*old)->offsetsstrm,(*old)->offsetsstrm_len);
+ close((*old)->offsetsstrm_fd);
+#endif
+ }
+
+ if ((*old)->offsetsmeta_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->offsetsmeta);
+ } else if ((*old)->offsetsmeta_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->offsetsmeta,(*old)->offsetsmeta_shmid,(*old)->offsetsmeta_key);
+#ifdef HAVE_MMAP
+ } else if ((*old)->offsetsmeta_access == MMAPPED) {
+ munmap((void *) (*old)->offsetsmeta,(*old)->offsetsmeta_len);
+ close((*old)->offsetsmeta_fd);
+#endif
+ }
FREE(*old);
}
return;
}
+#endif
+
Width_T
Indexdb_interval (T this) {
@@ -221,6 +282,16 @@ Indexdb_interval (T this) {
}
+#ifdef LARGE_GENOMES
+bool
+Indexdb_positions_fileio_p (T this) {
+ if (this->positions_high_access == FILEIO || this->positions_low_access == FILEIO) {
+ return true;
+ } else {
+ return false;
+ }
+}
+#else
bool
Indexdb_positions_fileio_p (T this) {
if (this->positions_access == FILEIO) {
@@ -229,6 +300,9 @@ Indexdb_positions_fileio_p (T this) {
return false;
}
}
+#endif
+
+
static Oligospace_T
power (int base, Width_T exponent) {
@@ -322,7 +396,10 @@ Indexdb_get_filenames_no_compression (Width_T *index1part, Width_T *index1interv
char *base_filename, *filename;
char *pattern, interval_char, digit_string[2], *p, *q;
- char tens, ones;
+#ifndef PMAP
+ char tens;
+#endif
+ char ones;
Width_T found_index1part, found_interval;
int rootlength, patternlength;
@@ -365,11 +442,8 @@ Indexdb_get_filenames_no_compression (Width_T *index1part, Width_T *index1interv
if ((q = strstr(p,offsets_suffix)) != NULL && !strcmp(q,offsets_suffix)) {
if (q - p == 3) {
#ifdef PMAP
- /* e.g., pf677 */
- if (sscanf(p,"%c%c%c",&ones0,&ones,&interval_char) == 3) {
- /* digit_string[0] = ones0; */
- /* found_basesize = atoi(digit_string); */
-
+ /* e.g., pf67offsets */
+ if (sscanf(p,"%c%c",&ones,&interval_char) == 2) {
digit_string[0] = ones;
found_index1part = atoi(digit_string);
@@ -572,7 +646,11 @@ Indexdb_get_filenames_no_compression (Width_T *index1part, Width_T *index1interv
Filenames_T
-Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
+Indexdb_get_filenames_bitpack (
+#ifdef PMAP
+ Alphabet_T *alphabet, Alphabet_T required_alphabet,
+#endif
+ Width_T *index1part, Width_T *index1interval,
char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
Width_T required_index1part, Width_T required_interval,
Blocksize_T blocksize, bool offsets_only_p) {
@@ -580,8 +658,9 @@ Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
*positions_high_filename, *positions_low_filename,
*offsetspages_basename_ptr, *offsetsmeta_basename_ptr, *offsetsstrm_basename_ptr,
*positions_high_basename_ptr, *positions_low_basename_ptr,
- *offsetspages_index1info_ptr, *offsetsmeta_index1info_ptr, *offsetsstrm_index1info_ptr,
+ *offsetsmeta_index1info_ptr, *offsetsstrm_index1info_ptr,
*positions_high_index1info_ptr, *positions_low_index1info_ptr;
+ /* char *offsetspages_index1info_ptr; */
char *base_filename, *filename;
#ifdef PMAP
@@ -697,8 +776,9 @@ Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
abort();
}
+#if 0
} else if (q - p == BASE_KMER_SAMPLING) {
- /* Previous style, e.g., pf677 */
+ /* Previous style, e.g., pf677. No longer supported. */
if (sscanf(p,"%c%c%c",&ones0,&ones,&interval_char) == 3) {
digit_string[0] = ones0;
found_basesize = atoi(digit_string);
@@ -711,6 +791,7 @@ Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
} else {
abort();
}
+#endif
} else {
/* fprintf(stderr,"Cannot parse part between %s and offsets in filename %s\n",idx_filesuffix,filename); */
@@ -735,7 +816,7 @@ Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
/* Skip, since we have already found a smaller interval */
} else {
patternlength = patternlength1 + alphabet_strlen + patternlength2;
- *basesize = found_basesize;
+ /* *basesize = found_basesize; */
*index1part = found_index1part;
*index1interval = found_interval;
*alphabet = found_alphabet;
@@ -889,7 +970,7 @@ Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
offsetspages_filename = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+rootlength+strlen(offsetspages_suffix)+1,sizeof(char));
offsetspages_basename_ptr = &(offsetspages_filename[strlen(genomesubdir)+strlen("/")]);
- offsetspages_index1info_ptr = &(offsetspages_basename_ptr[patternlength]);
+ /* offsetspages_index1info_ptr = &(offsetspages_basename_ptr[patternlength]); */
sprintf(offsetspages_filename,"%s/",genomesubdir);
strncpy(offsetspages_basename_ptr,base_filename,rootlength);
@@ -1026,6 +1107,7 @@ Indexdb_get_filenames (int *compression_type,
}
+#if 0
void
Indexdb_shmem_remove (char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
#ifdef PMAP
@@ -1074,6 +1156,7 @@ Indexdb_shmem_remove (char *genomesubdir, char *fileroot, char *idx_filesuffix,
return;
}
+#endif
T
@@ -1083,16 +1166,19 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
Alphabet_T *alphabet, int *alphabet_size, Alphabet_T required_alphabet,
#endif
Width_T required_index1part, Width_T required_interval, bool expand_offsets_p,
- Access_mode_T offsetsstrm_access, Access_mode_T positions_access, bool sharedp) {
+ Access_mode_T offsetsstrm_access, Access_mode_T positions_access, bool sharedp,
+ bool multiple_sequences_p) {
T new = (T) MALLOC(sizeof(*new));
Filenames_T filenames;
Oligospace_T basespace, base;
- unsigned int poly_T;
- Positionsptr_T ptr0, end0; /* UINT8 or UINT4 */
- off_t filesize;
+ Oligospace_T poly_T;
+ /* Positionsptr_T ptr0; -- UINT8 or UINT4 */
+ Positionsptr_T end0; /* UINT8 or UINT4 */
+ size_t filesize;
#ifdef LARGE_GENOMES
+ int offsetspages_fd;
size_t offsetspages_len;
#endif
@@ -1132,8 +1218,14 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
fprintf(stderr,"Allocating memory for %s offsets, kmer %d, interval %d...",
idx_filesuffix,new->index1part,new->index1interval);
}
- new->offsetsstrm = (UINT4 *) Access_allocate(&new->offsetsstrm_shmid,&new->offsetsstrm_len,&seconds,
- filenames->offsets_filename,sizeof(UINT4),sharedp);
+ if (sharedp == true) {
+ new->offsetsstrm = (UINT4 *) Access_allocate_shared(&new->offsetsstrm_access,&new->offsetsstrm_shmid,&new->offsetsstrm_key,
+ &new->offsetsstrm_fd,&new->offsetsstrm_len,&seconds,
+ filenames->offsets_filename,sizeof(UINT4));
+ } else {
+ new->offsetsstrm = (UINT4 *) Access_allocate_private(&new->offsetsstrm_access,&new->offsetsstrm_len,&seconds,
+ filenames->offsets_filename,sizeof(UINT4));
+ }
if (new->offsetsstrm == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B))\n");
exit(9);
@@ -1141,11 +1233,6 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
comma = Genomicpos_commafmt(new->offsetsstrm_len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
FREE(comma);
- if (sharedp == true) {
- new->offsetsstrm_access = ALLOCATED_SHARED;
- } else {
- new->offsetsstrm_access = ALLOCATED_PRIVATE;
- }
}
#ifdef HAVE_MMAP
@@ -1175,7 +1262,7 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
} else if (offsetsstrm_access == USE_MMAP_ONLY) {
new->offsetsstrm = (UINT4 *) Access_mmap(&new->offsetsstrm_fd,&new->offsetsstrm_len,
- filenames->offsets_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->offsets_filename,/*randomp*/false);
if (new->offsetsstrm == NULL) {
fprintf(stderr,"Insufficient memory for mmap of %s (will use disk file instead, but program may not run)\n",
filenames->offsets_filename);
@@ -1246,18 +1333,22 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
#ifdef PMAP
#else
/* Sanity check on positions filesize */
- poly_T = ~(~0UL << 2*new->index1part);
+#ifdef HAVE_64_BIT
+ poly_T = ~(~0ULL << 2*new->index1part);
+#else
+ poly_T = ~(~0U << 2*new->index1part);
+#endif
end0 = new->offsetsstrm[poly_T+1];
#ifdef LARGE_GENOMES
- if ((filesize = Access_filesize(filenames->positions_high_filename)) != end0 * (off_t) sizeof(unsigned char)) {
+ if ((filesize = Access_filesize(filenames->positions_high_filename)) != end0 * sizeof(unsigned char)) {
fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n",
- filenames->positions_high_filename,end0*sizeof(unsigned char),filesize);
+ filenames->positions_high_filename,(size_t) (end0*sizeof(unsigned char)),filesize);
abort();
}
#endif
- if ((filesize = Access_filesize(filenames->positions_low_filename)) != end0 * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(filenames->positions_low_filename)) != end0 * sizeof(UINT4)) {
fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n",
- filenames->positions_low_filename,end0*sizeof(UINT4),filesize);
+ filenames->positions_low_filename,(size_t) (end0*sizeof(UINT4)),filesize);
abort();
}
#endif /* PMAP */
@@ -1268,10 +1359,8 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
#ifdef PMAP
*alphabet_size = Alphabet_get_size(*alphabet);
- /* new->blocksize = power(*alphabet_size,(*index1part) - new->offsetsstrm_basesize); */
-#else
- new->blocksize = 64; /* power(4,(*index1part) - new->offsetsstrm_basesize); */
#endif
+ new->blocksize = 64; /* Used to be determined by 4^(kmer - basesize), but now fixed at 64 */
/* offsetsmeta and offsetsmeta always ALLOCATED */
if (snps_root) {
@@ -1281,17 +1370,29 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
fprintf(stderr,"Allocating memory for %s offset pointers, kmer %d, interval %d...",
idx_filesuffix,new->index1part,new->index1interval);
}
- new->offsetsmeta = (UINT4 *) Access_allocate(&new->offsetsmeta_shmid,&new->offsetsmeta_len,&seconds,
- filenames->pointers_filename,sizeof(UINT4),sharedp);
- if (sharedp == true) {
- new->offsetsmeta_access = ALLOCATED_SHARED;
- } else {
- new->offsetsmeta_access = ALLOCATED_PRIVATE;
- }
+#ifdef HAVE_MMAP
+ if (multiple_sequences_p == false) {
+ new->offsetsmeta = (UINT4 *) Access_mmap(&new->offsetsmeta_fd,&new->offsetsmeta_len,
+ filenames->pointers_filename,/*randomp*/false);
+ new->offsetsmeta_access = MMAPPED;
+ } else
+#endif
+ if (sharedp == true) {
+ new->offsetsmeta = (UINT4 *) Access_allocate_shared(&new->offsetsmeta_access,&new->offsetsmeta_shmid,&new->offsetsmeta_key,
+ &new->offsetsmeta_fd,&new->offsetsmeta_len,&seconds,
+ filenames->pointers_filename,sizeof(UINT4));
+ } else {
+ new->offsetsmeta = (UINT4 *) Access_allocate_private(&new->offsetsmeta_access,&new->offsetsmeta_len,&seconds,
+ filenames->pointers_filename,sizeof(UINT4));
+ }
comma = Genomicpos_commafmt(new->offsetsmeta_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
+ }
+ fprintf(stderr,")\n");
/* offsetsstrm could be ALLOCATED or MMAPPED +/- PRELOAD */
if (offsetsstrm_access == USE_ALLOCATE) {
@@ -1302,8 +1403,14 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
fprintf(stderr,"Allocating memory for %s offsets, kmer %d, interval %d...",
idx_filesuffix,new->index1part,new->index1interval);
}
- new->offsetsstrm = (UINT4 *) Access_allocate(&new->offsetsstrm_shmid,&new->offsetsstrm_len,&seconds,
- filenames->offsets_filename,sizeof(UINT4),sharedp);
+ if (sharedp == true) {
+ new->offsetsstrm = (UINT4 *) Access_allocate_shared(&new->offsetsstrm_access,&new->offsetsstrm_shmid,&new->offsetsstrm_key,
+ &new->offsetsstrm_fd,&new->offsetsstrm_len,&seconds,
+ filenames->offsets_filename,sizeof(UINT4));
+ } else {
+ new->offsetsstrm = (UINT4 *) Access_allocate_private(&new->offsetsstrm_access,&new->offsetsstrm_len,&seconds,
+ filenames->offsets_filename,sizeof(UINT4));
+ }
if (new->offsetsstrm == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B))\n");
exit(9);
@@ -1311,11 +1418,6 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
comma = Genomicpos_commafmt(new->offsetsstrm_len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
FREE(comma);
- if (sharedp == true) {
- new->offsetsstrm_access = ALLOCATED_SHARED;
- } else {
- new->offsetsstrm_access = ALLOCATED_PRIVATE;
- }
}
#ifdef HAVE_MMAP
@@ -1345,7 +1447,7 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
} else if (offsetsstrm_access == USE_MMAP_ONLY) {
new->offsetsstrm = (UINT4 *) Access_mmap(&new->offsetsstrm_fd,&new->offsetsstrm_len,
- filenames->offsets_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->offsets_filename,/*randomp*/false);
if (new->offsetsstrm == NULL) {
fprintf(stderr,"Insufficient memory for mmap of %s (will use disk file instead, but program may not run)\n",
filenames->offsets_filename);
@@ -1373,11 +1475,20 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
/* Sanity check on positions filesize */
#ifdef LARGE_GENOMES
if (filenames->pages_filename != NULL) {
- new->offsetspages = (UINT4 *) Access_allocate(&new->offsetspages_shmid,&offsetspages_len,&seconds,filenames->pages_filename,sizeof(UINT4),sharedp);
+#ifdef HAVE_MMAP
+ if (multiple_sequences_p == false) {
+ new->offsetspages = (UINT4 *) Access_mmap(&new->offsetspages_fd,&new->offsetspages_len,
+ filenames->pages_filename,/*randomp*/false);
+ new->offsetspages_access = MMAPPED;
+ } else
+#endif
if (sharedp == true) {
- new->offsetspages_access = ALLOCATED_SHARED;
+ new->offsetspages = (UINT4 *) Access_allocate_shared(&new->offsetspages_access,&new->offsetspages_shmid,&new->offsetspages_key,
+ &offsetspages_fd,&offsetspages_len,&seconds,
+ filenames->pages_filename,sizeof(UINT4));
} else {
- new->offsetspages_access = ALLOCATED_PRIVATE;
+ new->offsetspages = (UINT4 *) Access_allocate_private(&new->offsetspages_access,&offsetspages_len,&seconds,
+ filenames->pages_filename,sizeof(UINT4));
}
} else {
new->offsetspages_access = ALLOCATED_PRIVATE;
@@ -1385,24 +1496,29 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
new->offsetspages[0] = -1U;
}
#endif
- poly_T = ~(~0UL << 2*new->index1part);
+#ifdef HAVE_64_BIT
+ poly_T = ~(~0ULL << 2*new->index1part);
+#else
+ poly_T = ~(~0U << 2*new->index1part);
+#endif
+
#ifdef LARGE_GENOMES
- ptr0 = Bitpack64_read_two_huge(&end0,poly_T,new->offsetspages,new->offsetsmeta,new->offsetsstrm);
+ /*ptr0 =*/ Bitpack64_read_two_huge(&end0,poly_T,new->offsetspages,new->offsetsmeta,new->offsetsstrm);
#else
- ptr0 = Bitpack64_read_two(&end0,poly_T,new->offsetsmeta,new->offsetsstrm);
+ /*ptr0 =*/ Bitpack64_read_two(&end0,poly_T,new->offsetsmeta,new->offsetsstrm);
#endif
#ifdef LARGE_GENOMES
- ptr0 = Bitpack64_read_two_huge(&end0,poly_T,new->offsetspages,new->offsetsmeta,new->offsetsstrm);
- if ((filesize = Access_filesize(filenames->positions_high_filename)) != end0 * (off_t) sizeof(unsigned char)) {
+ /*ptr0 =*/ Bitpack64_read_two_huge(&end0,poly_T,new->offsetspages,new->offsetsmeta,new->offsetsstrm);
+ if ((filesize = Access_filesize(filenames->positions_high_filename)) != end0 * sizeof(unsigned char)) {
fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n",
- filenames->positions_high_filename,end0*sizeof(unsigned char),filesize);
+ filenames->positions_high_filename,(size_t) (end0*sizeof(unsigned char)),filesize);
abort();
}
#endif
- if ((filesize = Access_filesize(filenames->positions_low_filename)) != end0 * (off_t) sizeof(UINT4)) {
+ if ((filesize = Access_filesize(filenames->positions_low_filename)) != end0 * sizeof(UINT4)) {
fprintf(stderr,"Something is wrong with the genomic index: expected file size for %s is %zu, but observed %zu.\n",
- filenames->positions_low_filename,end0*sizeof(UINT4),filesize);
+ filenames->positions_low_filename,(size_t) (end0*sizeof(UINT4)),filesize);
abort();
}
#endif /* PMAP */
@@ -1425,48 +1541,92 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
idx_filesuffix,new->index1part,new->index1interval);
}
#ifdef LARGE_GENOMES
- new->positions_high = (unsigned char *) Access_allocate(&new->positions_high_shmid,&new->positions_high_len,&seconds,
- filenames->positions_high_filename,sizeof(unsigned char),sharedp);
+#ifdef HAVE_MMAP
+ if (multiple_sequences_p == false) {
+ new->positions_high = (unsigned char *) Access_mmap(&new->positions_high_fd,&new->positions_high_len,
+ filenames->positions_high_filename,/*randomp*/false);
+ } else
+#endif
+ if (sharedp == true) {
+ new->positions_high = (unsigned char *) Access_allocate_shared(&new->positions_high_access,&new->positions_high_shmid,&new->positions_high_key,
+ &new->positions_high_fd,&new->positions_high_len,&seconds,
+ filenames->positions_high_filename,sizeof(unsigned char));
+ } else {
+ new->positions_high = (unsigned char *) Access_allocate_private(&new->positions_high_access,&new->positions_high_len,&seconds,
+ filenames->positions_high_filename,sizeof(unsigned char));
+ }
+
if (new->positions_high == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B)\n");
exit(9);
} else {
comma = Genomicpos_commafmt(new->positions_high_len);
- fprintf(stderr,"done (%s bytes, %.2f sec), ",comma,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
+ }
+ fprintf(stderr,")\n");
+
+#ifdef HAVE_MMAP
+ if (multiple_sequences_p == false) {
+ new->positions_low = (UINT4 *) Access_mmap(&new->positions_low_fd,&new->positions_low_len,
+ filenames->positions_low_filename,/*randomp*/false);
+ new->positions_low_access = MMAPPED;
+ } else
+#endif
+ if (sharedp == true) {
+ new->positions_low = (UINT4 *) Access_allocate_shared(&new->positions_low_access,&new->positions_low_shmid,&new->positions_low_key,
+ &new->positions_low_fd,&new->positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
+ } else {
+ new->positions_low = (UINT4 *) Access_allocate_private(&new->positions_low_access,&new->positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
+ }
- new->positions_low = (UINT4 *) Access_allocate(&new->positions_low_shmid,&new->positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),sharedp);
if (new->positions_low == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B)\n");
exit(9);
} else {
comma = Genomicpos_commafmt(new->positions_low_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
-
- if (sharedp == true) {
- new->positions_access = ALLOCATED_SHARED;
- } else {
- new->positions_access = ALLOCATED_PRIVATE;
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
}
+ fprintf(stderr,")\n");
}
}
#else
- new->positions = (UINT4 *) Access_allocate(&new->positions_shmid,&new->positions_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),sharedp);
+
+#ifdef HAVE_MMAP
+ if (multiple_sequences_p == false) {
+ new->positions = (UINT4 *) Access_mmap(&new->positions_fd,&new->positions_len,
+ filenames->positions_low_filename,/*randomp*/false);
+ new->positions_access = MMAPPED;
+ } else
+#endif
+
+ if (sharedp == true) {
+ new->positions = (UINT4 *) Access_allocate_shared(&new->positions_access,&new->positions_shmid,&new->positions_key,
+ &new->positions_fd,&new->positions_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
+ } else {
+ new->positions = (UINT4 *) Access_allocate_private(&new->positions_access,&new->positions_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
+ }
+
if (new->positions == NULL) {
fprintf(stderr,"insufficient memory (need to use a lower batch mode (-B)\n");
exit(9);
} else {
comma = Genomicpos_commafmt(new->positions_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
- if (sharedp == true) {
- new->positions_access = ALLOCATED_SHARED;
- } else {
- new->positions_access = ALLOCATED_PRIVATE;
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
}
+ fprintf(stderr,")\n");
}
#endif
@@ -1485,23 +1645,31 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
filenames->positions_high_filename,sizeof(unsigned char));
if (new->positions_high == NULL) {
fprintf(stderr,"insufficient memory (will use disk file instead, but program will be slow)\n");
- new->positions_access = FILEIO;
+ new->positions_high_access = FILEIO;
} else {
comma = Genomicpos_commafmt(new->positions_high_len);
- fprintf(stderr,"done (%s bytes, %d pages, %.2f sec), ",comma,npages,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
+ }
+ fprintf(stderr,")\n");
new->positions_low = (UINT4 *) Access_mmap_and_preload(&new->positions_low_fd,&new->positions_low_len,&npages,&seconds,
filenames->positions_low_filename,sizeof(UINT4));
if (new->positions_low == NULL) {
fprintf(stderr,"insufficient memory (will use disk file instead, but program will be slow)\n");
- new->positions_access = FILEIO;
+ new->positions_low_access = FILEIO;
} else {
comma = Genomicpos_commafmt(new->positions_low_len);
- fprintf(stderr,"done (%s bytes, %d pages, %.2f sec)\n",comma,npages,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
+ }
+ fprintf(stderr,")\n");
- new->positions_access = MMAPPED;
+ new->positions_low_access = MMAPPED;
}
}
#else
@@ -1512,8 +1680,12 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
new->positions_access = FILEIO;
} else {
comma = Genomicpos_commafmt(new->positions_len);
- fprintf(stderr,"done (%s bytes, %d pages, %.2f sec)\n",comma,npages,seconds);
+ fprintf(stderr,"done (%s bytes",comma);
FREE(comma);
+ if (multiple_sequences_p == true) {
+ fprintf(stderr,", %.2f sec",seconds);
+ }
+ fprintf(stderr,")\n");
new->positions_access = MMAPPED;
}
#endif
@@ -1521,25 +1693,25 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
} else if (positions_access == USE_MMAP_ONLY) {
#ifdef LARGE_GENOMES
new->positions_high = (unsigned char *) Access_mmap(&new->positions_high_fd,&new->positions_high_len,
- filenames->positions_high_filename,sizeof(unsigned char),/*randomp*/true);
+ filenames->positions_high_filename,/*randomp*/true);
if (new->positions_high == NULL) {
fprintf(stderr,"Insufficient memory for mmap of %s (will use disk file instead, but program will be slow)\n",
filenames->positions_high_filename);
- new->positions_access = FILEIO;
+ new->positions_high_access = FILEIO;
} else {
new->positions_low = (UINT4 *) Access_mmap(&new->positions_low_fd,&new->positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/true);
+ filenames->positions_low_filename,/*randomp*/true);
if (new->positions_low == NULL) {
fprintf(stderr,"Insufficient memory for mmap of %s (will use disk file instead, but program will be slow)\n",
filenames->positions_low_filename);
- new->positions_access = FILEIO;
+ new->positions_low_access = FILEIO;
} else {
- new->positions_access = MMAPPED;
+ new->positions_low_access = MMAPPED;
}
}
#else
new->positions = (UINT4 *) Access_mmap(&new->positions_fd,&new->positions_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/true);
+ filenames->positions_low_filename,/*randomp*/true);
if (new->positions == NULL) {
fprintf(stderr,"Insufficient memory for mmap of %s (will use disk file instead, but program will be slow)\n",
@@ -1553,17 +1725,28 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
#endif
} else if (positions_access == USE_FILEIO) {
+#ifdef LARGE_GENOMES
+ new->positions_high_access = FILEIO;
+ new->positions_low_access = FILEIO;
+#else
new->positions_access = FILEIO;
+#endif
} else {
fprintf(stderr,"Don't recognize positions_access %d\n",positions_access);
abort();
}
#ifdef HAVE_PTHREAD
+#ifdef LARGE_GENOMES
+ if (new->positions_high_access == FILEIO || new->positions_low_access == FILEIO) {
+ pthread_mutex_init(&new->positions_read_mutex,NULL);
+ }
+#else
if (new->positions_access == FILEIO) {
pthread_mutex_init(&new->positions_read_mutex,NULL);
}
#endif
+#endif
Filenames_free(&filenames);
@@ -1577,21 +1760,15 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
#ifndef PMAP
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
#if (defined(DEBUG0) || defined(DEBUG1) || defined(DEBUG2))
static char *
-shortoligo_nt (Storedoligomer_T oligo, Width_T oligosize) {
+shortoligo_nt (Oligospace_T oligo, Width_T oligosize) {
char *nt;
Width_T i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -1620,12 +1797,12 @@ shortoligo_nt (Storedoligomer_T oligo, Width_T oligosize) {
static void
-positions_move_absolute_1 (int positions_fd, off_t ptr) {
- off_t offset = ptr*((off_t) sizeof(unsigned char));
+positions_move_absolute_1 (int positions_fd, size_t ptr) {
+ off_t offset = ptr*sizeof(unsigned char);
if (lseek(positions_fd,offset,SEEK_SET) < 0) {
- fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",
- ptr,(int) sizeof(unsigned char),offset);
+ fprintf(stderr,"Attempted to do lseek on offset %zu*%zu=%zu\n",
+ ptr,sizeof(unsigned char),(size_t) offset);
perror("Error in indexdb.c, positions_move_absolute");
exit(9);
}
@@ -1633,12 +1810,12 @@ positions_move_absolute_1 (int positions_fd, off_t ptr) {
}
static void
-positions_move_absolute_4 (int positions_fd, off_t ptr) {
- off_t offset = ptr*((off_t) sizeof(UINT4));
+positions_move_absolute_4 (int positions_fd, size_t ptr) {
+ off_t offset = ptr*sizeof(UINT4);
if (lseek(positions_fd,offset,SEEK_SET) < 0) {
- fprintf(stderr,"Attempted to do lseek on offset %jd*%d=%jd\n",
- ptr,(int) sizeof(UINT4),offset);
+ fprintf(stderr,"Attempted to do lseek on offset %zu*%zu=%zu\n",
+ ptr,sizeof(UINT4),(size_t) offset);
perror("Error in indexdb.c, positions_move_absolute");
exit(9);
}
@@ -1806,34 +1983,34 @@ Indexdb_offsets_from_bitpack (char *offsetsmetafile, char *offsetsstrmfile,
Width_T index1part
#endif
) {
-#ifndef HAVE_MMAP
- int shmid;
-#endif
UINT4 *offsetsmeta;
UINT4 *offsetsstrm;
- int offsetsmeta_fd, offsetsstrm_fd;
size_t offsetsmeta_len, offsetsstrm_len;
Positionsptr_T *offsets = NULL;
Oligospace_T oligospace, oligoi;
-#ifndef PMAP
Blocksize_T blocksize;
-#endif
+#ifdef HAVE_MMAP
+ int offsetsmeta_fd, offsetsstrm_fd;
+#else
+ Access_T offsetsmeta_access, offsetsstrm_access;
double seconds;
+#endif
+
#ifdef PMAP
oligospace = power(alphabet_size,index1part_aa);
#else
oligospace = power(4,index1part);
- blocksize = 64;
#endif
+ blocksize = 64; /* Used to be determined by 4^(kmer - basesize), but now fixed at 64 */
#ifdef HAVE_MMAP
- offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,sizeof(UINT4),/*randomp*/false);
- offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,sizeof(UINT4),/*randomp*/false);
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
#else
- offsetsmeta = (UINT4 *) Access_allocate(&shmid,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4),/*sharedp*/false);
- offsetsstrm = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4),/*sharedp*/false);
+ offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
#endif
#ifdef OLIGOSPACE_NOT_LONG
@@ -1906,38 +2083,43 @@ Indexdb_offsets_from_bitpack_huge (char *offsetspagesfile, char *offsetsmetafile
UINT4 *offsetsmeta;
UINT4 *offsetsstrm;
- int shmid;
- int offsetsmeta_fd, offsetsstrm_fd;
size_t offsetspages_len, offsetsmeta_len, offsetsstrm_len;
Hugepositionsptr_T *offsets = NULL;
Oligospace_T oligospace, oligoi;
Blocksize_T blocksize;
+#ifdef HAVE_MMAP
+ int offsetsmeta_fd, offsetsstrm_fd;
+#else
+ Access_T offsetsmeta_access;
+#endif
+ Access_T offsetspages_access, offsetsstrm_access;
double seconds;
+
#ifdef PMAP
oligospace = power(alphabet_size,index1part_aa);
- /* blocksize = power(alphabet_size,index1part_aa - offsetsstrm_basesize); */
#else
oligospace = power(4,index1part);
- blocksize = 64;
#endif
+ blocksize = 64; /* Used to be determined by 4^(kmer - basesize), but now fixed at 64 */
if (blocksize == 1) {
- return (Hugepositionsptr_T *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(Hugepositionsptr_T),/*sharedp*/false);
+ return (Hugepositionsptr_T *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,
+ offsetsstrmfile,sizeof(Hugepositionsptr_T));
} else {
if (offsetspagesfile == NULL) {
offsetspages = (UINT4 *) MALLOC(1*sizeof(UINT4));
offsetspages[0] = -1U;
} else {
- offsetspages = (UINT4 *) Access_allocate(&shmid,&offsetspages_len,&seconds,offsetspagesfile,sizeof(UINT4),/*sharedp*/false);
+ offsetspages = (UINT4 *) Access_allocate_private(&offsetspages_access,&offsetspages_len,&seconds,offsetspagesfile,sizeof(UINT4));
}
#ifdef HAVE_MMAP
- offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,sizeof(UINT4),/*randomp*/false);
- offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,sizeof(UINT4),/*randomp*/false);
+ offsetsmeta = (UINT4 *) Access_mmap(&offsetsmeta_fd,&offsetsmeta_len,offsetsmetafile,/*randomp*/false);
+ offsetsstrm = (UINT4 *) Access_mmap(&offsetsstrm_fd,&offsetsstrm_len,offsetsstrmfile,/*randomp*/false);
#else
- offsetsmeta = (UINT4 *) Access_allocate(&shmid,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4),/*sharedp*/false);
- offsetsstrm = (UINT4 *) Access_allocate(&shmid,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4),/*sharedp*/false);
+ offsetsmeta = (UINT4 *) Access_allocate_private(&offsetsmeta_access,&offsetsmeta_len,&seconds,offsetsmetafile,sizeof(UINT4));
+ offsetsstrm = (UINT4 *) Access_allocate_private(&offsetsstrm_access,&offsetsstrm_len,&seconds,offsetsstrmfile,sizeof(UINT4));
#endif
#ifdef OLIGOSPACE_NOT_LONG
@@ -1996,11 +2178,12 @@ Indexdb_offsets_from_bitpack_huge (char *offsetspagesfile, char *offsetsmetafile
#endif
+
#ifdef PMAP
/* PMAP version. Doesn't mask bottom 12 nt. */
Univcoord_T *
-Indexdb_read (int *nentries, T this, Storedoligomer_T aaindex) {
+Indexdb_read (int *nentries, T this, Oligospace_T aaindex) {
Univcoord_T *positions, bigendian, littleendian;
Positionsptr_T ptr, ptr0, end0;
int i;
@@ -2052,6 +2235,8 @@ Indexdb_read (int *nentries, T this, Storedoligomer_T aaindex) {
if ((*nentries = end0 - ptr0) == 0) {
return NULL;
} else {
+ debug0(printf("Indexdb_read: offset pointers are %u and %u\n",ptr0,end0));
+
positions = (Univcoord_T *) CALLOC(*nentries,sizeof(Univcoord_T));
if (this->positions_access == FILEIO) {
#ifdef HAVE_PTHREAD
@@ -2132,10 +2317,10 @@ Indexdb_read (int *nentries, T this, Storedoligomer_T aaindex) {
/* GMAP version: Allocates memory */
Univcoord_T *
-Indexdb_read (int *nentries, T this, Storedoligomer_T oligo) {
+Indexdb_read (int *nentries, T this, Oligospace_T oligo) {
Univcoord_T *positions;
Positionsptr_T ptr0, end0;
- Storedoligomer_T part0;
+ Oligospace_T part0;
#ifdef WORDS_BIGENDIAN
int i;
Positionsptr_T ptr;
@@ -2208,26 +2393,37 @@ Indexdb_read (int *nentries, T this, Storedoligomer_T oligo) {
debug0(printf("Indexdb_read: offset pointers are %u and %u\n",ptr0,end0));
positions = (Univcoord_T *) CALLOC(*nentries,sizeof(Univcoord_T));
- if (this->positions_access == FILEIO) {
+#ifdef LARGE_GENOMES
+ if (this->positions_high_access == FILEIO || this->positions_low_access == FILEIO) {
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&this->positions_read_mutex);
#endif
-#ifdef LARGE_GENOMES
positions_move_absolute_1(this->positions_high_fd,ptr0);
positions_move_absolute_4(this->positions_low_fd,ptr0);
positions_read_multiple_large(this->positions_high_fd,this->positions_low_fd,positions,*nentries);
+#ifdef HAVE_PTHREAD
+ pthread_mutex_unlock(&this->positions_read_mutex);
+#endif
+
+ } else if (this->positions_high_access == ALLOCATED_PRIVATE || this->positions_high_access == ALLOCATED_SHARED ||
+ this->positions_low_access == ALLOCATED_PRIVATE || this->positions_low_access == ALLOCATED_SHARED) {
+ positions_copy_multiple_large(positions,&(this->positions_high[ptr0]),&(this->positions_low[ptr0]),*nentries);
+
#else
+
+ if (this->positions_access == FILEIO) {
+#ifdef HAVE_PTHREAD
+ pthread_mutex_lock(&this->positions_read_mutex);
+#endif
positions_move_absolute_4(this->positions_fd,ptr0);
positions_read_multiple(this->positions_fd,positions,*nentries);
-#endif
#ifdef HAVE_PTHREAD
pthread_mutex_unlock(&this->positions_read_mutex);
#endif
+
} else if (this->positions_access == ALLOCATED_PRIVATE || this->positions_access == ALLOCATED_SHARED) {
-#ifdef LARGE_GENOMES
- positions_copy_multiple_large(positions,&(this->positions_high[ptr0]),&(this->positions_low[ptr0]),*nentries);
-#else
memcpy(positions,&(this->positions[ptr0]),(*nentries)*sizeof(Univcoord_T));
+
#endif
} else {
@@ -2290,9 +2486,9 @@ Indexdb_read_inplace (int *nentries,
#ifdef LARGE_GENOMES
unsigned char **positions_high,
#endif
- T this, Storedoligomer_T oligo) {
+ T this, Oligospace_T oligo) {
Positionsptr_T ptr0, end0;
- Storedoligomer_T part0;
+ Oligospace_T part0;
#ifdef DEBUG0
Positionsptr_T ptr;
#endif
@@ -2339,8 +2535,14 @@ Indexdb_read_inplace (int *nentries,
if (*nentries == 0) {
return NULL;
+#ifdef LARGE_GENOMES
+ } else if (this->positions_high_access == FILEIO || this->positions_low_access == FILEIO) {
+ abort();
+#else
} else if (this->positions_access == FILEIO) {
abort();
+#endif
+
} else {
#ifdef LARGE_GENOMES
debug0(
@@ -2372,7 +2574,7 @@ Indexdb_read_inplace (int *nentries,
/* Analogous to Indexdb_read, except this includes diagterm. Always allocates memory. */
Univcoord_T *
-Indexdb_read_with_diagterm (int *nentries, T this, Storedoligomer_T oligo, int diagterm) {
+Indexdb_read_with_diagterm (int *nentries, T this, Oligospace_T oligo, int diagterm) {
Univcoord_T *positions;
Positionsptr_T ptr0, end0, ptr;
int i;
@@ -2404,31 +2606,42 @@ Indexdb_read_with_diagterm (int *nentries, T this, Storedoligomer_T oligo, int d
return (Univcoord_T *) NULL;
} else {
positions = (Univcoord_T *) CALLOC(*nentries,sizeof(Univcoord_T));
- if (this->positions_access == FILEIO) {
+
+#ifdef LARGE_GENOMES
+ if (this->positions_high_access == FILEIO || this->positions_low_access == FILEIO) {
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&this->positions_read_mutex);
#endif
-#ifdef LARGE_GENOMES
positions_move_absolute_1(this->positions_high_fd,ptr0);
positions_move_absolute_4(this->positions_low_fd,ptr0);
positions_read_multiple_large(this->positions_high_fd,this->positions_low_fd,positions,*nentries);
-#else
- positions_move_absolute_4(this->positions_fd,ptr0);
- positions_read_multiple(this->positions_fd,positions,*nentries);
-#endif
#ifdef HAVE_PTHREAD
pthread_mutex_unlock(&this->positions_read_mutex);
#endif
- } else if (this->positions_access == ALLOCATED_PRIVATE || this->positions_access == ALLOCATED_SHARED) {
-#ifdef LARGE_GENOMES
+ } else if (this->positions_high_access == ALLOCATED_PRIVATE || this->positions_high_access == ALLOCATED_SHARED ||
+ this->positions_low_access == ALLOCATED_PRIVATE || this->positions_low_access == ALLOCATED_SHARED) {
for (ptr = ptr0, i = 0; ptr < end0; ptr++) {
positions[i++] = ((Univcoord_T) this->positions_high[ptr] << 32) + this->positions_low[ptr] + diagterm;
}
+
#else
+
+ if (this->positions_access == FILEIO) {
+#ifdef HAVE_PTHREAD
+ pthread_mutex_lock(&this->positions_read_mutex);
+#endif
+ positions_move_absolute_4(this->positions_fd,ptr0);
+ positions_read_multiple(this->positions_fd,positions,*nentries);
+#ifdef HAVE_PTHREAD
+ pthread_mutex_unlock(&this->positions_read_mutex);
+#endif
+
+ } else if (this->positions_access == ALLOCATED_PRIVATE || this->positions_access == ALLOCATED_SHARED) {
for (ptr = ptr0, i = 0; ptr < end0; ptr++) {
positions[i++] = this->positions[ptr] + diagterm;
}
+
#endif
} else {
@@ -2471,7 +2684,7 @@ Indexdb_read_with_diagterm (int *nentries, T this, Storedoligomer_T oligo, int d
/* Analogous to Indexdb_read, except this includes diagterm. Always allocates memory. */
Univcoord_T *
-Indexdb_read_with_diagterm_sizelimit (int *nentries, T this, Storedoligomer_T oligo, int diagterm,
+Indexdb_read_with_diagterm_sizelimit (int *nentries, T this, Oligospace_T oligo, int diagterm,
int size_threshold) {
Univcoord_T *positions;
Positionsptr_T ptr0, end0, ptr;
@@ -2510,29 +2723,40 @@ Indexdb_read_with_diagterm_sizelimit (int *nentries, T this, Storedoligomer_T ol
} else {
positions = (Univcoord_T *) CALLOC(*nentries,sizeof(Univcoord_T));
- if (this->positions_access == FILEIO) {
+
+#ifdef LARGE_GENOMES
+
+ if (this->positions_high_access == FILEIO || this->positions_low_access == FILEIO) {
#ifdef HAVE_PTHREAD
pthread_mutex_lock(&this->positions_read_mutex);
#endif
-#ifdef LARGE_GENOMES
positions_move_absolute_1(this->positions_high_fd,ptr0);
positions_move_absolute_4(this->positions_low_fd,ptr0);
positions_read_multiple_large(this->positions_high_fd,this->positions_low_fd,positions,*nentries);
+#ifdef HAVE_PTHREAD
+ pthread_mutex_unlock(&this->positions_read_mutex);
+#endif
+
+ } else if (this->positions_high_access == ALLOCATED_PRIVATE || this->positions_high_access == ALLOCATED_SHARED ||
+ this->positions_low_access == ALLOCATED_PRIVATE || this->positions_low_access == ALLOCATED_SHARED) {
+ for (ptr = ptr0, i = 0; ptr < end0; ptr++) {
+ positions[i++] = ((Univcoord_T) this->positions_high[ptr] << 32) + this->positions_low[ptr] + diagterm;
+ }
+
#else
+
+ if (this->positions_access == FILEIO) {
+#ifdef HAVE_PTHREAD
+ pthread_mutex_lock(&this->positions_read_mutex);
+#endif
positions_move_absolute_4(this->positions_fd,ptr0);
positions_read_multiple(this->positions_fd,positions,*nentries);
-#endif
#ifdef HAVE_PTHREAD
pthread_mutex_unlock(&this->positions_read_mutex);
#endif
} else if (this->positions_access == ALLOCATED_PRIVATE || this->positions_access == ALLOCATED_SHARED) {
-#ifdef LARGE_GENOMES
- for (ptr = ptr0, i = 0; ptr < end0; ptr++) {
- positions[i++] = ((Univcoord_T) this->positions_high[ptr] << 32) + this->positions_low[ptr] + diagterm;
- }
-#else
for (ptr = ptr0, i = 0; ptr < end0; ptr++) {
positions[i++] = this->positions[ptr] + diagterm;
}
@@ -2598,14 +2822,19 @@ Indexdb_new_segment (char *genomicseg,
Oligospace_T oligospace, oligoi;
char *p;
Univcoord_T position = 0UL;
+
+#ifdef HAVE_64_BIT
+ Oligospace_T oligo = 0U, masked, mask;
+#else
+ Shortoligomer_T high = 0U, low = 0U, carry;
+#endif
+
#ifdef PMAP
int frame = -1, between_counter[3], in_counter[3];
- Storedoligomer_T high = 0U, low = 0U, carry;
- Storedoligomer_T aaindex;
+ Oligospace_T aaindex;
int index1part_nt = 3*index1part_aa;
#else
- int between_counter = 0, in_counter = 0;
- Storedoligomer_T oligo = 0U, masked, mask;
+ int between_counter, in_counter;
#endif
uppercaseCode = UPPERCASE_U2T;
@@ -2615,13 +2844,19 @@ Indexdb_new_segment (char *genomicseg,
between_counter[0] = between_counter[1] = between_counter[2] = 0;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
new->index1part = index1part_aa;
+
+#else
+#ifdef HAVE_64_BIT
+ mask = ~(~0ULL << 2*index1part);
#else
- mask = ~(~0UL << 2*index1part);
+ mask = ~(~0U << 2*index1part);
+#endif
oligospace = power(4,index1part);
+ between_counter = in_counter = 0;
new->index1part = index1part;
#endif
- new->index1interval = 1;
+ new->index1interval = 1;
new->compression_type = NO_COMPRESSION;
new->offsetsmeta = (UINT4 *) CALLOC(oligospace+1,sizeof(UINT4));
@@ -2646,49 +2881,72 @@ Indexdb_new_segment (char *genomicseg,
in_counter++;
#endif
+#ifdef HAVE_64_BIT
+ switch (uppercaseCode[c]) {
+ case 'A': oligo = (oligo << 2); break;
+ case 'C': oligo = (oligo << 2) | 1U; break;
+ case 'G': oligo = (oligo << 2) | 2U; break;
+ case 'T': oligo = (oligo << 2) | 3U; break;
+ default:
+ oligo = 0U;
#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
+ }
+
+#else
carry = (low >> 30);
switch (uppercaseCode[c]) {
case 'A': low = (low << 2); break;
case 'C': low = (low << 2) | 1U; break;
case 'G': low = (low << 2) | 2U; break;
case 'T': low = (low << 2) | 3U; break;
- default:
- high = low = carry = 0U;
+ default:
+ high = low = carry = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
break;
}
high = (high << 2) | carry;
-#else
- switch (uppercaseCode[c]) {
- case 'A': oligo = (oligo << 2); break;
- case 'C': oligo = (oligo << 2) | 1U; break;
- case 'G': oligo = (oligo << 2) | 2U; break;
- case 'T': oligo = (oligo << 2) | 3U; break;
- default: oligo = 0U; in_counter = 0; break;
- }
#endif
- /*
- debug(printf("char=%c bc=%d ic=%d oligo=%016lX\n",
- c,between_counter,in_counter,oligo));
- */
-
#ifdef PMAP
if (in_counter[frame] > 0) {
if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_fwd(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
} else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_rev(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
}
}
if (in_counter[frame] == index1part_aa + 1) {
if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
+#endif
#ifdef OLIGOSPACE_NOT_LONG
oligoi = (Oligospace_T) aaindex + 1U;
#else
@@ -2742,14 +3000,18 @@ Indexdb_new_segment (char *genomicseg,
/* Create positions */
position = 0U;
+#ifdef HAVE_64_BIT
+ oligo = 0ULL;
+#else
+ high = low = 0U;
+#endif
+
#ifdef PMAP
frame = -1;
between_counter[0] = between_counter[1] = between_counter[2] = 0;
in_counter[0] = in_counter[1] = in_counter[2] = 0;
- high = low = 0U;
#else
between_counter = in_counter = 0;
- oligo = 0UL;
#endif
work_offsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
@@ -2782,50 +3044,73 @@ Indexdb_new_segment (char *genomicseg,
in_counter++;
#endif
-#ifdef PMAP
- carry = (low >> 30);
+#ifdef HAVE_64_BIT
switch (uppercaseCode[c]) {
- case 'A': low = (low << 2); break;
- case 'C': low = (low << 2) | 1; break;
- case 'G': low = (low << 2) | 2; break;
- case 'T': low = (low << 2) | 3; break;
+ case 'A': oligo = (oligo << 2); break;
+ case 'C': oligo = (oligo << 2) | 1U; break;
+ case 'G': oligo = (oligo << 2) | 2U; break;
+ case 'T': oligo = (oligo << 2) | 3U; break;
default:
- high = low = carry = 0U;
+ oligo = 0U;
+#ifdef PMAP
in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
break;
}
- high = (high << 2) | carry;
+
#else
+ carry = (low >> 30);
switch (uppercaseCode[c]) {
- case 'A': oligo = (oligo << 2); break;
- case 'C': oligo = (oligo << 2) | 1; break;
- case 'G': oligo = (oligo << 2) | 2; break;
- case 'T': oligo = (oligo << 2) | 3; break;
- default: oligo = 0U; in_counter = 0; break;
+ case 'A': low = (low << 2); break;
+ case 'C': low = (low << 2) | 1U; break;
+ case 'G': low = (low << 2) | 2U; break;
+ case 'T': low = (low << 2) | 3U; break;
+ default:
+ high = low = carry = 0U;
+#ifdef PMAP
+ in_counter[0] = in_counter[1] = in_counter[2] = 0;
+#else
+ in_counter = 0;
+#endif
+ break;
}
+ high = (high << 2) | carry;
#endif
- /*
- debug(printf("char=%c bc=%d ic=%d oligo=%06X\n",
- c,between_counter,in_counter,oligo));
- */
-
#ifdef PMAP
if (in_counter[frame] > 0) {
if (watsonp == true) {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_fwd(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_fwd(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
} else {
+#ifdef HAVE_64_BIT
+ if (Alphabet_get_codon_rev(oligo) == AA_STOP) {
+ in_counter[frame] = 0;
+ }
+#else
if (Alphabet_get_codon_rev(low) == AA_STOP) {
in_counter[frame] = 0;
}
+#endif
}
}
if (in_counter[frame] == index1part_aa + 1) {
if (between_counter[frame] >= index1interval) {
+#ifdef HAVE_64_BIT
+ aaindex = Alphabet_get_aa_index(oligo,watsonp,index1part_nt);
+#else
aaindex = Alphabet_get_aa_index(high,low,watsonp,index1part_nt);
+#endif
if (watsonp == true) {
new->positions[work_offsets[aaindex]++] = position-index1part_nt+1;
} else {
@@ -2869,6 +3154,7 @@ Indexdb_new_segment (char *genomicseg,
#endif
+#if 0
int
Storedoligomer_compare (const void *a, const void *b) {
Storedoligomer_T x = * (Storedoligomer_T *) a;
@@ -2882,4 +3168,5 @@ Storedoligomer_compare (const void *a, const void *b) {
return 0;
}
}
+#endif
diff --git a/src/indexdb.h b/src/indexdb.h
index fc83843..0335c57 100644
--- a/src/indexdb.h
+++ b/src/indexdb.h
@@ -1,4 +1,4 @@
-/* $Id: indexdb.h 161940 2015-03-25 20:36:59Z twu $ */
+/* $Id: indexdb.h 183995 2016-02-09 18:55:29Z twu $ */
#ifndef INDEXDB_INCLUDED
#define INDEXDB_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -90,7 +90,11 @@ Indexdb_get_filenames_no_compression (Width_T *index1part, Width_T *index1interv
char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
Width_T required_interval, bool offsets_only_p);
extern Filenames_T
-Indexdb_get_filenames_bitpack (Width_T *index1part, Width_T *index1interval,
+Indexdb_get_filenames_bitpack (
+#ifdef PMAP
+ Alphabet_T *alphabet, Alphabet_T required_alphabet,
+#endif
+ Width_T *index1part, Width_T *index1interval,
char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
Width_T required_index1part, Width_T required_interval,
Blocksize_T blocksize, bool offsets_only_p);
@@ -106,9 +110,9 @@ Indexdb_get_filenames (int *compression_type,
bool offsets_only_p);
extern Univcoord_T *
-Indexdb_point_one_shift (int *nentries, T this, Storedoligomer_T subst);
+Indexdb_point_one_shift (int *nentries, T this, Oligospace_T subst);
extern int
-Indexdb_count_one_shift (T this, Storedoligomer_T subst, int nadjacent);
+Indexdb_count_one_shift (T this, Oligospace_T subst, int nadjacent);
extern Positionsptr_T *
@@ -131,12 +135,14 @@ Indexdb_offsets_from_bitpack_huge (char *bitpackpagesfile, char *offsetsmetafile
);
#endif
+#if 0
extern void
Indexdb_shmem_remove (char *genomesubdir, char *fileroot, char *idx_filesuffix, char *snps_root,
#ifdef PMAP
Alphabet_T *alphabet, int *alphabet_size, Alphabet_T required_alphabet,
#endif
Width_T required_index1part, Width_T required_interval, bool expand_offsets_p);
+#endif
extern T
Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
@@ -145,7 +151,8 @@ Indexdb_new_genome (Width_T *index1part, Width_T *index1interval,
Alphabet_T *alphabet, int *alphabet_size, Alphabet_T required_alphabet,
#endif
Width_T required_index1part, Width_T required_interval, bool expand_offsets_p,
- Access_mode_T offsetsstrm_access, Access_mode_T positions_access, bool sharedp);
+ Access_mode_T offsetsstrm_access, Access_mode_T positions_access, bool sharedp,
+ bool multiple_sequences_p);
#ifndef UTILITYP
extern T
Indexdb_new_segment (char *genomicseg,
@@ -159,27 +166,24 @@ Indexdb_new_segment (char *genomicseg,
#ifdef PMAP
extern Univcoord_T *
-Indexdb_read (int *nentries, T this, Storedoligomer_T aaindex);
+Indexdb_read (int *nentries, T this, Oligospace_T aaindex);
#else
extern Univcoord_T *
-Indexdb_read (int *nentries, T this, Storedoligomer_T oligo);
+Indexdb_read (int *nentries, T this, Oligospace_T oligo);
extern UINT4 *
Indexdb_read_inplace (int *nentries,
#ifdef LARGE_GENOMES
unsigned char **positions_high,
#endif
- T this, Storedoligomer_T oligo);
+ T this, Oligospace_T oligo);
#endif
extern Univcoord_T *
-Indexdb_read_with_diagterm (int *nentries, T this, Storedoligomer_T oligo, int diagterm);
+Indexdb_read_with_diagterm (int *nentries, T this, Oligospace_T oligo, int diagterm);
extern Univcoord_T *
-Indexdb_read_with_diagterm_sizelimit (int *nentries, T this, Storedoligomer_T oligo, int diagterm,
+Indexdb_read_with_diagterm_sizelimit (int *nentries, T this, Oligospace_T oligo, int diagterm,
int size_threshold);
-extern int
-Storedoligomer_compare (const void *a, const void *b);
-
#undef T
#endif
diff --git a/src/indexdb_hr.c b/src/indexdb_hr.c
index 0ba9fb2..63bb08a 100644
--- a/src/indexdb_hr.c
+++ b/src/indexdb_hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: indexdb_hr.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: indexdb_hr.c 184203 2016-02-13 03:46:21Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -98,18 +98,30 @@ static char rcsid[] = "$Id: indexdb_hr.c 168395 2015-06-26 17:13:13Z twu $";
#define T Indexdb_T
static int index1part; /* For debugging */
-static unsigned int kmer_mask; /* Was LOW12MER 0x00FFFFFF */
+static Oligospace_T kmer_mask; /* Was LOW12MER 0x00FFFFFF */
+#ifdef HAVE_64_BIT
+ /*8765432187654321*/
+#define right_subst 0x0000000000000001
+#else
+ /*87654321*/
#define right_subst 0x00000001
-static unsigned int left_subst; /* Was LEFT_SUBST 0x00100000 */
-static unsigned int top_subst; /* Was TOP_SUBST 0x00400000 */
+#endif
+static Oligospace_T left_subst; /* Was LEFT_SUBST 0x00100000 */
+static Oligospace_T top_subst; /* Was TOP_SUBST 0x00400000 */
void
Indexdb_hr_setup (int index1part_in) {
index1part = index1part_in;
- kmer_mask = ~(~0UL << 2*index1part);
+#ifdef HAVE_64_BIT
+ kmer_mask = ~(~0ULL << 2*index1part);
+ top_subst = (1ULL << 2*(index1part-1));
+ left_subst = (1ULL << 2*(index1part-2));
+#else
+ kmer_mask = ~(~0U << 2*index1part);
+ top_subst = (1U << 2*(index1part-1));
+ left_subst = (1U << 2*(index1part-2));
+#endif
- top_subst = (1 << 2*(index1part-1));
- left_subst = (1 << 2*(index1part-2));
return;
}
@@ -581,7 +593,7 @@ merge_batches_one_heap_4_existing (int *nmerged, struct Batch_T *batchpool, int
/************************************************************************
- * The following positions functions are take from indexdb.c
+ * The following positions functions are taken from indexdb.c
************************************************************************/
#ifndef LARGE_GENOMES
@@ -590,7 +602,7 @@ positions_move_absolute (int positions_fd, Positionsptr_T ptr) {
off_t offset = ptr*((off_t) sizeof(Univcoord_T));
if (lseek(positions_fd,offset,SEEK_SET) < 0) {
- fprintf(stderr,"Attempted to do lseek on offset %zd*%d=%zd\n",
+ fprintf(stderr,"Attempted to do lseek on offset %u*%d=%zd\n",
ptr,(int) sizeof(Univcoord_T),offset);
perror("Error in indexdb.c, positions_move_absolute_4");
exit(9);
@@ -643,7 +655,7 @@ positions_read_multiple (int positions_fd, Univcoord_T *values, int n) {
#ifdef LARGE_GENOMES
static UINT4 *
-point_one_shift (int *nentries, unsigned char **positions_high, T this, Storedoligomer_T subst) {
+point_one_shift (int *nentries, unsigned char **positions_high, T this, Oligospace_T subst) {
UINT4 *positions_low;
Positionsptr_T ptr0, end0;
#ifdef DEBUG
@@ -669,7 +681,7 @@ point_one_shift (int *nentries, unsigned char **positions_high, T this, Storedol
*positions_high = (unsigned char *) NULL;
return (UINT4 *) NULL;
} else {
- if (this->positions_access == FILEIO) {
+ if (this->positions_high_access == FILEIO || this->positions_low_access == FILEIO) {
abort();
} else {
@@ -693,7 +705,7 @@ point_one_shift (int *nentries, unsigned char **positions_high, T this, Storedol
#else
static Univcoord_T *
-point_one_shift (int *nentries, T this, Storedoligomer_T subst) {
+point_one_shift (int *nentries, T this, Oligospace_T subst) {
Univcoord_T *positions;
Positionsptr_T ptr0, end0;
#ifdef DEBUG
@@ -769,22 +781,15 @@ point_one_shift (int *nentries, T this, Storedoligomer_T subst) {
#endif
-
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
#ifdef DEBUG
static char *
-shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
+shortoligo_nt (Oligospace_T oligo, int oligosize) {
char *nt;
int i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -807,7 +812,7 @@ shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
#ifdef LARGE_GENOMES
static int
-count_one_shift (T this, Storedoligomer_T subst, int nadjacent) {
+count_one_shift (T this, Oligospace_T subst, int nadjacent) {
Positionsptr_T ptr0, end0;
if (this->compression_type == NO_COMPRESSION) {
@@ -844,7 +849,7 @@ count_one_shift (T this, Storedoligomer_T subst, int nadjacent) {
#else
static int
-count_one_shift (T this, Storedoligomer_T subst, int nadjacent) {
+count_one_shift (T this, Oligospace_T subst, int nadjacent) {
Positionsptr_T ptr0, end0;
if (this->compression_type == NO_COMPRESSION) {
@@ -887,10 +892,11 @@ count_one_shift (T this, Storedoligomer_T subst, int nadjacent) {
************************************************************************/
/* Don't mask out leftmost nucleotides with LOWXXMER */
+/* TODO: Eliminate the loop by implementing a single procedure in bitpack64-readtwo that counts over the base */
int
-Indexdb_count_left_subst_2 (T this, Storedoligomer_T oligo) {
+Indexdb_count_left_subst_2 (T this, Oligospace_T oligo) {
int nentries = 0;
- Storedoligomer_T base;
+ Oligospace_T base;
int i;
debug(printf("count_left_subst_2: oligo = %06X (%s)\n",oligo,shortoligo_nt(oligo,index1part)));
@@ -919,10 +925,11 @@ Indexdb_count_left_subst_2 (T this, Storedoligomer_T oligo) {
/* Don't mask out leftmost nucleotides with LOWXXMER */
+/* TODO: Eliminate the loop by implementing a single procedure in bitpack64-readtwo that counts over the base */
int
-Indexdb_count_left_subst_1 (T this, Storedoligomer_T oligo) {
+Indexdb_count_left_subst_1 (T this, Oligospace_T oligo) {
int nentries = 0;
- Storedoligomer_T base;
+ Oligospace_T base;
int i;
debug(printf("count_left_subst_1: oligo = %06X (%s)\n",oligo,shortoligo_nt(oligo,index1part)));
@@ -950,9 +957,9 @@ Indexdb_count_left_subst_1 (T this, Storedoligomer_T oligo) {
int
-Indexdb_count_right_subst_2 (T this, Storedoligomer_T oligo) {
+Indexdb_count_right_subst_2 (T this, Oligospace_T oligo) {
int nentries;
- Storedoligomer_T base;
+ Oligospace_T base;
#ifdef ALLOW_DUPLICATES
int i;
#endif
@@ -988,9 +995,9 @@ Indexdb_count_right_subst_2 (T this, Storedoligomer_T oligo) {
int
-Indexdb_count_right_subst_1 (T this, Storedoligomer_T oligo) {
+Indexdb_count_right_subst_1 (T this, Oligospace_T oligo) {
int nentries;
- Storedoligomer_T base;
+ Oligospace_T base;
#ifdef ALLOW_DUPLICATES
int i;
#endif
@@ -1167,9 +1174,9 @@ Compoundpos_free (Compoundpos_T *old) {
Compoundpos_T
-Indexdb_compoundpos_left_subst_2 (T this, Storedoligomer_T oligo) {
+Indexdb_compoundpos_left_subst_2 (T this, Oligospace_T oligo) {
Compoundpos_T compoundpos = (Compoundpos_T) MALLOC(sizeof(*compoundpos));
- Storedoligomer_T base;
+ Oligospace_T base;
int i;
debug(printf("compoundpos_left_subst_2: %06X (%s)\n",oligo,shortoligo_nt(oligo,index1part)));
@@ -1193,9 +1200,9 @@ Indexdb_compoundpos_left_subst_2 (T this, Storedoligomer_T oligo) {
}
Compoundpos_T
-Indexdb_compoundpos_left_subst_1 (T this, Storedoligomer_T oligo) {
+Indexdb_compoundpos_left_subst_1 (T this, Oligospace_T oligo) {
Compoundpos_T compoundpos = (Compoundpos_T) MALLOC(sizeof(*compoundpos));
- Storedoligomer_T base;
+ Oligospace_T base;
int i;
debug(printf("compoundpos_left_subst_1: %06X (%s)\n",oligo,shortoligo_nt(oligo,index1part)));
@@ -1219,9 +1226,9 @@ Indexdb_compoundpos_left_subst_1 (T this, Storedoligomer_T oligo) {
}
Compoundpos_T
-Indexdb_compoundpos_right_subst_2 (T this, Storedoligomer_T oligo) {
+Indexdb_compoundpos_right_subst_2 (T this, Oligospace_T oligo) {
Compoundpos_T compoundpos = (Compoundpos_T) MALLOC(sizeof(*compoundpos));
- Storedoligomer_T base;
+ Oligospace_T base;
int i;
debug(printf("compoundpos_right_subst_2: %06X (%s)\n",oligo,shortoligo_nt(oligo,index1part)));
@@ -1245,9 +1252,9 @@ Indexdb_compoundpos_right_subst_2 (T this, Storedoligomer_T oligo) {
}
Compoundpos_T
-Indexdb_compoundpos_right_subst_1 (T this, Storedoligomer_T oligo) {
+Indexdb_compoundpos_right_subst_1 (T this, Oligospace_T oligo) {
Compoundpos_T compoundpos = (Compoundpos_T) MALLOC(sizeof(*compoundpos));
- Storedoligomer_T base;
+ Oligospace_T base;
int i;
debug(printf("compoundpos_right_subst_1: %06X (%s)\n",oligo,shortoligo_nt(oligo,index1part)));
@@ -1435,6 +1442,7 @@ Compoundpos_heap_init (Compoundpos_T compoundpos, int querylength, int diagterm)
}
+#if 0
/* Used by DEBUG3 and DEBUG6 */
static void
heap_even_dump (Batch_T *heap, int heapsize) {
@@ -1443,10 +1451,11 @@ heap_even_dump (Batch_T *heap, int heapsize) {
for (i = 1; i <= heapsize; i++) {
batch = heap[i];
- printf("#%d--%d:%u ",i,batch->nentries,batch->position);
+ printf("#%d--%d:%llu ",i,batch->nentries,(unsigned long long) batch->position);
}
printf("\n");
}
+#endif
@@ -1843,7 +1852,7 @@ Indexdb_merge_compoundpos (int *nmerged, Compoundpos_T compoundpos, int diagterm
/* Should be the same as count_one_shift(this,oligo,1) */
int
-Indexdb_count_no_subst (T this, Storedoligomer_T oligo) {
+Indexdb_count_no_subst (T this, Oligospace_T oligo) {
Positionsptr_T ptr0, end0;
if (this->compression_type == NO_COMPRESSION) {
diff --git a/src/indexdb_hr.h b/src/indexdb_hr.h
index f8224ff..1d9771c 100644
--- a/src/indexdb_hr.h
+++ b/src/indexdb_hr.h
@@ -1,4 +1,4 @@
-/* $Id: indexdb_hr.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: indexdb_hr.h 180341 2015-12-07 18:29:40Z twu $ */
#ifndef INDEXDB_HR_INCLUDED
#define INDEXDB_HR_INCLUDED
@@ -34,36 +34,36 @@ Compoundpos_find (bool *emptyp, Compoundpos_T compoundpos, Univcoord_T local_goa
extern int
Compoundpos_search (Univcoord_T *value, Compoundpos_T compoundpos, Univcoord_T local_goal);
extern Compoundpos_T
-Indexdb_compoundpos_left_subst_2 (T this, Storedoligomer_T oligo);
+Indexdb_compoundpos_left_subst_2 (T this, Oligospace_T oligo);
extern Compoundpos_T
-Indexdb_compoundpos_left_subst_1 (T this, Storedoligomer_T oligo);
+Indexdb_compoundpos_left_subst_1 (T this, Oligospace_T oligo);
extern Compoundpos_T
-Indexdb_compoundpos_right_subst_2 (T this, Storedoligomer_T oligo);
+Indexdb_compoundpos_right_subst_2 (T this, Oligospace_T oligo);
extern Compoundpos_T
-Indexdb_compoundpos_right_subst_1 (T this, Storedoligomer_T oligo);
+Indexdb_compoundpos_right_subst_1 (T this, Oligospace_T oligo);
extern Univcoord_T *
Indexdb_merge_compoundpos (int *nmerged, Compoundpos_T compoundpos, int diagterm);
extern Univcoord_T *
-Indexdb_read_left_subst_2 (int *npositions, T this, Storedoligomer_T oligo);
+Indexdb_read_left_subst_2 (int *npositions, T this, Oligospace_T oligo);
extern Univcoord_T *
-Indexdb_read_left_subst_1 (int *npositions, T this, Storedoligomer_T oligo);
+Indexdb_read_left_subst_1 (int *npositions, T this, Oligospace_T oligo);
extern Univcoord_T *
-Indexdb_read_right_subst_2 (int *npositions, T this, Storedoligomer_T oligo);
+Indexdb_read_right_subst_2 (int *npositions, T this, Oligospace_T oligo);
extern Univcoord_T *
-Indexdb_read_right_subst_1 (int *npositions, T this, Storedoligomer_T oligo);
+Indexdb_read_right_subst_1 (int *npositions, T this, Oligospace_T oligo);
extern int
-Indexdb_count_no_subst (T this, Storedoligomer_T oligo);
+Indexdb_count_no_subst (T this, Oligospace_T oligo);
extern int
-Indexdb_count_left_subst_2 (T this, Storedoligomer_T oligo);
+Indexdb_count_left_subst_2 (T this, Oligospace_T oligo);
extern int
-Indexdb_count_left_subst_1 (T this, Storedoligomer_T oligo);
+Indexdb_count_left_subst_1 (T this, Oligospace_T oligo);
extern int
-Indexdb_count_right_subst_2 (T this, Storedoligomer_T oligo);
+Indexdb_count_right_subst_2 (T this, Oligospace_T oligo);
extern int
-Indexdb_count_right_subst_1 (T this, Storedoligomer_T oligo);
+Indexdb_count_right_subst_1 (T this, Oligospace_T oligo);
#undef T
#endif
diff --git a/src/indexdbdef.h b/src/indexdbdef.h
index cfc8d5c..27dc76f 100644
--- a/src/indexdbdef.h
+++ b/src/indexdbdef.h
@@ -1,4 +1,4 @@
-/* $Id: indexdbdef.h 161940 2015-03-25 20:36:59Z twu $ */
+/* $Id: indexdbdef.h 183995 2016-02-09 18:55:29Z twu $ */
#ifndef INDEXDBDEF_INCLUDED
#define INDEXDBDEF_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -36,35 +36,45 @@ struct T {
#ifdef LARGE_GENOMES
Access_T offsetspages_access;
int offsetspages_shmid;
+ key_t offsetspages_key;
+ int offsetspages_fd;
+ size_t offsetspages_len;
UINT4 *offsetspages;
#endif
Access_T offsetsmeta_access;
int offsetsmeta_shmid;
+ key_t offsetsmeta_key;
int offsetsmeta_fd;
size_t offsetsmeta_len;
UINT4 *offsetsmeta;
Access_T offsetsstrm_access;
int offsetsstrm_shmid;
+ key_t offsetsstrm_key;
int offsetsstrm_fd;
size_t offsetsstrm_len;
UINT4 *offsetsstrm;
- Access_T positions_access;
#ifdef LARGE_GENOMES
+ Access_T positions_high_access;
int positions_high_shmid;
+ key_t positions_high_key;
int positions_high_fd;
size_t positions_high_len;
+ Access_T positions_low_access;
int positions_low_shmid;
+ key_t positions_low_key;
int positions_low_fd;
size_t positions_low_len;
unsigned char *positions_high;
UINT4 *positions_low;
#else
+ Access_T positions_access;
int positions_shmid;
+ key_t positions_key;
int positions_fd;
size_t positions_len;
UINT4 *positions; /* For small genomes, same as Univcoord_T */
diff --git a/src/junction.c b/src/junction.c
index f59feb4..5c1e3c1 100644
--- a/src/junction.c
+++ b/src/junction.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: junction.c 166641 2015-05-29 21:13:04Z twu $";
+static char rcsid[] = "$Id: junction.c 183888 2016-02-05 20:33:29Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -28,7 +28,7 @@ Junction_print (T this) {
} else if (this->type == INS_JUNCTION) {
printf("Insertion of %d\n",this->nindels);
} else if (this->type == DEL_JUNCTION) {
- printf("Deletion of %d at %u\n",this->nindels,this->deletionpos);
+ printf("Deletion of %d at %llu\n",this->nindels,(unsigned long long) this->deletionpos);
} else if (this->type == SPLICE_JUNCTION) {
if (this->splice_distance == 0) {
printf("Splice ambiguous with sense %d, prob %f and %f\n",
diff --git a/src/mapq.c b/src/mapq.c
index d28f2bd..397c897 100644
--- a/src/mapq.c
+++ b/src/mapq.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: mapq.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: mapq.c 184376 2016-02-16 23:39:30Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -96,7 +96,7 @@ MAPQ_max_quality_score (char *quality_string, int querylength) {
}
-
+#if 0
float
MAPQ_loglik_exact (char *quality_string, int querystart, int queryend) {
@@ -136,9 +136,10 @@ MAPQ_loglik_exact (char *quality_string, int querystart, int queryend) {
#endif
}
+#endif
-
+#if 0
static bool
check_badchar (char c) {
if (c == 'A' || c == 'a' || c == 'C' || c == 'c' || c == 'G' || c == 'g' || c == 'T' || c == 't' || c == 'N' || c == 'n') {
@@ -147,12 +148,12 @@ check_badchar (char c) {
return true;
}
}
-
+#endif
float
MAPQ_loglik (Compress_T query_compress, Univcoord_T left, int querystart, int queryend,
- int querylength, char *quality_string, bool plusp, int genestrand, bool first_read_p) {
+ int querylength, char *quality_string, bool plusp, int genestrand) {
float loglik = 0.0;
int Q;
int querypos;
@@ -185,7 +186,7 @@ MAPQ_loglik (Compress_T query_compress, Univcoord_T left, int querystart, int qu
querystart,queryend,alignlength));
nmismatches = Genome_mismatches_left(mismatch_positions,/*max_mismatches*/alignlength,
query_compress,left,/*pos5*/querystart,/*pos3*/queryend,plusp,
- genestrand,first_read_p);
+ genestrand);
debug(printf("%d mismatches:",nmismatches));
debug(
@@ -221,7 +222,7 @@ MAPQ_loglik (Compress_T query_compress, Univcoord_T left, int querystart, int qu
querylength - queryend,querylength - querystart,alignlength));
nmismatches = Genome_mismatches_left(mismatch_positions,/*max_mismatches*/alignlength,
query_compress,left,/*pos5*/querylength - queryend,
- /*pos3*/querylength - querystart,plusp,genestrand,first_read_p);
+ /*pos3*/querylength - querystart,plusp,genestrand);
debug(printf("%d mismatches (adjusted for querylength %d):",nmismatches,querylength));
debug(
diff --git a/src/mapq.h b/src/mapq.h
index e700388..e05faaa 100644
--- a/src/mapq.h
+++ b/src/mapq.h
@@ -1,4 +1,4 @@
-/* $Id: mapq.h 133760 2014-04-20 05:16:56Z twu $ */
+/* $Id: mapq.h 184376 2016-02-16 23:39:30Z twu $ */
#ifndef MAPQ_INCLUDED
#define MAPQ_INCLUDED
@@ -15,10 +15,8 @@ MAPQ_init (int quality_score_adj_in);
extern int
MAPQ_max_quality_score (char *quality_string, int querylength);
extern float
-MAPQ_loglik_exact (char *quality_string, int querystart, int queryend);
-extern float
MAPQ_loglik (Compress_T query_compress, Univcoord_T left, int querystart, int queryend,
- int querylength, char *quality_string, bool plusp, int genestrand, bool first_read_p);
+ int querylength, char *quality_string, bool plusp, int genestrand);
#endif
diff --git a/src/oligo.c b/src/oligo.c
index f6e3174..e9fe8f9 100644
--- a/src/oligo.c
+++ b/src/oligo.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: oligo.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: oligo.c 184203 2016-02-13 03:46:21Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -33,7 +33,7 @@ static char rcsid[] = "$Id: oligo.c 145990 2014-08-25 21:47:32Z twu $";
#define NREPETITIVE 76 /* same for 6 through 15 */
-static Storedoligomer_T repetitive_oligos_6[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_6[NREPETITIVE] =
{0, /* AAAAAA */
65, /* AACAAC */
130, /* AAGAAG */
@@ -112,7 +112,7 @@ static Storedoligomer_T repetitive_oligos_6[NREPETITIVE] =
4095, /* TTTTTT */
};
-static Storedoligomer_T repetitive_oligos_7[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_7[NREPETITIVE] =
{0, /* AAAAAAA */
260, /* AACAACA */
520, /* AAGAAGA */
@@ -191,7 +191,7 @@ static Storedoligomer_T repetitive_oligos_7[NREPETITIVE] =
16383, /* TTTTTTT */
};
-static Storedoligomer_T repetitive_oligos_8[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_8[NREPETITIVE] =
{0, /* AAAAAAAA */
1040, /* AACAACAA */
2080, /* AAGAAGAA */
@@ -270,7 +270,7 @@ static Storedoligomer_T repetitive_oligos_8[NREPETITIVE] =
65535, /* TTTTTTTT */
};
-static Storedoligomer_T repetitive_oligos_9[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_9[NREPETITIVE] =
{0, /* AAAAAAAAA */
4161, /* AACAACAAC */
8322, /* AAGAAGAAG */
@@ -350,7 +350,7 @@ static Storedoligomer_T repetitive_oligos_9[NREPETITIVE] =
};
-static Storedoligomer_T repetitive_oligos_10[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_10[NREPETITIVE] =
{0, /* AAAAAAAAAA */
16644, /* AACAACAACA */
33288, /* AAGAAGAAGA */
@@ -430,7 +430,7 @@ static Storedoligomer_T repetitive_oligos_10[NREPETITIVE] =
};
-static Storedoligomer_T repetitive_oligos_11[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_11[NREPETITIVE] =
{0, /* AAAAAAAAAAA */
66576, /* AACAACAACAA */
133152, /* AAGAAGAAGAA */
@@ -510,7 +510,7 @@ static Storedoligomer_T repetitive_oligos_11[NREPETITIVE] =
};
-static Storedoligomer_T repetitive_oligos_12[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_12[NREPETITIVE] =
{0, /* AAAAAAAAAAAA */
266305, /* AACAACAACAAC */
532610, /* AAGAAGAAGAAG */
@@ -589,7 +589,7 @@ static Storedoligomer_T repetitive_oligos_12[NREPETITIVE] =
16777215, /* TTTTTTTTTTTT */
};
-static Storedoligomer_T repetitive_oligos_13[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_13[NREPETITIVE] =
{0, /* AAAAAAAAAAAAA */
1065220, /* AACAACAACAACA */
2130440, /* AAGAAGAAGAAGA */
@@ -669,7 +669,7 @@ static Storedoligomer_T repetitive_oligos_13[NREPETITIVE] =
};
-static Storedoligomer_T repetitive_oligos_14[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_14[NREPETITIVE] =
{0, /* AAAAAAAAAAAAAA */
4260880, /* AACAACAACAACAA */
8521760, /* AAGAAGAAGAAGAA */
@@ -748,7 +748,7 @@ static Storedoligomer_T repetitive_oligos_14[NREPETITIVE] =
268435455, /* TTTTTTTTTTTTTT */
};
-static Storedoligomer_T repetitive_oligos_15[NREPETITIVE] =
+static Oligospace_T repetitive_oligos_15[NREPETITIVE] =
{0, /* AAAAAAAAAAAAAAA */
17043521, /* AACAACAACAACAAC */
34087042, /* AAGAAGAAGAAGAAG */
@@ -827,83 +827,400 @@ static Storedoligomer_T repetitive_oligos_15[NREPETITIVE] =
1073741823, /* TTTTTTTTTTTTTTT */
};
-static Storedoligomer_T repetitive_oligos_16[NREPETITIVE] =
- {0U, /* AAAAAAAAAAAAAAAA */
- 68174084U, /* AACAACAACAACAACA */
- 136348168U, /* AAGAAGAAGAAGAAGA */
- 204522252U, /* AATAATAATAATAATA */
- 272696336U, /* ACAACAACAACAACAA */
- 286331153U, /* ACACACACACACACAC */
- 340870420U, /* ACCACCACCACCACCA */
- 409044504U, /* ACGACGACGACGACGA */
- 477218588U, /* ACTACTACTACTACTA */
- 545392672U, /* AGAAGAAGAAGAAGAA */
- 572662306U, /* AGAGAGAGAGAGAGAG */
- 613566756U, /* AGCAGCAGCAGCAGCA */
- 681740840U, /* AGGAGGAGGAGGAGGA */
- 749914924U, /* AGTAGTAGTAGTAGTA */
- 818089008U, /* ATAATAATAATAATAA */
- 858993459U, /* ATATATATATATATAT */
- 886263092U, /* ATCATCATCATCATCA */
- 954437176U, /* ATGATGATGATGATGA */
- 1022611260U, /* ATTATTATTATTATTA */
- 1090785345U, /* CAACAACAACAACAAC */
- 1145324612U, /* CACACACACACACACA */
- 1158959429U, /* CACCACCACCACCACC */
- 1227133513U, /* CAGCAGCAGCAGCAGC */
- 1295307597U, /* CATCATCATCATCATC */
- 1363481681U, /* CCACCACCACCACCAC */
- 1431655765U, /* CCCCCCCCCCCCCCCC */
- 1499829849U, /* CCGCCGCCGCCGCCGC */
- 1568003933U, /* CCTCCTCCTCCTCCTC */
- 1636178017U, /* CGACGACGACGACGAC */
- 1704352101U, /* CGCCGCCGCCGCCGCC */
- 1717986918U, /* CGCGCGCGCGCGCGCG */
- 1772526185U, /* CGGCGGCGGCGGCGGC */
- 1840700269U, /* CGTCGTCGTCGTCGTC */
- 1908874353U, /* CTACTACTACTACTAC */
- 1977048437U, /* CTCCTCCTCCTCCTCC */
- 2004318071U, /* CTCTCTCTCTCTCTCT */
- 2045222521U, /* CTGCTGCTGCTGCTGC */
- 2113396605U, /* CTTCTTCTTCTTCTTC */
- 2181570690U, /* GAAGAAGAAGAAGAAG */
- 2249744774U, /* GACGACGACGACGACG */
- 2290649224U, /* GAGAGAGAGAGAGAGA */
- 2317918858U, /* GAGGAGGAGGAGGAGG */
- 2386092942U, /* GATGATGATGATGATG */
- 2454267026U, /* GCAGCAGCAGCAGCAG */
- 2522441110U, /* GCCGCCGCCGCCGCCG */
- 2576980377U, /* GCGCGCGCGCGCGCGC */
- 2590615194U, /* GCGGCGGCGGCGGCGG */
- 2658789278U, /* GCTGCTGCTGCTGCTG */
- 2726963362U, /* GGAGGAGGAGGAGGAG */
- 2795137446U, /* GGCGGCGGCGGCGGCG */
- 2863311530U, /* GGGGGGGGGGGGGGGG */
- 2931485614U, /* GGTGGTGGTGGTGGTG */
- 2999659698U, /* GTAGTAGTAGTAGTAG */
- 3067833782U, /* GTCGTCGTCGTCGTCG */
- 3136007866U, /* GTGGTGGTGGTGGTGG */
- 3149642683U, /* GTGTGTGTGTGTGTGT */
- 3204181950U, /* GTTGTTGTTGTTGTTG */
- 3272356035U, /* TAATAATAATAATAAT */
- 3340530119U, /* TACTACTACTACTACT */
- 3408704203U, /* TAGTAGTAGTAGTAGT */
- 3435973836U, /* TATATATATATATATA */
- 3476878287U, /* TATTATTATTATTATT */
- 3545052371U, /* TCATCATCATCATCAT */
- 3613226455U, /* TCCTCCTCCTCCTCCT */
- 3681400539U, /* TCGTCGTCGTCGTCGT */
- 3722304989U, /* TCTCTCTCTCTCTCTC */
- 3749574623U, /* TCTTCTTCTTCTTCTT */
- 3817748707U, /* TGATGATGATGATGAT */
- 3885922791U, /* TGCTGCTGCTGCTGCT */
- 3954096875U, /* TGGTGGTGGTGGTGGT */
- 4008636142U, /* TGTGTGTGTGTGTGTG */
- 4022270959U, /* TGTTGTTGTTGTTGTT */
- 4090445043U, /* TTATTATTATTATTAT */
- 4158619127U, /* TTCTTCTTCTTCTTCT */
- 4226793211U, /* TTGTTGTTGTTGTTGT */
- 4294967295U, /* TTTTTTTTTTTTTTTT */
+static Oligospace_T repetitive_oligos_16[NREPETITIVE] =
+ {0, /* AAAAAAAAAAAAAAAA */
+ 68174084, /* AACAACAACAACAACA */
+ 136348168, /* AAGAAGAAGAAGAAGA */
+ 204522252, /* AATAATAATAATAATA */
+ 272696336, /* ACAACAACAACAACAA */
+ 286331153, /* ACACACACACACACAC */
+ 340870420, /* ACCACCACCACCACCA */
+ 409044504, /* ACGACGACGACGACGA */
+ 477218588, /* ACTACTACTACTACTA */
+ 545392672, /* AGAAGAAGAAGAAGAA */
+ 572662306, /* AGAGAGAGAGAGAGAG */
+ 613566756, /* AGCAGCAGCAGCAGCA */
+ 681740840, /* AGGAGGAGGAGGAGGA */
+ 749914924, /* AGTAGTAGTAGTAGTA */
+ 818089008, /* ATAATAATAATAATAA */
+ 858993459, /* ATATATATATATATAT */
+ 886263092, /* ATCATCATCATCATCA */
+ 954437176, /* ATGATGATGATGATGA */
+ 1022611260, /* ATTATTATTATTATTA */
+ 1090785345, /* CAACAACAACAACAAC */
+ 1145324612, /* CACACACACACACACA */
+ 1158959429, /* CACCACCACCACCACC */
+ 1227133513, /* CAGCAGCAGCAGCAGC */
+ 1295307597, /* CATCATCATCATCATC */
+ 1363481681, /* CCACCACCACCACCAC */
+ 1431655765, /* CCCCCCCCCCCCCCCC */
+ 1499829849, /* CCGCCGCCGCCGCCGC */
+ 1568003933, /* CCTCCTCCTCCTCCTC */
+ 1636178017, /* CGACGACGACGACGAC */
+ 1704352101, /* CGCCGCCGCCGCCGCC */
+ 1717986918, /* CGCGCGCGCGCGCGCG */
+ 1772526185, /* CGGCGGCGGCGGCGGC */
+ 1840700269, /* CGTCGTCGTCGTCGTC */
+ 1908874353, /* CTACTACTACTACTAC */
+ 1977048437, /* CTCCTCCTCCTCCTCC */
+ 2004318071, /* CTCTCTCTCTCTCTCT */
+ 2045222521, /* CTGCTGCTGCTGCTGC */
+ 2113396605, /* CTTCTTCTTCTTCTTC */
+ 2181570690, /* GAAGAAGAAGAAGAAG */
+ 2249744774, /* GACGACGACGACGACG */
+ 2290649224, /* GAGAGAGAGAGAGAGA */
+ 2317918858, /* GAGGAGGAGGAGGAGG */
+ 2386092942, /* GATGATGATGATGATG */
+ 2454267026, /* GCAGCAGCAGCAGCAG */
+ 2522441110, /* GCCGCCGCCGCCGCCG */
+ 2576980377, /* GCGCGCGCGCGCGCGC */
+ 2590615194, /* GCGGCGGCGGCGGCGG */
+ 2658789278, /* GCTGCTGCTGCTGCTG */
+ 2726963362, /* GGAGGAGGAGGAGGAG */
+ 2795137446, /* GGCGGCGGCGGCGGCG */
+ 2863311530, /* GGGGGGGGGGGGGGGG */
+ 2931485614, /* GGTGGTGGTGGTGGTG */
+ 2999659698, /* GTAGTAGTAGTAGTAG */
+ 3067833782, /* GTCGTCGTCGTCGTCG */
+ 3136007866, /* GTGGTGGTGGTGGTGG */
+ 3149642683, /* GTGTGTGTGTGTGTGT */
+ 3204181950, /* GTTGTTGTTGTTGTTG */
+ 3272356035, /* TAATAATAATAATAAT */
+ 3340530119, /* TACTACTACTACTACT */
+ 3408704203, /* TAGTAGTAGTAGTAGT */
+ 3435973836, /* TATATATATATATATA */
+ 3476878287, /* TATTATTATTATTATT */
+ 3545052371, /* TCATCATCATCATCAT */
+ 3613226455, /* TCCTCCTCCTCCTCCT */
+ 3681400539, /* TCGTCGTCGTCGTCGT */
+ 3722304989, /* TCTCTCTCTCTCTCTC */
+ 3749574623, /* TCTTCTTCTTCTTCTT */
+ 3817748707, /* TGATGATGATGATGAT */
+ 3885922791, /* TGCTGCTGCTGCTGCT */
+ 3954096875, /* TGGTGGTGGTGGTGGT */
+ 4008636142, /* TGTGTGTGTGTGTGTG */
+ 4022270959, /* TGTTGTTGTTGTTGTT */
+ 4090445043, /* TTATTATTATTATTAT */
+ 4158619127, /* TTCTTCTTCTTCTTCT */
+ 4226793211, /* TTGTTGTTGTTGTTGT */
+ 4294967295, /* TTTTTTTTTTTTTTTT */
+ };
+
+
+static Oligospace_T repetitive_oligos_17[NREPETITIVE] =
+ {0, /* AAAAAAAAAAAAAAAAA */
+ 272696336, /* AACAACAACAACAACAA */
+ 545392672, /* AAGAAGAAGAAGAAGAA */
+ 818089008, /* AATAATAATAATAATAA */
+ 1090785345, /* ACAACAACAACAACAAC */
+ 1145324612, /* ACACACACACACACACA */
+ 1363481681, /* ACCACCACCACCACCAC */
+ 1636178017, /* ACGACGACGACGACGAC */
+ 1908874353, /* ACTACTACTACTACTAC */
+ 2181570690, /* AGAAGAAGAAGAAGAAG */
+ 2290649224, /* AGAGAGAGAGAGAGAGA */
+ 2454267026, /* AGCAGCAGCAGCAGCAG */
+ 2726963362, /* AGGAGGAGGAGGAGGAG */
+ 2999659698, /* AGTAGTAGTAGTAGTAG */
+ 3272356035, /* ATAATAATAATAATAAT */
+ 3435973836, /* ATATATATATATATATA */
+ 3545052371, /* ATCATCATCATCATCAT */
+ 3817748707, /* ATGATGATGATGATGAT */
+ 4090445043, /* ATTATTATTATTATTAT */
+ 4363141380, /* CAACAACAACAACAACA */
+ 4581298449, /* CACACACACACACACAC */
+ 4635837716, /* CACCACCACCACCACCA */
+ 4908534052, /* CAGCAGCAGCAGCAGCA */
+ 5181230388, /* CATCATCATCATCATCA */
+ 5453926725, /* CCACCACCACCACCACC */
+ 5726623061, /* CCCCCCCCCCCCCCCCC */
+ 5999319397, /* CCGCCGCCGCCGCCGCC */
+ 6272015733, /* CCTCCTCCTCCTCCTCC */
+ 6544712070, /* CGACGACGACGACGACG */
+ 6817408406, /* CGCCGCCGCCGCCGCCG */
+ 6871947673, /* CGCGCGCGCGCGCGCGC */
+ 7090104742, /* CGGCGGCGGCGGCGGCG */
+ 7362801078, /* CGTCGTCGTCGTCGTCG */
+ 7635497415, /* CTACTACTACTACTACT */
+ 7908193751, /* CTCCTCCTCCTCCTCCT */
+ 8017272285, /* CTCTCTCTCTCTCTCTC */
+ 8180890087, /* CTGCTGCTGCTGCTGCT */
+ 8453586423, /* CTTCTTCTTCTTCTTCT */
+ 8726282760, /* GAAGAAGAAGAAGAAGA */
+ 8998979096, /* GACGACGACGACGACGA */
+ 9162596898, /* GAGAGAGAGAGAGAGAG */
+ 9271675432, /* GAGGAGGAGGAGGAGGA */
+ 9544371768, /* GATGATGATGATGATGA */
+ 9817068105, /* GCAGCAGCAGCAGCAGC */
+ 10089764441, /* GCCGCCGCCGCCGCCGC */
+ 10307921510, /* GCGCGCGCGCGCGCGCG */
+ 10362460777, /* GCGGCGGCGGCGGCGGC */
+ 10635157113, /* GCTGCTGCTGCTGCTGC */
+ 10907853450, /* GGAGGAGGAGGAGGAGG */
+ 11180549786, /* GGCGGCGGCGGCGGCGG */
+ 11453246122, /* GGGGGGGGGGGGGGGGG */
+ 11725942458, /* GGTGGTGGTGGTGGTGG */
+ 11998638795, /* GTAGTAGTAGTAGTAGT */
+ 12271335131, /* GTCGTCGTCGTCGTCGT */
+ 12544031467, /* GTGGTGGTGGTGGTGGT */
+ 12598570734, /* GTGTGTGTGTGTGTGTG */
+ 12816727803, /* GTTGTTGTTGTTGTTGT */
+ 13089424140, /* TAATAATAATAATAATA */
+ 13362120476, /* TACTACTACTACTACTA */
+ 13634816812, /* TAGTAGTAGTAGTAGTA */
+ 13743895347, /* TATATATATATATATAT */
+ 13907513148, /* TATTATTATTATTATTA */
+ 14180209485, /* TCATCATCATCATCATC */
+ 14452905821, /* TCCTCCTCCTCCTCCTC */
+ 14725602157, /* TCGTCGTCGTCGTCGTC */
+ 14889219959, /* TCTCTCTCTCTCTCTCT */
+ 14998298493, /* TCTTCTTCTTCTTCTTC */
+ 15270994830, /* TGATGATGATGATGATG */
+ 15543691166, /* TGCTGCTGCTGCTGCTG */
+ 15816387502, /* TGGTGGTGGTGGTGGTG */
+ 16034544571, /* TGTGTGTGTGTGTGTGT */
+ 16089083838, /* TGTTGTTGTTGTTGTTG */
+ 16361780175, /* TTATTATTATTATTATT */
+ 16634476511, /* TTCTTCTTCTTCTTCTT */
+ 16907172847, /* TTGTTGTTGTTGTTGTT */
+ 17179869183, /* TTTTTTTTTTTTTTTTT */
+ };
+
+static Oligospace_T repetitive_oligos_18[NREPETITIVE] =
+ {0, /* AAAAAAAAAAAAAAAAAA */
+ 1090785345, /* AACAACAACAACAACAAC */
+ 2181570690, /* AAGAAGAAGAAGAAGAAG */
+ 3272356035, /* AATAATAATAATAATAAT */
+ 4363141380, /* ACAACAACAACAACAACA */
+ 4581298449, /* ACACACACACACACACAC */
+ 5453926725, /* ACCACCACCACCACCACC */
+ 6544712070, /* ACGACGACGACGACGACG */
+ 7635497415, /* ACTACTACTACTACTACT */
+ 8726282760, /* AGAAGAAGAAGAAGAAGA */
+ 9162596898, /* AGAGAGAGAGAGAGAGAG */
+ 9817068105, /* AGCAGCAGCAGCAGCAGC */
+ 10907853450, /* AGGAGGAGGAGGAGGAGG */
+ 11998638795, /* AGTAGTAGTAGTAGTAGT */
+ 13089424140, /* ATAATAATAATAATAATA */
+ 13743895347, /* ATATATATATATATATAT */
+ 14180209485, /* ATCATCATCATCATCATC */
+ 15270994830, /* ATGATGATGATGATGATG */
+ 16361780175, /* ATTATTATTATTATTATT */
+ 17452565520, /* CAACAACAACAACAACAA */
+ 18325193796, /* CACACACACACACACACA */
+ 18543350865, /* CACCACCACCACCACCAC */
+ 19634136210, /* CAGCAGCAGCAGCAGCAG */
+ 20724921555, /* CATCATCATCATCATCAT */
+ 21815706900, /* CCACCACCACCACCACCA */
+ 22906492245, /* CCCCCCCCCCCCCCCCCC */
+ 23997277590, /* CCGCCGCCGCCGCCGCCG */
+ 25088062935, /* CCTCCTCCTCCTCCTCCT */
+ 26178848280, /* CGACGACGACGACGACGA */
+ 27269633625, /* CGCCGCCGCCGCCGCCGC */
+ 27487790694, /* CGCGCGCGCGCGCGCGCG */
+ 28360418970, /* CGGCGGCGGCGGCGGCGG */
+ 29451204315, /* CGTCGTCGTCGTCGTCGT */
+ 30541989660, /* CTACTACTACTACTACTA */
+ 31632775005, /* CTCCTCCTCCTCCTCCTC */
+ 32069089143, /* CTCTCTCTCTCTCTCTCT */
+ 32723560350, /* CTGCTGCTGCTGCTGCTG */
+ 33814345695, /* CTTCTTCTTCTTCTTCTT */
+ 34905131040, /* GAAGAAGAAGAAGAAGAA */
+ 35995916385, /* GACGACGACGACGACGAC */
+ 36650387592, /* GAGAGAGAGAGAGAGAGA */
+ 37086701730, /* GAGGAGGAGGAGGAGGAG */
+ 38177487075, /* GATGATGATGATGATGAT */
+ 39268272420, /* GCAGCAGCAGCAGCAGCA */
+ 40359057765, /* GCCGCCGCCGCCGCCGCC */
+ 41231686041, /* GCGCGCGCGCGCGCGCGC */
+ 41449843110, /* GCGGCGGCGGCGGCGGCG */
+ 42540628455, /* GCTGCTGCTGCTGCTGCT */
+ 43631413800, /* GGAGGAGGAGGAGGAGGA */
+ 44722199145, /* GGCGGCGGCGGCGGCGGC */
+ 45812984490, /* GGGGGGGGGGGGGGGGGG */
+ 46903769835, /* GGTGGTGGTGGTGGTGGT */
+ 47994555180, /* GTAGTAGTAGTAGTAGTA */
+ 49085340525, /* GTCGTCGTCGTCGTCGTC */
+ 50176125870, /* GTGGTGGTGGTGGTGGTG */
+ 50394282939, /* GTGTGTGTGTGTGTGTGT */
+ 51266911215, /* GTTGTTGTTGTTGTTGTT */
+ 52357696560, /* TAATAATAATAATAATAA */
+ 53448481905, /* TACTACTACTACTACTAC */
+ 54539267250, /* TAGTAGTAGTAGTAGTAG */
+ 54975581388, /* TATATATATATATATATA */
+ 55630052595, /* TATTATTATTATTATTAT */
+ 56720837940, /* TCATCATCATCATCATCA */
+ 57811623285, /* TCCTCCTCCTCCTCCTCC */
+ 58902408630, /* TCGTCGTCGTCGTCGTCG */
+ 59556879837, /* TCTCTCTCTCTCTCTCTC */
+ 59993193975, /* TCTTCTTCTTCTTCTTCT */
+ 61083979320, /* TGATGATGATGATGATGA */
+ 62174764665, /* TGCTGCTGCTGCTGCTGC */
+ 63265550010, /* TGGTGGTGGTGGTGGTGG */
+ 64138178286, /* TGTGTGTGTGTGTGTGTG */
+ 64356335355, /* TGTTGTTGTTGTTGTTGT */
+ 65447120700, /* TTATTATTATTATTATTA */
+ 66537906045, /* TTCTTCTTCTTCTTCTTC */
+ 67628691390, /* TTGTTGTTGTTGTTGTTG */
+ 68719476735, /* TTTTTTTTTTTTTTTTTT */
+ };
+
+static Oligospace_T repetitive_oligos_19[NREPETITIVE] =
+ {0, /* AAAAAAAAAAAAAAAAAAA */
+ 4363141380, /* AACAACAACAACAACAACA */
+ 8726282760, /* AAGAAGAAGAAGAAGAAGA */
+ 13089424140, /* AATAATAATAATAATAATA */
+ 17452565520, /* ACAACAACAACAACAACAA */
+ 18325193796, /* ACACACACACACACACACA */
+ 21815706900, /* ACCACCACCACCACCACCA */
+ 26178848280, /* ACGACGACGACGACGACGA */
+ 30541989660, /* ACTACTACTACTACTACTA */
+ 34905131040, /* AGAAGAAGAAGAAGAAGAA */
+ 36650387592, /* AGAGAGAGAGAGAGAGAGA */
+ 39268272420, /* AGCAGCAGCAGCAGCAGCA */
+ 43631413800, /* AGGAGGAGGAGGAGGAGGA */
+ 47994555180, /* AGTAGTAGTAGTAGTAGTA */
+ 52357696560, /* ATAATAATAATAATAATAA */
+ 54975581388, /* ATATATATATATATATATA */
+ 56720837940, /* ATCATCATCATCATCATCA */
+ 61083979320, /* ATGATGATGATGATGATGA */
+ 65447120700, /* ATTATTATTATTATTATTA */
+ 69810262081, /* CAACAACAACAACAACAAC */
+ 73300775185, /* CACACACACACACACACAC */
+ 74173403461, /* CACCACCACCACCACCACC */
+ 78536544841, /* CAGCAGCAGCAGCAGCAGC */
+ 82899686221, /* CATCATCATCATCATCATC */
+ 87262827601, /* CCACCACCACCACCACCAC */
+ 91625968981, /* CCCCCCCCCCCCCCCCCCC */
+ 95989110361, /* CCGCCGCCGCCGCCGCCGC */
+ 100352251741, /* CCTCCTCCTCCTCCTCCTC */
+ 104715393121, /* CGACGACGACGACGACGAC */
+ 109078534501, /* CGCCGCCGCCGCCGCCGCC */
+ 109951162777, /* CGCGCGCGCGCGCGCGCGC */
+ 113441675881, /* CGGCGGCGGCGGCGGCGGC */
+ 117804817261, /* CGTCGTCGTCGTCGTCGTC */
+ 122167958641, /* CTACTACTACTACTACTAC */
+ 126531100021, /* CTCCTCCTCCTCCTCCTCC */
+ 128276356573, /* CTCTCTCTCTCTCTCTCTC */
+ 130894241401, /* CTGCTGCTGCTGCTGCTGC */
+ 135257382781, /* CTTCTTCTTCTTCTTCTTC */
+ 139620524162, /* GAAGAAGAAGAAGAAGAAG */
+ 143983665542, /* GACGACGACGACGACGACG */
+ 146601550370, /* GAGAGAGAGAGAGAGAGAG */
+ 148346806922, /* GAGGAGGAGGAGGAGGAGG */
+ 152709948302, /* GATGATGATGATGATGATG */
+ 157073089682, /* GCAGCAGCAGCAGCAGCAG */
+ 161436231062, /* GCCGCCGCCGCCGCCGCCG */
+ 164926744166, /* GCGCGCGCGCGCGCGCGCG */
+ 165799372442, /* GCGGCGGCGGCGGCGGCGG */
+ 170162513822, /* GCTGCTGCTGCTGCTGCTG */
+ 174525655202, /* GGAGGAGGAGGAGGAGGAG */
+ 178888796582, /* GGCGGCGGCGGCGGCGGCG */
+ 183251937962, /* GGGGGGGGGGGGGGGGGGG */
+ 187615079342, /* GGTGGTGGTGGTGGTGGTG */
+ 191978220722, /* GTAGTAGTAGTAGTAGTAG */
+ 196341362102, /* GTCGTCGTCGTCGTCGTCG */
+ 200704503482, /* GTGGTGGTGGTGGTGGTGG */
+ 201577131758, /* GTGTGTGTGTGTGTGTGTG */
+ 205067644862, /* GTTGTTGTTGTTGTTGTTG */
+ 209430786243, /* TAATAATAATAATAATAAT */
+ 213793927623, /* TACTACTACTACTACTACT */
+ 218157069003, /* TAGTAGTAGTAGTAGTAGT */
+ 219902325555, /* TATATATATATATATATAT */
+ 222520210383, /* TATTATTATTATTATTATT */
+ 226883351763, /* TCATCATCATCATCATCAT */
+ 231246493143, /* TCCTCCTCCTCCTCCTCCT */
+ 235609634523, /* TCGTCGTCGTCGTCGTCGT */
+ 238227519351, /* TCTCTCTCTCTCTCTCTCT */
+ 239972775903, /* TCTTCTTCTTCTTCTTCTT */
+ 244335917283, /* TGATGATGATGATGATGAT */
+ 248699058663, /* TGCTGCTGCTGCTGCTGCT */
+ 253062200043, /* TGGTGGTGGTGGTGGTGGT */
+ 256552713147, /* TGTGTGTGTGTGTGTGTGT */
+ 257425341423, /* TGTTGTTGTTGTTGTTGTT */
+ 261788482803, /* TTATTATTATTATTATTAT */
+ 266151624183, /* TTCTTCTTCTTCTTCTTCT */
+ 270514765563, /* TTGTTGTTGTTGTTGTTGT */
+ 274877906943, /* TTTTTTTTTTTTTTTTTTT */
+ };
+
+static Oligospace_T repetitive_oligos_20[NREPETITIVE] =
+ {0, /* AAAAAAAAAAAAAAAAAAAA */
+ 17452565520, /* AACAACAACAACAACAACAA */
+ 34905131040, /* AAGAAGAAGAAGAAGAAGAA */
+ 52357696560, /* AATAATAATAATAATAATAA */
+ 69810262081, /* ACAACAACAACAACAACAAC */
+ 73300775185, /* ACACACACACACACACACAC */
+ 87262827601, /* ACCACCACCACCACCACCAC */
+ 104715393121, /* ACGACGACGACGACGACGAC */
+ 122167958641, /* ACTACTACTACTACTACTAC */
+ 139620524162, /* AGAAGAAGAAGAAGAAGAAG */
+ 146601550370, /* AGAGAGAGAGAGAGAGAGAG */
+ 157073089682, /* AGCAGCAGCAGCAGCAGCAG */
+ 174525655202, /* AGGAGGAGGAGGAGGAGGAG */
+ 191978220722, /* AGTAGTAGTAGTAGTAGTAG */
+ 209430786243, /* ATAATAATAATAATAATAAT */
+ 219902325555, /* ATATATATATATATATATAT */
+ 226883351763, /* ATCATCATCATCATCATCAT */
+ 244335917283, /* ATGATGATGATGATGATGAT */
+ 261788482803, /* ATTATTATTATTATTATTAT */
+ 279241048324, /* CAACAACAACAACAACAACA */
+ 293203100740, /* CACACACACACACACACACA */
+ 296693613844, /* CACCACCACCACCACCACCA */
+ 314146179364, /* CAGCAGCAGCAGCAGCAGCA */
+ 331598744884, /* CATCATCATCATCATCATCA */
+ 349051310405, /* CCACCACCACCACCACCACC */
+ 366503875925, /* CCCCCCCCCCCCCCCCCCCC */
+ 383956441445, /* CCGCCGCCGCCGCCGCCGCC */
+ 401409006965, /* CCTCCTCCTCCTCCTCCTCC */
+ 418861572486, /* CGACGACGACGACGACGACG */
+ 436314138006, /* CGCCGCCGCCGCCGCCGCCG */
+ 439804651110, /* CGCGCGCGCGCGCGCGCGCG */
+ 453766703526, /* CGGCGGCGGCGGCGGCGGCG */
+ 471219269046, /* CGTCGTCGTCGTCGTCGTCG */
+ 488671834567, /* CTACTACTACTACTACTACT */
+ 506124400087, /* CTCCTCCTCCTCCTCCTCCT */
+ 513105426295, /* CTCTCTCTCTCTCTCTCTCT */
+ 523576965607, /* CTGCTGCTGCTGCTGCTGCT */
+ 541029531127, /* CTTCTTCTTCTTCTTCTTCT */
+ 558482096648, /* GAAGAAGAAGAAGAAGAAGA */
+ 575934662168, /* GACGACGACGACGACGACGA */
+ 586406201480, /* GAGAGAGAGAGAGAGAGAGA */
+ 593387227688, /* GAGGAGGAGGAGGAGGAGGA */
+ 610839793208, /* GATGATGATGATGATGATGA */
+ 628292358729, /* GCAGCAGCAGCAGCAGCAGC */
+ 645744924249, /* GCCGCCGCCGCCGCCGCCGC */
+ 659706976665, /* GCGCGCGCGCGCGCGCGCGC */
+ 663197489769, /* GCGGCGGCGGCGGCGGCGGC */
+ 680650055289, /* GCTGCTGCTGCTGCTGCTGC */
+ 698102620810, /* GGAGGAGGAGGAGGAGGAGG */
+ 715555186330, /* GGCGGCGGCGGCGGCGGCGG */
+ 733007751850, /* GGGGGGGGGGGGGGGGGGGG */
+ 750460317370, /* GGTGGTGGTGGTGGTGGTGG */
+ 767912882891, /* GTAGTAGTAGTAGTAGTAGT */
+ 785365448411, /* GTCGTCGTCGTCGTCGTCGT */
+ 802818013931, /* GTGGTGGTGGTGGTGGTGGT */
+ 806308527035, /* GTGTGTGTGTGTGTGTGTGT */
+ 820270579451, /* GTTGTTGTTGTTGTTGTTGT */
+ 837723144972, /* TAATAATAATAATAATAATA */
+ 855175710492, /* TACTACTACTACTACTACTA */
+ 872628276012, /* TAGTAGTAGTAGTAGTAGTA */
+ 879609302220, /* TATATATATATATATATATA */
+ 890080841532, /* TATTATTATTATTATTATTA */
+ 907533407053, /* TCATCATCATCATCATCATC */
+ 924985972573, /* TCCTCCTCCTCCTCCTCCTC */
+ 942438538093, /* TCGTCGTCGTCGTCGTCGTC */
+ 952910077405, /* TCTCTCTCTCTCTCTCTCTC */
+ 959891103613, /* TCTTCTTCTTCTTCTTCTTC */
+ 977343669134, /* TGATGATGATGATGATGATG */
+ 994796234654, /* TGCTGCTGCTGCTGCTGCTG */
+ 1012248800174, /* TGGTGGTGGTGGTGGTGGTG */
+ 1026210852590, /* TGTGTGTGTGTGTGTGTGTG */
+ 1029701365694, /* TGTTGTTGTTGTTGTTGTTG */
+ 1047153931215, /* TTATTATTATTATTATTATT */
+ 1064606496735, /* TTCTTCTTCTTCTTCTTCTT */
+ 1082059062255, /* TTGTTGTTGTTGTTGTTGTT */
+ 1099511627775, /* TTTTTTTTTTTTTTTTTTTT */
};
@@ -1458,7 +1775,7 @@ static Storedoligomer_T all_repetitive_oligos[ALL_NREPETITIVE] =
static int oligosize;
-static Storedoligomer_T *repetitive_oligos;
+static Oligospace_T *repetitive_oligos;
void
Oligo_setup (int index1part) {
@@ -1486,40 +1803,22 @@ Oligo_setup (int index1part) {
repetitive_oligos = repetitive_oligos_15;
} else if (index1part == 16) {
repetitive_oligos = repetitive_oligos_16;
+ } else if (index1part == 17) {
+ repetitive_oligos = repetitive_oligos_17;
+ } else if (index1part == 18) {
+ repetitive_oligos = repetitive_oligos_18;
+ } else if (index1part == 19) {
+ repetitive_oligos = repetitive_oligos_19;
+ } else if (index1part == 20) {
+ repetitive_oligos = repetitive_oligos_20;
} else {
- fprintf(stderr,"Oligo_setup can handle only values of 6 through 16\n");
+ fprintf(stderr,"Oligo_setup can handle only values of 6 through 20\n");
abort();
}
return;
}
-/* 87654321 */
-#define LEFT_A 0x00000000
-#define LEFT_C 0x40000000
-#define LEFT_G 0x80000000
-#define LEFT_T 0xC0000000
-
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
-
-/* 87654321 */
-#define LEFT_0 0x00000000
-#define LEFT_1 0x40000000
-#define LEFT_2 0x80000000
-#define LEFT_3 0xC0000000
-
-/* 87654321 */
-#define RIGHT_0 0x00000000
-#define RIGHT_1 0x00000001
-#define RIGHT_2 0x00000002
-#define RIGHT_3 0x00000003
-
-
/************************************************************************
* Check
************************************************************************/
@@ -1529,10 +1828,10 @@ Oligo_setup (int index1part) {
/* For debugging purposes only */
char *
-Oligo_one_nt (Storedoligomer_T oligo, int oligosize) {
+Oligo_one_nt (Oligospace_T oligo, int oligosize) {
char *nt;
int i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -1556,7 +1855,7 @@ Oligo_one_nt (Storedoligomer_T oligo, int oligosize) {
positions is allocated by system malloc() */
/* No longer seems to be called by GMAP either */
int
-Oligo_lookup (Univcoord_T **positions, Indexdb_T indexdb, Storedoligomer_T storedoligo) {
+Oligo_lookup (Univcoord_T **positions, Indexdb_T indexdb, Oligospace_T storedoligo) {
int nentries;
debug(char *nt);
debug1(int i);
@@ -1584,7 +1883,7 @@ Oligo_lookup (Univcoord_T **positions, Indexdb_T indexdb, Storedoligomer_T store
}
static Oligostate_T
-oligo_read (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *revcomp,
+oligo_read (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp,
Reader_T reader, cDNAEnd_T cdnaend) {
int count = 0;
int c;
@@ -1646,7 +1945,7 @@ oligo_read (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *revcomp,
#if 0
static Oligostate_T
-oligo_read_dibase (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *revcomp,
+oligo_read_dibase (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp,
Reader_T reader, cDNAEnd_T cdnaend) {
int count = 0;
int c;
@@ -1710,7 +2009,7 @@ oligo_read_dibase (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *r
#if 0
-typedef Oligostate_T (*oligo_read_proc_t) (int *, Storedoligomer_T *, Storedoligomer_T *,
+typedef Oligostate_T (*oligo_read_proc_t) (int *, Oligospace_T *, Oligospace_T *,
int, Reader_T, cDNAEnd_T);
static oligo_read_proc_t oligo_read;
#endif
@@ -1718,7 +2017,7 @@ static oligo_read_proc_t oligo_read;
static Oligostate_T
-oligo_revise (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *revcomp,
+oligo_revise (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp,
Reader_T reader, cDNAEnd_T cdnaend) {
char c;
@@ -1774,7 +2073,7 @@ oligo_revise (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *revcom
#if 0
static Oligostate_T
-oligo_revise_dibase (int *querypos, Storedoligomer_T *forward, Storedoligomer_T *revcomp,
+oligo_revise_dibase (int *querypos, Oligospace_T *forward, Oligospace_T *revcomp,
Reader_T reader, cDNAEnd_T cdnaend) {
char c;
@@ -1831,7 +2130,7 @@ oligo_revise_dibase (int *querypos, Storedoligomer_T *forward, Storedoligomer_T
#endif
#if 0
-typedef Oligostate_T (*oligo_revise_proc_t) (int *, Storedoligomer_T *, Storedoligomer_T *,
+typedef Oligostate_T (*oligo_revise_proc_t) (int *, Oligospace_T *, Oligospace_T *,
int, Reader_T, cDNAEnd_T);
static oligo_revise_proc_t oligo_revise;
#endif
@@ -1839,8 +2138,8 @@ static oligo_revise_proc_t oligo_revise;
Oligostate_T
-Oligo_next (Oligostate_T last_state, int *querypos, Storedoligomer_T *forward,
- Storedoligomer_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) {
+Oligo_next (Oligostate_T last_state, int *querypos, Oligospace_T *forward,
+ Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend) {
Oligostate_T state;
if (last_state == DONE) {
@@ -1863,8 +2162,8 @@ Oligo_next (Oligostate_T last_state, int *querypos, Storedoligomer_T *forward,
}
Oligostate_T
-Oligo_skip (Oligostate_T last_state, int *querypos, Storedoligomer_T *forward,
- Storedoligomer_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend, int nskip) {
+Oligo_skip (Oligostate_T last_state, int *querypos, Oligospace_T *forward,
+ Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend, int nskip) {
int i = 0;
while (i < nskip && last_state != DONE) {
@@ -1883,10 +2182,10 @@ Oligo_skip (Oligostate_T last_state, int *querypos, Storedoligomer_T *forward,
#if 0
/* Procedure used by oligo-count.c. oligosize here is expected to be > 12. */
char *
-Oligo_nt (Storedoligomer_T oligo1, Storedoligomer_T oligo2, int oligosize, int index1part) {
+Oligo_nt (Oligospace_T oligo1, Oligospace_T oligo2, int oligosize, int index1part) {
char *nt;
int i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -1919,11 +2218,14 @@ Oligo_nt (Storedoligomer_T oligo1, Storedoligomer_T oligo2, int oligosize, int i
#endif
+#if 0
struct Cell_T {
int querypos;
- Storedoligomer_T oligo;
+ Oligospace_T oligo;
};
+#endif
+#if 0
/* Taken from oligo_hr.c */
static int
Cell_compare (const void *a, const void *b) {
@@ -1938,12 +2240,13 @@ Cell_compare (const void *a, const void *b) {
return 0;
}
}
+#endif
#define BINARY_FOLDDIFF 16
static int
-binary_search (int lowi, int highi, Storedoligomer_T *oligos, Storedoligomer_T goal) {
+binary_search (int lowi, int highi, Oligospace_T *oligos, Oligospace_T goal) {
bool foundp = false;
int middlei;
@@ -1975,12 +2278,12 @@ binary_search (int lowi, int highi, Storedoligomer_T *oligos, Storedoligomer_T g
#if 0
bool
-Oligo_mark_repetitive (bool **repetitivep, Storedoligomer_T *oligos,
+Oligo_mark_repetitive (bool **repetitivep, Oligospace_T *oligos,
int first_querypos, int last_querypos) {
bool any_repetitive_p = false;
struct Cell_T *cells;
int n, i, j, querypos, nremaining, binary_threshold;
- Storedoligomer_T *q;
+ Oligospace_T *q;
n = last_querypos - first_querypos + 1;
cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T));
@@ -2023,7 +2326,7 @@ Oligo_mark_repetitive (bool **repetitivep, Storedoligomer_T *oligos,
bool
-Oligo_repetitive_p (Storedoligomer_T oligo) {
+Oligo_repetitive_p (Oligospace_T oligo) {
int j;
j = binary_search(0,NREPETITIVE,repetitive_oligos,oligo);
@@ -2037,12 +2340,12 @@ Oligo_repetitive_p (Storedoligomer_T oligo) {
#if 0
bool
-Oligo_mark_frequent (bool **frequentp, Storedoligomer_T *oligos, int n,
- Storedoligomer_T *frequent_oligos, int nfrequent) {
+Oligo_mark_frequent (bool **frequentp, Oligospace_T *oligos, int n,
+ Oligospace_T *frequent_oligos, int nfrequent) {
bool any_frequent_p = false;
struct Cell_T *cells;
int i, j, nremaining, binary_threshold;
- Storedoligomer_T *q;
+ Oligospace_T *q;
cells = (struct Cell_T *) MALLOCA(n * sizeof(struct Cell_T));
for (i = 0; i < n; i++) {
@@ -2081,9 +2384,9 @@ Oligo_mark_frequent (bool **frequentp, Storedoligomer_T *oligos, int n,
return any_frequent_p;
}
-Storedoligomer_T *
+Oligospace_T *
Oligo_frequent_oligos (int *nfrequent, Indexdb_T indexdb, int size_threshold) {
- Storedoligomer_T *frequent_oligos, oligo;
+ Oligospace_T *frequent_oligos, oligo;
int npositions, i, k;
bool *frequentp[NREPETITIVE];
@@ -2108,7 +2411,7 @@ Oligo_frequent_oligos (int *nfrequent, Indexdb_T indexdb, int size_threshold) {
(*nfrequent) += 1;
}
- frequent_oligos = (Storedoligomer_T *) CALLOC(*nfrequent,sizeof(Storedoligomer_T));
+ frequent_oligos = (Oligospace_T *) CALLOC(*nfrequent,sizeof(Oligospace_T));
k = 0;
for (i = 0; i < NREPETITIVE; i++) {
if (frequentp[i] == true) {
diff --git a/src/oligo.h b/src/oligo.h
index 2ea5776..4f8045e 100644
--- a/src/oligo.h
+++ b/src/oligo.h
@@ -1,4 +1,4 @@
-/* $Id: oligo.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: oligo.h 180341 2015-12-07 18:29:40Z twu $ */
#ifndef OLIGO_INCLUDED
#define OLIGO_INCLUDED
@@ -13,19 +13,19 @@ extern void
Oligo_setup (int index1part);
extern char *
-Oligo_one_nt (Storedoligomer_T oligo, int oligosize);
+Oligo_one_nt (Oligospace_T oligo, int oligosize);
extern int
-Oligo_lookup (Univcoord_T **positions, Indexdb_T indexdb, Storedoligomer_T storedoligo);
+Oligo_lookup (Univcoord_T **positions, Indexdb_T indexdb, Oligospace_T storedoligo);
extern Oligostate_T
-Oligo_next (Oligostate_T last_state, int *querypos, Storedoligomer_T *forward,
- Storedoligomer_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend);
+Oligo_next (Oligostate_T last_state, int *querypos, Oligospace_T *forward,
+ Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend);
extern Oligostate_T
-Oligo_skip (Oligostate_T last_state, int *querypos, Storedoligomer_T *forward,
- Storedoligomer_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend, int nskip);
+Oligo_skip (Oligostate_T last_state, int *querypos, Oligospace_T *forward,
+ Oligospace_T *revcomp, Reader_T reader, cDNAEnd_T cdnaend, int nskip);
extern bool
-Oligo_repetitive_p (Storedoligomer_T oligo);
+Oligo_repetitive_p (Oligospace_T oligo);
#endif
diff --git a/src/oligoindex_hr.c b/src/oligoindex_hr.c
index 3c0b489..acb86f5 100644
--- a/src/oligoindex_hr.c
+++ b/src/oligoindex_hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: oligoindex_hr.c 175547 2015-09-28 21:31:01Z twu $";
+static char rcsid[] = "$Id: oligoindex_hr.c 184484 2016-02-18 03:11:53Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -36,6 +36,9 @@ static char rcsid[] = "$Id: oligoindex_hr.c 175547 2015-09-28 21:31:01Z twu $";
#ifdef HAVE_SSE4_1
#include <smmintrin.h>
#endif
+#ifdef HAVE_AVX2
+#include <immintrin.h>
+#endif
#ifdef HAVE_SSE2
@@ -47,8 +50,11 @@ static char rcsid[] = "$Id: oligoindex_hr.c 175547 2015-09-28 21:31:01Z twu $";
#elif !defined(HAVE_SSE4_1)
#define SIMD_MASK_THEN_STORE
#define EXTRACT(x,i) x[i]
+#elif !defined(HAVE_AVX2)
+#define EXTRACT(x,i) _mm_extract_epi32(x,i)
#else
#define EXTRACT(x,i) _mm_extract_epi32(x,i)
+#define EXTRACT256(x,i) _mm256_extract_epi32(x,i)
#endif
@@ -56,6 +62,9 @@ static char rcsid[] = "$Id: oligoindex_hr.c 175547 2015-09-28 21:31:01Z twu $";
#define THETADIFF2 20.0
#define REPOLIGOCOUNT 8
+/* For PMAP, use oligoindex_pmap.c */
+/* #define NT_PER_MATCH 1 */
+
struct Genomicdiag_T {
int i;
@@ -71,13 +80,8 @@ typedef struct Genomicdiag_T *Genomicdiag_T;
#define T Oligoindex_T
struct T {
-#ifdef PMAP
- int indexsize_aa;
- Shortoligomer_T msb;
-#else
int indexsize;
Shortoligomer_T mask;
-#endif
int diag_lookback;
int suffnconsecutive;
@@ -85,21 +89,20 @@ struct T {
/* bool query_evaluated_p; */
Oligospace_T oligospace;
-#ifdef HAVE_SSE2
+#ifdef HAVE_AVX2
+ __m256i *inquery_allocated;
+ __m256i *counts_allocated;
+#elif defined(HAVE_SSE2)
__m128i *inquery_allocated;
__m128i *counts_allocated;
- Count_T *inquery;
-#else
- bool *inquery;
#endif
+ Inquery_T *inquery;
Count_T *counts;
-#ifdef PMAP
- int *relevant_counts;
-#endif
- Chrpos_T **positions;
- Chrpos_T *positions_space;
- Chrpos_T **pointers;
- Chrpos_T **pointers_allocated;
+
+ Chrpos_T *table;
+ UINT4 *positions;
+ UINT4 *pointers;
+ UINT4 *pointers_allocated;
};
struct Oligoindex_array_T {
@@ -165,10 +168,10 @@ print_vector (__m128i x, char *label) {
_mm_store_si128(a,x);
_mm_mfence();
- printf("%s: %u\n",label,s[0]);
- printf("%s: %u\n",label,s[1]);
- printf("%s: %u\n",label,s[2]);
- printf("%s: %u\n",label,s[3]);
+ printf("%s: %08X %u\n",label,s[0],s[0]);
+ printf("%s: %08X %u\n",label,s[1],s[1]);
+ printf("%s: %08X %u\n",label,s[2],s[2]);
+ printf("%s: %08X %u\n",label,s[3],s[3]);
return;
}
@@ -181,6 +184,12 @@ print_counts (__m128i x, char *label) {
_mm_store_si128(a,x);
_mm_mfence();
printf("%s:",label);
+#ifdef HAVE_AVX2
+ printf(" %u",s[0]);
+ printf(" %u",s[1]);
+ printf(" %u",s[2]);
+ printf(" %u",s[3]);
+#else
printf(" %hd",s[0]);
printf(" %hd",s[1]);
printf(" %hd",s[2]);
@@ -197,10 +206,53 @@ print_counts (__m128i x, char *label) {
printf(" %hd",s[13]);
printf(" %hd",s[14]);
printf(" %hd",s[15]);
+#endif
+ printf("\n");
+ return;
+}
+#endif
+
+#ifdef HAVE_AVX2
+static void
+print_counts_256 (__m256i x, char *label) {
+ __m256i a[1];
+ Count_T *s = a;
+
+ _mm256_store_si256(a,x);
+ _mm_mfence();
+ printf("%s:",label);
+ printf(" %u",s[0]);
+ printf(" %u",s[1]);
+ printf(" %u",s[2]);
+ printf(" %u",s[3]);
+ printf(" %u",s[4]);
+ printf(" %u",s[5]);
+ printf(" %u",s[6]);
+ printf(" %u",s[7]);
printf("\n");
return;
}
+
+/* For debugging of SIMD procedures*/
+static void
+print_vector_256 (__m256i x, char *label) {
+ __m256i a[1];
+ unsigned int *s = a;
+
+ _mm256_store_si256(a,x);
+ _mm_mfence();
+ printf("%s: %08X %u\n",label,s[0],s[0]);
+ printf("%s: %08X %u\n",label,s[1],s[1]);
+ printf("%s: %08X %u\n",label,s[2],s[2]);
+ printf("%s: %08X %u\n",label,s[3],s[3]);
+ printf("%s: %08X %u\n",label,s[4],s[4]);
+ printf("%s: %08X %u\n",label,s[5],s[5]);
+ printf("%s: %08X %u\n",label,s[6],s[6]);
+ printf("%s: %08X %u\n",label,s[7],s[7]);
+ return;
+}
#endif
+
#endif
@@ -8405,6 +8457,9 @@ static const Genomecomp_T reverse_nt[] =
/* Code starts here */
+/* Shortoligmer_T is a short oligomer, representing 3 amino acids, or
+ 9 nt, requiring 18 bits or 2.25 bytes */
+
#define STRAIGHT_MASK_2 0x0000000F /* 2-mer: 1111 */
#define STRAIGHT_MASK_3 0x0000003F /* 3-mer: 11 1111 */
#define STRAIGHT_MASK_4 0x000000FF /* 4-mer: 1111 1111 */
@@ -8472,6 +8527,7 @@ static int suffnconsecutives_minor[NOLIGOINDICES_MINOR] = {10, 10, 10};
static Genomecomp_T *ref_blocks;
static Mode_T mode;
+#define USE_GATHER 1
#ifdef USE_SIMD_FOR_COUNTS
static __m128i mask9;
@@ -8481,6 +8537,26 @@ static __m128i mask6;
static __m128i mask5;
#endif
+#ifdef HAVE_AVX2
+#ifdef CHECK_FOR_OVERFLOW
+static __m128i maxcount128;
+static __m256i maxcount256;
+#endif
+static __m256i shift0to14;
+/* static __m256i low8; */
+static __m256i low7;
+static __m256i low6;
+static __m256i low5;
+static __m256i low4;
+static __m256i bigmask9;
+static __m256i bigmask8;
+static __m256i bigmask7;
+static __m256i bigmask6;
+static __m256i bigmask5;
+static __m256i byfours;
+static __m256i byeights;
+#endif
+
void
Oligoindex_hr_setup (Genomecomp_T *ref_blocks_in, Mode_T mode_in) {
@@ -8494,6 +8570,26 @@ Oligoindex_hr_setup (Genomecomp_T *ref_blocks_in, Mode_T mode_in) {
mask5 = _mm_set1_epi32(1023U);
#endif
+#ifdef HAVE_AVX2
+#ifdef CHECK_FOR_OVERFLOW
+ maxcount128 = _mm_set1_epi32(MAXCOUNT);
+ maxcount256 = _mm256_set1_epi32(MAXCOUNT);
+#endif
+ shift0to14 = _mm256_setr_epi32(0,2,4,6,8,10,12,14);
+ /* low8 = _mm256_setr_epi32(-1U,-1U,-1U,-1U,-1U,-1U,-1U,-1U); */
+ low7 = _mm256_setr_epi32(-1U,-1U,-1U,-1U,-1U,-1U,-1U, 0U);
+ low6 = _mm256_setr_epi32(-1U,-1U,-1U,-1U,-1U,-1U, 0U, 0U);
+ low5 = _mm256_setr_epi32(-1U,-1U,-1U,-1U,-1U, 0U, 0U, 0U);
+ low4 = _mm256_setr_epi32(-1U,-1U,-1U,-1U, 0U, 0U, 0U, 0U);
+ bigmask9 = _mm256_set1_epi32(262143U);
+ bigmask8 = _mm256_set1_epi32(65535U);
+ bigmask7 = _mm256_set1_epi32(16383U);
+ bigmask6 = _mm256_set1_epi32(4095U);
+ bigmask5 = _mm256_set1_epi32(1023U);
+ byfours = _mm256_setr_epi32(28,24,20,16,12,8,4,0);
+ byeights = _mm256_setr_epi32(56,48,40,32,24,16,8,0);
+#endif
+
#ifdef DEBUG14
Oligoindex_old_setup(ref_blocks_in,mode_in);
#endif
@@ -8520,55 +8616,43 @@ power (int base, int exponent) {
static T
-Oligoindex_new (int indexsize, int diag_lookback, int suffnconsecutive
-#ifndef PMAP
- , Shortoligomer_T mask
-#endif
- ) {
+Oligoindex_new (int indexsize, int diag_lookback, int suffnconsecutive, Shortoligomer_T mask) {
T new = (T) MALLOC(sizeof(*new));
-#ifdef PMAP
- new->indexsize_aa = indexsize;
- new->msb = power(NAMINOACIDS_STAGE2,indexsize-1);
- debug(printf("msb for indexsize %d is %u\n",indexsize,new->msb));
- new->oligospace = power(NAMINOACIDS_STAGE2,indexsize);
-#else
new->indexsize = indexsize;
new->mask = mask;
new->oligospace = power(4,indexsize);
-#endif
new->diag_lookback = diag_lookback;
new->suffnconsecutive = suffnconsecutive;
/* new->query_evaluated_p = false; */
-#ifdef HAVE_SSE2
- new->inquery_allocated = (__m128i *) _mm_malloc(new->oligospace * sizeof(Count_T),16);
+#ifdef HAVE_AVX2
+ new->inquery_allocated = (__m256i *) _mm_malloc(new->oligospace * sizeof(Inquery_T),32);
+ new->counts_allocated = (__m256i *) _mm_malloc(new->oligospace * sizeof(Count_T),32);
+ assert((long) new->inquery_allocated % 32 == 0);
+ assert((long) new->counts_allocated % 32 == 0);
+ new->inquery = (Inquery_T *) new->inquery_allocated;
+ new->counts = (Count_T *) new->counts_allocated;
+#elif defined(HAVE_SSE2)
+ new->inquery_allocated = (__m128i *) _mm_malloc(new->oligospace * sizeof(Inquery_T),16);
new->counts_allocated = (__m128i *) _mm_malloc(new->oligospace * sizeof(Count_T),16);
assert((long) new->inquery_allocated % 16 == 0);
assert((long) new->counts_allocated % 16 == 0);
- new->inquery = (Count_T *) new->inquery_allocated;
+ new->inquery = (Inquery_T *) new->inquery_allocated;
new->counts = (Count_T *) new->counts_allocated;
#else
- new->inquery = (bool *) CALLOC(new->oligospace,sizeof(bool));
- new->counts = (Count_T *) CALLOC(new->oligospace,sizeof(int));
+ new->inquery = (Inquery_T *) CALLOC(new->oligospace,sizeof(Inquery_T));
+ new->counts = (Count_T *) CALLOC(new->oligospace,sizeof(Count_T));
#endif
-#ifdef HAVE_SSE2
- memset((void *) new->inquery,INQUERY_FALSE,new->oligospace*sizeof(Count_T));
-#else
- memset((void *) new->inquery,false,new->oligospace*sizeof(bool));
-#endif
+ memset((void *) new->inquery,INQUERY_FALSE,new->oligospace*sizeof(Inquery_T));
memset((void *) new->counts,0,new->oligospace*sizeof(Count_T));
-
-#ifdef PMAP
- new->relevant_counts = (int *) CALLOC(new->oligospace,sizeof(int));
-#endif
- new->pointers_allocated = (Chrpos_T **) MALLOC((new->oligospace+1) * sizeof(Chrpos_T *));
+ new->pointers_allocated = (UINT4 *) MALLOC((new->oligospace+1) * sizeof(UINT4));
new->pointers = &(new->pointers_allocated[1]);
- new->positions_space = (Chrpos_T *) NULL;
- new->positions = (Chrpos_T **) MALLOC(new->oligospace * sizeof(Chrpos_T *));
+ new->positions = (UINT4 *) MALLOC(new->oligospace * sizeof(UINT4));
+ new->table = (Chrpos_T *) NULL;
return new;
}
@@ -8595,7 +8679,8 @@ Oligoindex_array_new_major (int max_querylength, int max_genomiclength) {
new->array = (T *) CALLOC(NOLIGOINDICES_MAJOR,sizeof(T));
for (source = 0; source < NOLIGOINDICES_MAJOR; source++) {
new->array[source] = Oligoindex_new(indexsizes_major[source],diag_lookbacks_major[source],
- suffnconsecutives_major[source],masks_major[source]);
+ suffnconsecutives_major[source],
+ masks_major[source]);
if (indexsizes_major[source] > max_indexsize) {
max_indexsize = indexsizes_major[source];
}
@@ -8621,7 +8706,8 @@ Oligoindex_array_new_minor (int max_querylength, int max_genomiclength) {
new->array = (T *) CALLOC(NOLIGOINDICES_MINOR,sizeof(T));
for (source = 0; source < NOLIGOINDICES_MINOR; source++) {
new->array[source] = Oligoindex_new(indexsizes_minor[source],diag_lookbacks_minor[source],
- suffnconsecutives_minor[source],masks_minor[source]);
+ suffnconsecutives_minor[source],
+ masks_minor[source]);
if (indexsizes_minor[source] > max_indexsize) {
max_indexsize = indexsizes_minor[source];
}
@@ -8711,12 +8797,6 @@ Genome_print_blocks (Genomecomp_T *blocks, Univcoord_T startpos, Univcoord_T end
#endif
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
@@ -8774,7 +8854,7 @@ dump_allocations (Chrpos_T **positions, Count_T *counts, int oligospace, int ind
#if defined(DEBUG) || defined(DEBUG9)
static void
-dump_positions (Chrpos_T **positions, Count_T *counts, Count_T *inquery, int oligospace, int indexsize) {
+dump_positions (Chrpos_T *table, UINT4 *positions, Count_T *counts, Inquery_T *inquery, int oligospace, int indexsize) {
int i;
char *nt;
@@ -8787,7 +8867,7 @@ dump_positions (Chrpos_T **positions, Count_T *counts, Count_T *inquery, int oli
printf("Oligo_hr %s => 0 entries\n",nt);
} else {
printf("Oligo_hr %s => %d entries: %u...%u\n",
- nt,counts[i],positions[i][0],positions[i][counts[i]-1]);
+ nt,counts[i],table[positions[i]],table[positions[i]+counts[i]-1]);
}
FREE(nt);
}
@@ -8819,6 +8899,9 @@ dump_positions (Chrpos_T **positions, Count_T *counts, Count_T *inquery, int oli
* count_fwdrev_simd
* store_fwdrev_simd
*
+ * Now, extract_*mers_{fwd|rev}_simd plus count_fwdrev_simd has been merged
+ * into count_*mers_{fwd|rev}_simd. However, we retain extract/store.
+ *
* Use a special procedure to compute an odd block of 32 k-mers
* count_*mers_{fwd|rev}
* This procedure can use SIMD if we compute backwards
@@ -8833,43 +8916,44 @@ dump_positions (Chrpos_T **positions, Count_T *counts, Count_T *inquery, int oli
************************************************************************/
static void
-count_9mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
- int startdiscard, int enddiscard) {
+count_9mers_fwd_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev,
+ Genomecomp_T nexthigh_rev, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 24) {
- masked = nexthigh_rev >> (78 - 2*pos);
- masked |= low_rev << (2*pos - 46);
+ masked = nexthigh_rev >> ((96 - 2*9) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*9));
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (46 - 2*pos);
+ masked = low_rev >> ((64 - 2*9) - 2*pos);
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 8) {
- masked = low_rev >> (46 - 2*pos);
- masked |= high_rev << (2*pos - 14);
+ masked = low_rev >> ((64 - 2*9) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*9));
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (14 - 2*pos);
+ masked = high_rev >> ((32 - 2*9) - 2*pos);
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
@@ -8877,70 +8961,59 @@ count_9mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T lo
}
static int
-store_9mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_9mers_fwd_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 24) {
- masked = nexthigh_rev >> (78 - 2*pos);
- masked |= low_rev << (2*pos - 46);
+ masked = nexthigh_rev >> ((96 - 2*9) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*9));
masked &= MASK9;
- debug(printf("%d %04X\n",pos,masked));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (46 - 2*pos);
+ masked = low_rev >> ((64 - 2*9) - 2*pos);
masked &= MASK9;
- debug(printf("%d %04X\n",pos,masked));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 8) {
- masked = low_rev >> (46 - 2*pos);
- masked |= high_rev << (2*pos - 14);
+ masked = low_rev >> ((64 - 2*9) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*9));
masked &= MASK9;
- debug(printf("%d %04X\n",pos,masked));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (14 - 2*pos);
+ masked = high_rev >> ((32 - 2*9) - 2*pos);
masked &= MASK9;
- debug(printf("%d %04X\n",pos,masked));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
@@ -8950,45 +9023,45 @@ store_9mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
}
-
static void
-count_8mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
- int startdiscard, int enddiscard) {
+count_8mers_fwd_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev,
+ Genomecomp_T nexthigh_rev, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 25) {
- masked = nexthigh_rev >> (80 - 2*pos);
- masked |= low_rev << (2*pos - 48);
+ masked = nexthigh_rev >> ((96 - 2*8) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*8));
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (48 - 2*pos);
+ masked = low_rev >> ((64 - 2*8) - 2*pos);
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 9) {
- masked = low_rev >> (48 - 2*pos);
- masked |= high_rev << (2*pos - 16);
+ masked = low_rev >> ((64 - 2*8) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*8));
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (16 - 2*pos);
+ masked = high_rev >> ((32 - 2*8) - 2*pos);
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
@@ -8996,70 +9069,59 @@ count_8mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T lo
}
static int
-store_8mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_8mers_fwd_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 25) {
- masked = nexthigh_rev >> (80 - 2*pos);
- masked |= low_rev << (2*pos - 48);
+ masked = nexthigh_rev >> ((96 - 2*8) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*8));
masked &= MASK8;
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (48 - 2*pos);
+ masked = low_rev >> ((64 - 2*8) - 2*pos);
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 9) {
- masked = low_rev >> (48 - 2*pos);
- masked |= high_rev << (2*pos - 16);
+ masked = low_rev >> ((64 - 2*8) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*8));
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (16 - 2*pos);
+ masked = high_rev >> ((32 - 2*8) - 2*pos);
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
@@ -9070,43 +9132,44 @@ store_8mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
static void
-count_7mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
- int startdiscard, int enddiscard) {
+count_7mers_fwd_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev,
+ Genomecomp_T nexthigh_rev, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 26) {
- masked = nexthigh_rev >> (82 - 2*pos);
- masked |= low_rev << (2*pos - 50);
+ masked = nexthigh_rev >> ((96 - 2*7) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*7));
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (50 - 2*pos);
+ masked = low_rev >> ((64 - 2*7) - 2*pos);
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 10) {
- masked = low_rev >> (50 - 2*pos);
- masked |= high_rev << (2*pos - 18);
+ masked = low_rev >> ((64 - 2*7) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*7));
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (18 - 2*pos);
+ masked = high_rev >> ((32 - 2*7) - 2*pos);
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
@@ -9114,66 +9177,59 @@ count_7mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T lo
}
static int
-store_7mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_7mers_fwd_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 26) {
- masked = nexthigh_rev >> (82 - 2*pos);
- masked |= low_rev << (2*pos - 50);
+ masked = nexthigh_rev >> ((96 - 2*7) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*7));
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (50 - 2*pos);
+ masked = low_rev >> ((64 - 2*7) - 2*pos);
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 10) {
- masked = low_rev >> (50 - 2*pos);
- masked |= high_rev << (2*pos - 18);
+ masked = low_rev >> ((64 - 2*7) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*7));
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (18 - 2*pos);
+ masked = high_rev >> ((32 - 2*7) - 2*pos);
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
@@ -9184,111 +9240,104 @@ store_7mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
static void
-count_6mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
- int startdiscard, int enddiscard) {
+count_6mers_fwd_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev,
+ Genomecomp_T nexthigh_rev, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 27) {
- masked = nexthigh_rev >> (84 - 2*pos);
- masked |= low_rev << (2*pos - 52);
+ masked = nexthigh_rev >> ((96 - 2*6) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*6));
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (52 - 2*pos);
+ masked = low_rev >> ((64 - 2*6) - 2*pos);
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 11) {
- masked = low_rev >> (52 - 2*pos);
- masked |= high_rev << (2*pos - 20);
+ masked = low_rev >> ((64 - 2*6) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*6));
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (20 - 2*pos);
+ masked = high_rev >> ((32 - 2*6) - 2*pos);
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
return;
}
-
static int
-store_6mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_6mers_fwd_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 27) {
- masked = nexthigh_rev >> (84 - 2*pos);
- masked |= low_rev << (2*pos - 52);
+ masked = nexthigh_rev >> ((96 - 2*6) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*6));
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (52 - 2*pos);
+ masked = low_rev >> ((64 - 2*6) - 2*pos);
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 11) {
- masked = low_rev >> (52 - 2*pos);
- masked |= high_rev << (2*pos - 20);
+ masked = low_rev >> ((64 - 2*6) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*6));
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (20 - 2*pos);
+ masked = high_rev >> ((32 - 2*6) - 2*pos);
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
@@ -9299,111 +9348,104 @@ store_6mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
static void
-count_5mers_fwd_partial (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
- int startdiscard, int enddiscard) {
+count_5mers_fwd_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev,
+ Genomecomp_T nexthigh_rev, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 28) {
- masked = nexthigh_rev >> (86 - 2*pos);
- masked |= low_rev << (2*pos - 54);
+ masked = nexthigh_rev >> ((96 - 2*5) - 2*pos);
+ masked |= low_rev << (2*pos - (64 - 2*5));
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (54 - 2*pos);
+ masked = low_rev >> ((64 - 2*5) - 2*pos);
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard && pos >= 12) {
- masked = low_rev >> (54 - 2*pos);
- masked |= high_rev << (2*pos - 22);
+ masked = low_rev >> ((64 - 2*5) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*5));
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (22 - 2*pos);
+ masked = high_rev >> ((32 - 2*5) - 2*pos);
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos--;
}
return;
}
-
static int
-store_5mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_5mers_fwd_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
pos = enddiscard;
+
while (pos >= startdiscard && pos >= 28) {
- masked = nexthigh_rev >> (86 - 2*pos);
- masked |= low_rev << (2*pos - 54);
+ masked = nexthigh_rev >> ((96 - 2*5) - 2*pos);
+ masked |= low_rev << (2*pos - (64- 2*5));
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
- while (pos >= startdiscard && pos >= 16) {
- masked = low_rev >> (54 - 2*pos);
+ while (pos >= startdiscard && pos >= 48) {
+ masked = low_rev >> ((64 - 2*5) - 2*pos);
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard && pos >= 12) {
- masked = low_rev >> (54 - 2*pos);
- masked |= high_rev << (2*pos - 22);
+ masked = low_rev >> ((64 - 2*5) - 2*pos);
+ masked |= high_rev << (2*pos - (32 - 2*5));
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
}
while (pos >= startdiscard) {
- masked = high_rev >> (22 - 2*pos);
+ masked = high_rev >> ((32 - 2*5) - 2*pos);
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos--;
@@ -9413,6 +9455,7 @@ store_5mers_fwd_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
}
+
#if 0
/* Note; for AVX2 and AVX512 */
/* Variable bit shift right logical (VPSRLVD/Q) */
@@ -9423,6 +9466,48 @@ _high_rev is broadcast in eight 32-bit quantities in __m256i
Then need to mask
(Gather in AVX2)
(Scatter in AVX-512)
+
+
+ Previously, did
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ _counts = _mm256_add_epi32(_counts,ones256);
+
+ Problem: Cannot add ones if any oligo repeats itself within the same SIMD register
+ Need to wait for conflict instructions from AVX512:
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _conflict = _mm256_conflict_epi32(_masked);
+ if (_conflict is zero) then
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ _counts = _mm256_add_epi32(_counts,ones256);
+ } else {
+ Increment counts manually, or account for conflict
+ }
+
+
+
+ _counts = _mm_i32gather_epi32(counts,_masked,/*scale*/4);
+ _counts = _mm_add_epi32(_counts,ones);
+ _mm_i32scatter_epi32(counts,_masked,/*scale*/4);
+
+ /* Need to change pointers and positions to be indices into a set of values */
+ _pointers = _mm256_i32gather_epi32(pointers,_masked,/*scale*/4);
+ _positions = _mm256_i32gather_epi32(positions,_masked,/*scale*/4);
+ _space = _mm256_sub_epi32(_positions,_pointers);
+ _pointers = _mm256_sub_epi32(_pointers,ones); /* New pointers */
+ _chrpos = _mm256_sub_epi32(_mm256_set1_epi32(chrpos),ramp);
+
+ _mm256_mask_i32scatter_epi32(pointers,_masked,_pointers,/*scale*/4);
+ _mm256_mask_i32scatter_epi32(values,_pointers,_chrpos,/*scale*/4);
+
+ if (EXTRACT256(_space,0)) {
+ pointer = EXTRACT256(_pointers,0);
+ *pointer = EXTRACT256(_chrpos,0);
+ }
+
#endif
@@ -9559,816 +9644,2672 @@ count_fwdrev_simd (Count_T *counts, UINT4 *array) {
chrpos ascending from left and reverse has chrpos ascending from
right */
static Chrpos_T
-store_fwdrev_simd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_fwdrev_simd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
UINT4 *array) {
+#if defined(HAVE_AVX2) && defined(USE_GATHER)
+ __m256i _counts, _masked;
+#else
Genomecomp_T masked;
+#endif
- /* Row 4 */
+ /* Row 3 */
+#if defined(HAVE_AVX2) && defined(USE_GATHER)
+ _masked = _mm256_i32gather_epi32((int *) &(array[32+3]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[63]]);
+ assert(EXTRACT256(_counts,1) == counts[array[59]]);
+ assert(EXTRACT256(_counts,2) == counts[array[55]]);
+ assert(EXTRACT256(_counts,3) == counts[array[51]]);
+ assert(EXTRACT256(_counts,4) == counts[array[47]]);
+ assert(EXTRACT256(_counts,5) == counts[array[43]]);
+ assert(EXTRACT256(_counts,6) == counts[array[39]]);
+ assert(EXTRACT256(_counts,7) == counts[array[35]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos,chrpos,0));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 1,chrpos,1));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 1;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 2,chrpos,2));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 2;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 3,chrpos,3));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 3;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 4,chrpos,4));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 4;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 5,chrpos,5));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 5;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 6,chrpos,6));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 6;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 7,chrpos,7));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 7;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[3]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[31]]);
+ assert(EXTRACT256(_counts,1) == counts[array[27]]);
+ assert(EXTRACT256(_counts,2) == counts[array[23]]);
+ assert(EXTRACT256(_counts,3) == counts[array[19]]);
+ assert(EXTRACT256(_counts,4) == counts[array[15]]);
+ assert(EXTRACT256(_counts,5) == counts[array[11]]);
+ assert(EXTRACT256(_counts,6) == counts[array[7]]);
+ assert(EXTRACT256(_counts,7) == counts[array[3]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 8,chrpos,8));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 8;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 9,chrpos,9));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 9;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 10,chrpos,10));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 10;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 11,chrpos,11));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 11;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 12,chrpos,12));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 12;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 13,chrpos,13));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 13;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 14,chrpos,14));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 14;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 15,chrpos,15));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 15;
+ }
+ }
+#else
masked = array[63];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos,chrpos,0));
+ table[--pointers[masked]] = chrpos;
}
masked = array[59];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 1,chrpos,1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = array[55];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 2,chrpos,2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = array[51];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 3,chrpos,3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = array[47];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 4,chrpos,4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = array[43];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 5,chrpos,5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = array[39];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 6,chrpos,6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = array[35];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 7,chrpos,7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = array[31];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 8,chrpos,8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = array[27];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 9,chrpos,9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = array[23];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 10,chrpos,10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = array[19];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 11,chrpos,11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = array[15];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 12,chrpos,12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = array[11];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 13,chrpos,13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = array[7];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 14,chrpos,14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = array[3];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 15,chrpos,15));
+ table[--pointers[masked]] = chrpos - 15;
}
+#endif
- /* Row 3 */
+ /* Row 2 */
+#if defined(HAVE_AVX2) && defined(USE_GATHER)
+ _masked = _mm256_i32gather_epi32((int *) &(array[32+2]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[62]]);
+ assert(EXTRACT256(_counts,1) == counts[array[58]]);
+ assert(EXTRACT256(_counts,2) == counts[array[54]]);
+ assert(EXTRACT256(_counts,3) == counts[array[50]]);
+ assert(EXTRACT256(_counts,4) == counts[array[46]]);
+ assert(EXTRACT256(_counts,5) == counts[array[42]]);
+ assert(EXTRACT256(_counts,6) == counts[array[38]]);
+ assert(EXTRACT256(_counts,7) == counts[array[34]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 16,chrpos,16));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 16;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 17,chrpos,17));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 17;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 18,chrpos,18));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 18;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 19,chrpos,19));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 19;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 20,chrpos,20));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 20;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 21,chrpos,21));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 21;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 22,chrpos,22));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 22;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 23,chrpos,23));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 23;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[2]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[30]]);
+ assert(EXTRACT256(_counts,1) == counts[array[26]]);
+ assert(EXTRACT256(_counts,2) == counts[array[22]]);
+ assert(EXTRACT256(_counts,3) == counts[array[18]]);
+ assert(EXTRACT256(_counts,4) == counts[array[14]]);
+ assert(EXTRACT256(_counts,5) == counts[array[10]]);
+ assert(EXTRACT256(_counts,6) == counts[array[6]]);
+ assert(EXTRACT256(_counts,7) == counts[array[2]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 24,chrpos,24));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 24;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 25,chrpos,25));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 25;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 26,chrpos,26));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 26;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 27,chrpos,27));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 27;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 28,chrpos,28));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 28;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 29,chrpos,29));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 29;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 30,chrpos,30));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 30;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 31,chrpos,31));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 31;
+ }
+ }
+#else
masked = array[62];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 16,chrpos,16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = array[58];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 17,chrpos,17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = array[54];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 18,chrpos,18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = array[50];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 19,chrpos,19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = array[46];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 20,chrpos,20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = array[42];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 21,chrpos,21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = array[38];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 22,chrpos,22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = array[34];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 23,chrpos,23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = array[30];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 24,chrpos,24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = array[26];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 25,chrpos,25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = array[22];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 26,chrpos,26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = array[18];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 27,chrpos,27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = array[14];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 28,chrpos,28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = array[10];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 29,chrpos,29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = array[6];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 30,chrpos,30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = array[2];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 31,chrpos,31));
+ table[--pointers[masked]] = chrpos - 31;
}
+#endif
/* Row 1 */
+#if defined(HAVE_AVX2) && defined(USE_GATHER)
+ _masked = _mm256_i32gather_epi32((int *) &(array[32+1]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[61]]);
+ assert(EXTRACT256(_counts,1) == counts[array[57]]);
+ assert(EXTRACT256(_counts,2) == counts[array[53]]);
+ assert(EXTRACT256(_counts,3) == counts[array[49]]);
+ assert(EXTRACT256(_counts,4) == counts[array[45]]);
+ assert(EXTRACT256(_counts,5) == counts[array[41]]);
+ assert(EXTRACT256(_counts,6) == counts[array[37]]);
+ assert(EXTRACT256(_counts,7) == counts[array[33]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 32,chrpos,32));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 32;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 33,chrpos,33));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 33;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 34,chrpos,34));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 34;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 35,chrpos,35));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 35;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 36,chrpos,36));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 36;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 37,chrpos,37));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 37;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 38,chrpos,38));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 38;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 39,chrpos,39));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 39;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[1]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[29]]);
+ assert(EXTRACT256(_counts,1) == counts[array[25]]);
+ assert(EXTRACT256(_counts,2) == counts[array[21]]);
+ assert(EXTRACT256(_counts,3) == counts[array[17]]);
+ assert(EXTRACT256(_counts,4) == counts[array[13]]);
+ assert(EXTRACT256(_counts,5) == counts[array[9]]);
+ assert(EXTRACT256(_counts,6) == counts[array[5]]);
+ assert(EXTRACT256(_counts,7) == counts[array[1]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 40,chrpos,40));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 40;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 41,chrpos,41));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 41;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 42,chrpos,42));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 42;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 43,chrpos,43));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 43;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 44,chrpos,44));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 44;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 45,chrpos,45));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 45;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 46,chrpos,46));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 46;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 47,chrpos,47));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 47;
+ }
+ }
+#else
masked = array[61];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 32));
- *(--pointers[masked]) = chrpos - 32;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 32,chrpos,32));
+ table[--pointers[masked]] = chrpos - 32;
}
masked = array[57];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 33));
- *(--pointers[masked]) = chrpos - 33;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 33,chrpos,33));
+ table[--pointers[masked]] = chrpos - 33;
}
masked = array[53];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 34));
- *(--pointers[masked]) = chrpos - 34;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 34,chrpos,34));
+ table[--pointers[masked]] = chrpos - 34;
}
masked = array[49];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 35));
- *(--pointers[masked]) = chrpos - 35;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 35,chrpos,35));
+ table[--pointers[masked]] = chrpos - 35;
}
masked = array[45];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 36));
- *(--pointers[masked]) = chrpos - 36;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 36,chrpos,36));
+ table[--pointers[masked]] = chrpos - 36;
}
masked = array[41];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 37));
- *(--pointers[masked]) = chrpos - 37;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 37,chrpos,37));
+ table[--pointers[masked]] = chrpos - 37;
}
masked = array[37];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 38));
- *(--pointers[masked]) = chrpos - 38;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 38,chrpos,38));
+ table[--pointers[masked]] = chrpos - 38;
}
masked = array[33];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 39));
- *(--pointers[masked]) = chrpos - 39;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 39,chrpos,39));
+ table[--pointers[masked]] = chrpos - 39;
}
masked = array[29];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 40));
- *(--pointers[masked]) = chrpos - 40;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 40,chrpos,40));
+ table[--pointers[masked]] = chrpos - 40;
}
masked = array[25];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 41));
- *(--pointers[masked]) = chrpos - 41;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 41,chrpos,41));
+ table[--pointers[masked]] = chrpos - 41;
}
masked = array[21];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 42));
- *(--pointers[masked]) = chrpos - 42;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 42,chrpos,42));
+ table[--pointers[masked]] = chrpos - 42;
}
masked = array[17];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 43));
- *(--pointers[masked]) = chrpos - 43;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 43,chrpos,43));
+ table[--pointers[masked]] = chrpos - 43;
}
masked = array[13];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 44));
- *(--pointers[masked]) = chrpos - 44;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 44,chrpos,44));
+ table[--pointers[masked]] = chrpos - 44;
}
masked = array[9];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 45));
- *(--pointers[masked]) = chrpos - 45;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 45,chrpos,45));
+ table[--pointers[masked]] = chrpos - 45;
}
masked = array[5];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 46));
- *(--pointers[masked]) = chrpos - 46;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 46,chrpos,46));
+ table[--pointers[masked]] = chrpos - 46;
}
masked = array[1];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 47));
- *(--pointers[masked]) = chrpos - 47;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 47,chrpos,47));
+ table[--pointers[masked]] = chrpos - 47;
}
+#endif
/* Row 0 */
- masked = array[60];
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 48));
- *(--pointers[masked]) = chrpos - 48;
+#if defined(HAVE_AVX2) && defined(USE_GATHER)
+ _masked = _mm256_i32gather_epi32((int *) &(array[32+0]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[60]]);
+ assert(EXTRACT256(_counts,1) == counts[array[56]]);
+ assert(EXTRACT256(_counts,2) == counts[array[52]]);
+ assert(EXTRACT256(_counts,3) == counts[array[48]]);
+ assert(EXTRACT256(_counts,4) == counts[array[44]]);
+ assert(EXTRACT256(_counts,5) == counts[array[40]]);
+ assert(EXTRACT256(_counts,6) == counts[array[36]]);
+ assert(EXTRACT256(_counts,7) == counts[array[32]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 48,chrpos,48));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 48;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 49,chrpos,49));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 49;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 50,chrpos,50));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 50;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 51,chrpos,51));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 51;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 52,chrpos,52));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 52;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 53,chrpos,53));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 53;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 54,chrpos,54));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 54;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 55,chrpos,55));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 55;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[0]),byfours,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[28]]);
+ assert(EXTRACT256(_counts,1) == counts[array[24]]);
+ assert(EXTRACT256(_counts,2) == counts[array[20]]);
+ assert(EXTRACT256(_counts,3) == counts[array[16]]);
+ assert(EXTRACT256(_counts,4) == counts[array[12]]);
+ assert(EXTRACT256(_counts,5) == counts[array[8]]);
+ assert(EXTRACT256(_counts,6) == counts[array[4]]);
+ assert(EXTRACT256(_counts,7) == counts[array[0]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 56,chrpos,56));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 56;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 57,chrpos,57));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 57;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 58,chrpos,58));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 58;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 59,chrpos,59));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 59;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 60,chrpos,60));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 60;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 61,chrpos,61));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 61;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 62,chrpos,62));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 62;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 63,chrpos,63));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 63;
}
}
+#else
+ masked = array[60];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 48,chrpos,48));
+ table[--pointers[masked]] = chrpos - 48;
+ }
masked = array[56];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 49));
- *(--pointers[masked]) = chrpos - 49;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 49,chrpos,49));
+ table[--pointers[masked]] = chrpos - 49;
}
masked = array[52];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 50));
- *(--pointers[masked]) = chrpos - 50;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 50,chrpos,50));
+ table[--pointers[masked]] = chrpos - 50;
}
masked = array[48];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 51));
- *(--pointers[masked]) = chrpos - 51;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 51,chrpos,51));
+ table[--pointers[masked]] = chrpos - 51;
}
masked = array[44];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 52));
- *(--pointers[masked]) = chrpos - 52;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 52,chrpos,52));
+ table[--pointers[masked]] = chrpos - 52;
}
masked = array[40];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 53));
- *(--pointers[masked]) = chrpos - 53;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 53,chrpos,53));
+ table[--pointers[masked]] = chrpos - 53;
}
masked = array[36];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 54));
- *(--pointers[masked]) = chrpos - 54;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 54,chrpos,54));
+ table[--pointers[masked]] = chrpos - 54;
}
masked = array[32];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 55));
- *(--pointers[masked]) = chrpos - 55;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 55,chrpos,55));
+ table[--pointers[masked]] = chrpos - 55;
}
masked = array[28];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 56));
- *(--pointers[masked]) = chrpos - 56;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 56,chrpos,56));
+ table[--pointers[masked]] = chrpos - 56;
}
masked = array[24];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 57));
- *(--pointers[masked]) = chrpos - 57;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 57,chrpos,57));
+ table[--pointers[masked]] = chrpos - 57;
}
masked = array[20];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 58));
- *(--pointers[masked]) = chrpos - 58;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 58,chrpos,58));
+ table[--pointers[masked]] = chrpos - 58;
}
masked = array[16];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 59));
- *(--pointers[masked]) = chrpos - 59;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 59,chrpos,59));
+ table[--pointers[masked]] = chrpos - 59;
}
masked = array[12];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 60));
- *(--pointers[masked]) = chrpos - 60;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 60,chrpos,60));
+ table[--pointers[masked]] = chrpos - 60;
}
masked = array[8];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 61));
- *(--pointers[masked]) = chrpos - 61;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 61,chrpos,61));
+ table[--pointers[masked]] = chrpos - 61;
}
masked = array[4];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 62));
- *(--pointers[masked]) = chrpos - 62;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 62,chrpos,62));
+ table[--pointers[masked]] = chrpos - 62;
}
masked = array[0];
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 63));
- *(--pointers[masked]) = chrpos - 63;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 63,chrpos,63));
+ table[--pointers[masked]] = chrpos - 63;
}
+#endif
return chrpos - 64;
}
-#endif
+#ifdef HAVE_AVX2
-static void
-count_9mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
- Genomecomp_T masked, oligo;
-#ifdef INDIVIDUAL_SHIFTS
-#elif defined(SIMD_MASK_THEN_STORE)
- UINT4 _masked[4] __attribute__ ((aligned (16)));
- __m128i _oligo;
+/* testz(counts,counts) == 0 implies there is a nonzero count */
+static Chrpos_T
+store_fwdrev_simd_128 (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ UINT4 *array) {
+#ifdef USE_GATHER
+ __m256i _counts, _masked;
#else
- __m128i _oligo, _masked;
+ Genomecomp_T masked;
#endif
+#ifdef DEBUG
+ int i;
+ for (i = 0; i < 128; i += 8) {
+ printf("%d: %08X %08X %08X %08X %08X %08X %08X %08X\n",
+ i,array[i],array[i+1],array[i+2],array[i+3],array[i+4],array[i+5],array[i+6],array[i+7]);
+ }
+#endif
- oligo = nexthigh_rev >> 16; /* For 31..24 */
- oligo |= low_rev << 16;
-
-#ifdef INDIVIDUAL_SHIFTS
- masked = oligo & MASK9; /* 31 */
- counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 2) & MASK9; /* 30 */
- counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
+ /* Row 7 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+7]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[127]]);
+ assert(EXTRACT256(_counts,1) == counts[array[119]]);
+ assert(EXTRACT256(_counts,2) == counts[array[111]]);
+ assert(EXTRACT256(_counts,3) == counts[array[103]]);
+ assert(EXTRACT256(_counts,4) == counts[array[95]]);
+ assert(EXTRACT256(_counts,5) == counts[array[87]]);
+ assert(EXTRACT256(_counts,6) == counts[array[79]]);
+ assert(EXTRACT256(_counts,7) == counts[array[71]]);
- masked = (oligo >> 4) & MASK9; /* 29 */
- counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos,chrpos,0));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 1,chrpos,1));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 1;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 2,chrpos,2));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 2;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 3,chrpos,3));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 3;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 4,chrpos,4));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 4;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 5,chrpos,5));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 5;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 6,chrpos,6));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 6;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 7,chrpos,7));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 7;
+ }
+ }
- masked = (oligo >> 6) & MASK9; /* 28 */
- counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
+ _masked = _mm256_i32gather_epi32((int *) &(array[7]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[63]]);
+ assert(EXTRACT256(_counts,1) == counts[array[55]]);
+ assert(EXTRACT256(_counts,2) == counts[array[47]]);
+ assert(EXTRACT256(_counts,3) == counts[array[39]]);
+ assert(EXTRACT256(_counts,4) == counts[array[31]]);
+ assert(EXTRACT256(_counts,5) == counts[array[23]]);
+ assert(EXTRACT256(_counts,6) == counts[array[15]]);
+ assert(EXTRACT256(_counts,7) == counts[array[7]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 8,chrpos,8));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 8;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 9,chrpos,9));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 9;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 10,chrpos,10));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 10;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 11,chrpos,11));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 11;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 12,chrpos,12));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 12;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 13,chrpos,13));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 13;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 14,chrpos,14));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 14;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 15,chrpos,15));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 15;
+ }
+ }
+#else
+ masked = array[127];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos,chrpos,0));
+ table[--pointers[masked]] = chrpos;
+ }
- masked = (oligo >> 8) & MASK9; /* 27 */
- counts[masked] += 1;
- debug(printf("27 %04X => %d\n",masked,counts[masked]));
+ masked = array[119];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 1,chrpos,1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
- masked = (oligo >> 10) & MASK9; /* 26 */
- counts[masked] += 1;
- debug(printf("26 %04X => %d\n",masked,counts[masked]));
+ masked = array[111];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 2,chrpos,2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
- masked = (oligo >> 12) & MASK9; /* 25 */
- counts[masked] += 1;
- debug(printf("25 %04X => %d\n",masked,counts[masked]));
+ masked = array[103];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 3,chrpos,3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
- masked = (oligo >> 14) & MASK9; /* 24 */
- counts[masked] += 1;
- debug(printf("24 %04X => %d\n",masked,counts[masked]));
+ masked = array[95];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 4,chrpos,4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
-#else
- _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+ masked = array[87];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 5,chrpos,5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
+ masked = array[79];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 6,chrpos,6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
+ masked = array[71];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 7,chrpos,7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
+ masked = array[63];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 8,chrpos,8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
- masked = EXTRACT(_masked,3);
- counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
+ masked = array[55];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 9,chrpos,9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+ masked = array[47];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 10,chrpos,10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+ masked = array[39];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 11,chrpos,11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
- debug(printf("27 %04X => %d\n",masked,counts[masked]));
+ masked = array[31];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 12,chrpos,12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
- debug(printf("26 %04X => %d\n",masked,counts[masked]));
+ masked = array[23];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 13,chrpos,13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
- debug(printf("25 %04X => %d\n",masked,counts[masked]));
+ masked = array[15];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 14,chrpos,14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
- masked = EXTRACT(_masked,3);
- counts[masked] += 1;
- debug(printf("24 %04X => %d\n",masked,counts[masked]));
+ masked = array[7];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 15,chrpos,15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
#endif
-#ifdef INDIVIDUAL_SHIFTS
- masked = low_rev & MASK9; /* 23 */
- counts[masked] += 1;
- debug(printf("23 %04X => %d\n",masked,counts[masked]));
+ /* Row 6 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+6]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[126]]);
+ assert(EXTRACT256(_counts,1) == counts[array[118]]);
+ assert(EXTRACT256(_counts,2) == counts[array[110]]);
+ assert(EXTRACT256(_counts,3) == counts[array[102]]);
+ assert(EXTRACT256(_counts,4) == counts[array[94]]);
+ assert(EXTRACT256(_counts,5) == counts[array[86]]);
+ assert(EXTRACT256(_counts,6) == counts[array[78]]);
+ assert(EXTRACT256(_counts,7) == counts[array[70]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 16,chrpos,16));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 16;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 17,chrpos,17));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 17;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 18,chrpos,18));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 18;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 19,chrpos,19));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 19;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 20,chrpos,20));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 20;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 21,chrpos,21));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 21;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 22,chrpos,22));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 22;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 23,chrpos,23));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 23;
+ }
+ }
- masked = (low_rev >> 2) & MASK9; /* 22 */
- counts[masked] += 1;
- debug(printf("22 %04X => %d\n",masked,counts[masked]));
+ _masked = _mm256_i32gather_epi32((int *) &(array[6]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[62]]);
+ assert(EXTRACT256(_counts,1) == counts[array[54]]);
+ assert(EXTRACT256(_counts,2) == counts[array[46]]);
+ assert(EXTRACT256(_counts,3) == counts[array[38]]);
+ assert(EXTRACT256(_counts,4) == counts[array[30]]);
+ assert(EXTRACT256(_counts,5) == counts[array[22]]);
+ assert(EXTRACT256(_counts,6) == counts[array[14]]);
+ assert(EXTRACT256(_counts,7) == counts[array[6]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 24,chrpos,24));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 24;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 25,chrpos,25));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 25;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 26,chrpos,26));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 26;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 27,chrpos,27));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 27;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 28,chrpos,28));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 28;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 29,chrpos,29));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 29;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 30,chrpos,30));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 30;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 31,chrpos,31));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 31;
+ }
+ }
+#else
+ masked = array[126];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 16,chrpos,16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
- masked = (low_rev >> 4) & MASK9; /* 21 */
- counts[masked] += 1;
- debug(printf("21 %04X => %d\n",masked,counts[masked]));
+ masked = array[118];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 17,chrpos,17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
- masked = (low_rev >> 6) & MASK9; /* 20 */
- counts[masked] += 1;
- debug(printf("20 %04X => %d\n",masked,counts[masked]));
+ masked = array[110];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 18,chrpos,18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
- masked = (low_rev >> 8) & MASK9; /* 19 */
- counts[masked] += 1;
- debug(printf("19 %04X => %d\n",masked,counts[masked]));
+ masked = array[102];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 19,chrpos,19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
- masked = (low_rev >> 10) & MASK9; /* 18 */
- counts[masked] += 1;
- debug(printf("18 %04X => %d\n",masked,counts[masked]));
+ masked = array[94];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 20,chrpos,20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
- masked = (low_rev >> 12) & MASK9; /* 17 */
- counts[masked] += 1;
- debug(printf("17 %04X => %d\n",masked,counts[masked]));
+ masked = array[86];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 21,chrpos,21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
- masked = low_rev >> 14; /* 16, No mask necessary */
- counts[masked] += 1;
- debug(printf("16 %04X => %d\n",masked,counts[masked]));
+ masked = array[78];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 22,chrpos,22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
-#else
- _oligo = _mm_setr_epi32(low_rev, low_rev >> 2, low_rev >> 4, low_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+ masked = array[70];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 23,chrpos,23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
- debug(printf("23 %04X => %d\n",masked,counts[masked]));
+ masked = array[62];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 24,chrpos,24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
- debug(printf("22 %04X => %d\n",masked,counts[masked]));
+ masked = array[54];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 25,chrpos,25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
- debug(printf("21 %04X => %d\n",masked,counts[masked]));
+ masked = array[46];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 26,chrpos,26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = array[38];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 27,chrpos,27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = array[30];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 28,chrpos,28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = array[22];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 29,chrpos,29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = array[14];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 30,chrpos,30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = array[6];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 31,chrpos,31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ /* Row 5 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+5]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[125]]);
+ assert(EXTRACT256(_counts,1) == counts[array[117]]);
+ assert(EXTRACT256(_counts,2) == counts[array[109]]);
+ assert(EXTRACT256(_counts,3) == counts[array[101]]);
+ assert(EXTRACT256(_counts,4) == counts[array[93]]);
+ assert(EXTRACT256(_counts,5) == counts[array[85]]);
+ assert(EXTRACT256(_counts,6) == counts[array[77]]);
+ assert(EXTRACT256(_counts,7) == counts[array[69]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 32,chrpos,32));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 32;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 33,chrpos,33));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 33;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 34,chrpos,34));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 34;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 35,chrpos,35));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 35;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 36,chrpos,36));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 36;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 37,chrpos,37));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 37;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 38,chrpos,38));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 38;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 39,chrpos,39));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 39;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[5]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[61]]);
+ assert(EXTRACT256(_counts,1) == counts[array[53]]);
+ assert(EXTRACT256(_counts,2) == counts[array[45]]);
+ assert(EXTRACT256(_counts,3) == counts[array[37]]);
+ assert(EXTRACT256(_counts,4) == counts[array[29]]);
+ assert(EXTRACT256(_counts,5) == counts[array[21]]);
+ assert(EXTRACT256(_counts,6) == counts[array[13]]);
+ assert(EXTRACT256(_counts,7) == counts[array[5]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 40,chrpos,40));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 40;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 41,chrpos,41));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 41;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 42,chrpos,42));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 42;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 43,chrpos,43));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 43;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 44,chrpos,44));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 44;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 45,chrpos,45));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 45;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 46,chrpos,46));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 46;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 47,chrpos,47));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 47;
+ }
+ }
+#else
+ masked = array[125];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 32,chrpos,32));
+ table[--pointers[masked]] = chrpos - 32;
+ }
+
+ masked = array[117];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 33,chrpos,33));
+ table[--pointers[masked]] = chrpos - 33;
+ }
+
+ masked = array[109];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 34,chrpos,34));
+ table[--pointers[masked]] = chrpos - 34;
+ }
+
+ masked = array[101];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 35,chrpos,35));
+ table[--pointers[masked]] = chrpos - 35;
+ }
+
+ masked = array[93];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 36,chrpos,36));
+ table[--pointers[masked]] = chrpos - 36;
+ }
+
+ masked = array[85];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 37,chrpos,37));
+ table[--pointers[masked]] = chrpos - 37;
+ }
+
+ masked = array[77];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 38,chrpos,38));
+ table[--pointers[masked]] = chrpos - 38;
+ }
+
+ masked = array[69];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 39,chrpos,39));
+ table[--pointers[masked]] = chrpos - 39;
+ }
+
+ masked = array[61];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 40,chrpos,40));
+ table[--pointers[masked]] = chrpos - 40;
+ }
+
+ masked = array[53];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 41,chrpos,41));
+ table[--pointers[masked]] = chrpos - 41;
+ }
+
+ masked = array[45];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 42,chrpos,42));
+ table[--pointers[masked]] = chrpos - 42;
+ }
+
+ masked = array[37];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 43,chrpos,43));
+ table[--pointers[masked]] = chrpos - 43;
+ }
+
+ masked = array[29];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 44,chrpos,44));
+ table[--pointers[masked]] = chrpos - 44;
+ }
+
+ masked = array[21];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 45,chrpos,45));
+ table[--pointers[masked]] = chrpos - 45;
+ }
+
+ masked = array[13];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 46,chrpos,46));
+ table[--pointers[masked]] = chrpos - 46;
+ }
+
+ masked = array[5];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 47,chrpos,47));
+ table[--pointers[masked]] = chrpos - 47;
+ }
+#endif
+
+
+ /* Row 4 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+4]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[124]]);
+ assert(EXTRACT256(_counts,1) == counts[array[116]]);
+ assert(EXTRACT256(_counts,2) == counts[array[108]]);
+ assert(EXTRACT256(_counts,3) == counts[array[100]]);
+ assert(EXTRACT256(_counts,4) == counts[array[92]]);
+ assert(EXTRACT256(_counts,5) == counts[array[84]]);
+ assert(EXTRACT256(_counts,6) == counts[array[76]]);
+ assert(EXTRACT256(_counts,7) == counts[array[68]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 48,chrpos,48));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 48;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 49,chrpos,49));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 49;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 50,chrpos,50));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 50;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 51,chrpos,51));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 51;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 52,chrpos,52));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 52;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 53,chrpos,53));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 53;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 54,chrpos,54));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 54;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 55,chrpos,55));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 55;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[4]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[60]]);
+ assert(EXTRACT256(_counts,1) == counts[array[52]]);
+ assert(EXTRACT256(_counts,2) == counts[array[44]]);
+ assert(EXTRACT256(_counts,3) == counts[array[36]]);
+ assert(EXTRACT256(_counts,4) == counts[array[28]]);
+ assert(EXTRACT256(_counts,5) == counts[array[20]]);
+ assert(EXTRACT256(_counts,6) == counts[array[12]]);
+ assert(EXTRACT256(_counts,7) == counts[array[4]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 56,chrpos,56));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 56;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 57,chrpos,57));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 57;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 58,chrpos,58));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 58;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 59,chrpos,59));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 59;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 60,chrpos,60));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 60;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 61,chrpos,61));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 61;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 62,chrpos,62));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 62;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 63,chrpos,63));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 63;
+ }
+ }
+#else
+ masked = array[124];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 48,chrpos,48));
+ table[--pointers[masked]] = chrpos - 48;
+ }
+
+ masked = array[116];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 49,chrpos,49));
+ table[--pointers[masked]] = chrpos - 49;
+ }
+
+ masked = array[108];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 50,chrpos,50));
+ table[--pointers[masked]] = chrpos - 50;
+ }
+
+ masked = array[100];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 51,chrpos,51));
+ table[--pointers[masked]] = chrpos - 51;
+ }
+
+ masked = array[92];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 52,chrpos,52));
+ table[--pointers[masked]] = chrpos - 52;
+ }
+
+ masked = array[84];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 53,chrpos,53));
+ table[--pointers[masked]] = chrpos - 53;
+ }
+
+ masked = array[76];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 54,chrpos,54));
+ table[--pointers[masked]] = chrpos - 54;
+ }
+
+ masked = array[68];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 55,chrpos,55));
+ table[--pointers[masked]] = chrpos - 55;
+ }
+
+ masked = array[60];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 56,chrpos,56));
+ table[--pointers[masked]] = chrpos - 56;
+ }
+
+ masked = array[52];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 57,chrpos,57));
+ table[--pointers[masked]] = chrpos - 57;
+ }
+
+ masked = array[44];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 58,chrpos,58));
+ table[--pointers[masked]] = chrpos - 58;
+ }
+
+ masked = array[36];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 59,chrpos,59));
+ table[--pointers[masked]] = chrpos - 59;
+ }
+
+ masked = array[28];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 60,chrpos,60));
+ table[--pointers[masked]] = chrpos - 60;
+ }
+
+ masked = array[20];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 61,chrpos,61));
+ table[--pointers[masked]] = chrpos - 61;
+ }
+
+ masked = array[12];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 62,chrpos,62));
+ table[--pointers[masked]] = chrpos - 62;
+ }
+
+ masked = array[4];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 63,chrpos,63));
+ table[--pointers[masked]] = chrpos - 63;
+ }
+#endif
+
+
+ /* Row 3 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+3]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[123]]);
+ assert(EXTRACT256(_counts,1) == counts[array[115]]);
+ assert(EXTRACT256(_counts,2) == counts[array[107]]);
+ assert(EXTRACT256(_counts,3) == counts[array[99]]);
+ assert(EXTRACT256(_counts,4) == counts[array[91]]);
+ assert(EXTRACT256(_counts,5) == counts[array[83]]);
+ assert(EXTRACT256(_counts,6) == counts[array[75]]);
+ assert(EXTRACT256(_counts,7) == counts[array[67]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 64,chrpos,64));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 64;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 65,chrpos,65));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 65;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 66,chrpos,66));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 66;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 67,chrpos,67));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 67;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 68,chrpos,68));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 68;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 69,chrpos,69));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 69;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 70,chrpos,70));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 70;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 71,chrpos,71));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 71;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[3]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[59]]);
+ assert(EXTRACT256(_counts,1) == counts[array[51]]);
+ assert(EXTRACT256(_counts,2) == counts[array[43]]);
+ assert(EXTRACT256(_counts,3) == counts[array[35]]);
+ assert(EXTRACT256(_counts,4) == counts[array[27]]);
+ assert(EXTRACT256(_counts,5) == counts[array[19]]);
+ assert(EXTRACT256(_counts,6) == counts[array[11]]);
+ assert(EXTRACT256(_counts,7) == counts[array[3]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 72,chrpos,72));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 72;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 73,chrpos,73));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 73;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 74,chrpos,74));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 74;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 75,chrpos,75));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 75;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 76,chrpos,76));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 76;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 77,chrpos,77));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 77;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 78,chrpos,78));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 78;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 79,chrpos,79));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 79;
+ }
+ }
+#else
+ masked = array[123];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 64,chrpos,64));
+ table[--pointers[masked]] = chrpos - 64;
+ }
+
+ masked = array[115];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 65,chrpos,65));
+ table[--pointers[masked]] = chrpos - 65;
+ }
+
+ masked = array[107];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 66,chrpos,66));
+ table[--pointers[masked]] = chrpos - 66;
+ }
+
+ masked = array[99];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 67,chrpos,67));
+ table[--pointers[masked]] = chrpos - 67;
+ }
+
+ masked = array[91];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 68,chrpos,68));
+ table[--pointers[masked]] = chrpos - 68;
+ }
+
+ masked = array[83];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 69,chrpos,69));
+ table[--pointers[masked]] = chrpos - 69;
+ }
+
+ masked = array[75];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 70,chrpos,70));
+ table[--pointers[masked]] = chrpos - 70;
+ }
+
+ masked = array[67];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 71,chrpos,71));
+ table[--pointers[masked]] = chrpos - 71;
+ }
+
+ masked = array[59];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 72,chrpos,72));
+ table[--pointers[masked]] = chrpos - 72;
+ }
+
+ masked = array[51];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 73,chrpos,73));
+ table[--pointers[masked]] = chrpos - 73;
+ }
+
+ masked = array[43];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 74,chrpos,74));
+ table[--pointers[masked]] = chrpos - 74;
+ }
+
+ masked = array[35];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 75,chrpos,75));
+ table[--pointers[masked]] = chrpos - 75;
+ }
+
+ masked = array[27];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 76,chrpos,76));
+ table[--pointers[masked]] = chrpos - 76;
+ }
+
+ masked = array[19];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 77,chrpos,77));
+ table[--pointers[masked]] = chrpos - 77;
+ }
+
+ masked = array[11];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 78,chrpos,78));
+ table[--pointers[masked]] = chrpos - 78;
+ }
+
+ masked = array[3];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 79,chrpos,79));
+ table[--pointers[masked]] = chrpos - 79;
+ }
+#endif
+
+
+ /* Row 2 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+2]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[122]]);
+ assert(EXTRACT256(_counts,1) == counts[array[114]]);
+ assert(EXTRACT256(_counts,2) == counts[array[106]]);
+ assert(EXTRACT256(_counts,3) == counts[array[98]]);
+ assert(EXTRACT256(_counts,4) == counts[array[90]]);
+ assert(EXTRACT256(_counts,5) == counts[array[82]]);
+ assert(EXTRACT256(_counts,6) == counts[array[74]]);
+ assert(EXTRACT256(_counts,7) == counts[array[66]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 80,chrpos,80));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 80;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 81,chrpos,81));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 81;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 82,chrpos,82));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 82;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 83,chrpos,83));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 83;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 84,chrpos,84));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 84;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 85,chrpos,85));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 85;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 86,chrpos,86));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 86;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 87,chrpos,87));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 87;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[2]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[58]]);
+ assert(EXTRACT256(_counts,1) == counts[array[50]]);
+ assert(EXTRACT256(_counts,2) == counts[array[42]]);
+ assert(EXTRACT256(_counts,3) == counts[array[34]]);
+ assert(EXTRACT256(_counts,4) == counts[array[26]]);
+ assert(EXTRACT256(_counts,5) == counts[array[18]]);
+ assert(EXTRACT256(_counts,6) == counts[array[10]]);
+ assert(EXTRACT256(_counts,7) == counts[array[2]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 88,chrpos,88));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 88;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 89,chrpos,89));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 89;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 90,chrpos,90));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 90;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 91,chrpos,91));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 91;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 92,chrpos,92));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 92;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 93,chrpos,93));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 93;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 94,chrpos,94));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 94;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 95,chrpos,95));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 95;
+ }
+ }
+#else
+ masked = array[122];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 80,chrpos,80));
+ table[--pointers[masked]] = chrpos - 80;
+ }
+
+ masked = array[114];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 81,chrpos,81));
+ table[--pointers[masked]] = chrpos - 81;
+ }
+
+ masked = array[106];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 82,chrpos,82));
+ table[--pointers[masked]] = chrpos - 82;
+ }
+
+ masked = array[98];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 83,chrpos,83));
+ table[--pointers[masked]] = chrpos - 83;
+ }
+
+ masked = array[90];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 84,chrpos,84));
+ table[--pointers[masked]] = chrpos - 84;
+ }
+
+ masked = array[82];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 85,chrpos,85));
+ table[--pointers[masked]] = chrpos - 85;
+ }
+
+ masked = array[74];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 86,chrpos,86));
+ table[--pointers[masked]] = chrpos - 86;
+ }
+
+ masked = array[66];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 87,chrpos,87));
+ table[--pointers[masked]] = chrpos - 87;
+ }
+
+ masked = array[58];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 88,chrpos,88));
+ table[--pointers[masked]] = chrpos - 88;
+ }
+
+ masked = array[50];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 89,chrpos,89));
+ table[--pointers[masked]] = chrpos - 89;
+ }
+
+ masked = array[42];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 90,chrpos,90));
+ table[--pointers[masked]] = chrpos - 90;
+ }
+
+ masked = array[34];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 91,chrpos,91));
+ table[--pointers[masked]] = chrpos - 91;
+ }
+
+ masked = array[26];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 92,chrpos,92));
+ table[--pointers[masked]] = chrpos - 92;
+ }
+
+ masked = array[18];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 93,chrpos,93));
+ table[--pointers[masked]] = chrpos - 93;
+ }
+
+ masked = array[10];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 94,chrpos,94));
+ table[--pointers[masked]] = chrpos - 94;
+ }
+
+ masked = array[2];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 95,chrpos,95));
+ table[--pointers[masked]] = chrpos - 95;
+ }
+#endif
+
+
+ /* Row 1 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+1]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[121]]);
+ assert(EXTRACT256(_counts,1) == counts[array[113]]);
+ assert(EXTRACT256(_counts,2) == counts[array[105]]);
+ assert(EXTRACT256(_counts,3) == counts[array[97]]);
+ assert(EXTRACT256(_counts,4) == counts[array[89]]);
+ assert(EXTRACT256(_counts,5) == counts[array[81]]);
+ assert(EXTRACT256(_counts,6) == counts[array[73]]);
+ assert(EXTRACT256(_counts,7) == counts[array[65]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 96,chrpos,96));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 96;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 97,chrpos,97));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 97;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 98,chrpos,98));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 98;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 99,chrpos,99));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 99;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 100,chrpos,100));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 100;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 101,chrpos,101));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 101;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 102,chrpos,102));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 102;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 103,chrpos,103));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 103;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[1]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[57]]);
+ assert(EXTRACT256(_counts,1) == counts[array[49]]);
+ assert(EXTRACT256(_counts,2) == counts[array[41]]);
+ assert(EXTRACT256(_counts,3) == counts[array[33]]);
+ assert(EXTRACT256(_counts,4) == counts[array[25]]);
+ assert(EXTRACT256(_counts,5) == counts[array[17]]);
+ assert(EXTRACT256(_counts,6) == counts[array[9]]);
+ assert(EXTRACT256(_counts,7) == counts[array[1]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 104,chrpos,104));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 104;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 105,chrpos,105));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 105;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 106,chrpos,106));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 106;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 107,chrpos,107));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 107;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 108,chrpos,108));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 108;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 109,chrpos,109));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 109;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 110,chrpos,110));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 110;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 111,chrpos,111));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 111;
+ }
+ }
+#else
+ masked = array[121];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 96,chrpos,96));
+ table[--pointers[masked]] = chrpos - 96;
+ }
+
+ masked = array[113];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 97,chrpos,97));
+ table[--pointers[masked]] = chrpos - 97;
+ }
+
+ masked = array[105];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 98,chrpos,98));
+ table[--pointers[masked]] = chrpos - 98;
+ }
+
+ masked = array[97];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 99,chrpos,99));
+ table[--pointers[masked]] = chrpos - 99;
+ }
+
+ masked = array[89];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 100,chrpos,100));
+ table[--pointers[masked]] = chrpos - 100;
+ }
+
+ masked = array[81];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 101,chrpos,101));
+ table[--pointers[masked]] = chrpos - 101;
+ }
+
+ masked = array[73];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 102,chrpos,102));
+ table[--pointers[masked]] = chrpos - 102;
+ }
+
+ masked = array[65];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 103,chrpos,103));
+ table[--pointers[masked]] = chrpos - 103;
+ }
+
+ masked = array[57];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 104,chrpos,104));
+ table[--pointers[masked]] = chrpos - 104;
+ }
+
+ masked = array[49];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 105,chrpos,105));
+ table[--pointers[masked]] = chrpos - 105;
+ }
+
+ masked = array[41];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 106,chrpos,106));
+ table[--pointers[masked]] = chrpos - 106;
+ }
+
+ masked = array[33];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 107,chrpos,107));
+ table[--pointers[masked]] = chrpos - 107;
+ }
+
+ masked = array[25];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 108,chrpos,108));
+ table[--pointers[masked]] = chrpos - 108;
+ }
+
+ masked = array[17];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 109,chrpos,109));
+ table[--pointers[masked]] = chrpos - 109;
+ }
+
+ masked = array[9];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 110,chrpos,110));
+ table[--pointers[masked]] = chrpos - 110;
+ }
+
+ masked = array[1];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 111,chrpos,111));
+ table[--pointers[masked]] = chrpos - 111;
+ }
+#endif
+
+
+ /* Row 0 */
+#ifdef USE_GATHER
+ _masked = _mm256_i32gather_epi32((int *) &(array[64+0]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[120]]);
+ assert(EXTRACT256(_counts,1) == counts[array[112]]);
+ assert(EXTRACT256(_counts,2) == counts[array[104]]);
+ assert(EXTRACT256(_counts,3) == counts[array[96]]);
+ assert(EXTRACT256(_counts,4) == counts[array[88]]);
+ assert(EXTRACT256(_counts,5) == counts[array[80]]);
+ assert(EXTRACT256(_counts,6) == counts[array[72]]);
+ assert(EXTRACT256(_counts,7) == counts[array[64]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 112,chrpos,112));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 112;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 113,chrpos,113));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 113;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 114,chrpos,114));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 114;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 115,chrpos,115));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 115;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 116,chrpos,116));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 116;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 117,chrpos,117));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 117;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 118,chrpos,118));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 118;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 119,chrpos,119));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 119;
+ }
+ }
+
+ _masked = _mm256_i32gather_epi32((int *) &(array[0]),byeights,/*scale*/4);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+ assert(EXTRACT256(_counts,0) == counts[array[56]]);
+ assert(EXTRACT256(_counts,1) == counts[array[48]]);
+ assert(EXTRACT256(_counts,2) == counts[array[40]]);
+ assert(EXTRACT256(_counts,3) == counts[array[32]]);
+ assert(EXTRACT256(_counts,4) == counts[array[24]]);
+ assert(EXTRACT256(_counts,5) == counts[array[16]]);
+ assert(EXTRACT256(_counts,6) == counts[array[8]]);
+ assert(EXTRACT256(_counts,7) == counts[array[0]]);
+ if (_mm256_testz_si256(_counts,_counts) == 0) {
+ if (EXTRACT256(_counts,0)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,0),chrpos - 120,chrpos,120));
+ table[--pointers[EXTRACT256(_masked,0)]] = chrpos - 120;
+ }
+ if (EXTRACT256(_counts,1)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,1),chrpos - 121,chrpos,121));
+ table[--pointers[EXTRACT256(_masked,1)]] = chrpos - 121;
+ }
+ if (EXTRACT256(_counts,2)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,2),chrpos - 122,chrpos,122));
+ table[--pointers[EXTRACT256(_masked,2)]] = chrpos - 122;
+ }
+ if (EXTRACT256(_counts,3)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,3),chrpos - 123,chrpos,123));
+ table[--pointers[EXTRACT256(_masked,3)]] = chrpos - 123;
+ }
+ if (EXTRACT256(_counts,4)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,4),chrpos - 124,chrpos,124));
+ table[--pointers[EXTRACT256(_masked,4)]] = chrpos - 124;
+ }
+ if (EXTRACT256(_counts,5)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,5),chrpos - 125,chrpos,125));
+ table[--pointers[EXTRACT256(_masked,5)]] = chrpos - 125;
+ }
+ if (EXTRACT256(_counts,6)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,6),chrpos - 126,chrpos,126));
+ table[--pointers[EXTRACT256(_masked,6)]] = chrpos - 126;
+ }
+ if (EXTRACT256(_counts,7)) {
+ debug(printf("Storing masked %u at %u (%u - %d)\n",EXTRACT256(_masked,7),chrpos - 127,chrpos,127));
+ table[--pointers[EXTRACT256(_masked,7)]] = chrpos - 127;
+ }
+ }
+#else
+ masked = array[120];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 112,chrpos,112));
+ table[--pointers[masked]] = chrpos - 112;
+ }
+
+ masked = array[112];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 113,chrpos,113));
+ table[--pointers[masked]] = chrpos - 113;
+ }
+
+ masked = array[104];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 114,chrpos,114));
+ table[--pointers[masked]] = chrpos - 114;
+ }
+
+ masked = array[96];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 115,chrpos,115));
+ table[--pointers[masked]] = chrpos - 115;
+ }
+
+ masked = array[88];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 116,chrpos,116));
+ table[--pointers[masked]] = chrpos - 116;
+ }
+
+ masked = array[80];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 117,chrpos,117));
+ table[--pointers[masked]] = chrpos - 117;
+ }
+
+ masked = array[72];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 118,chrpos,118));
+ table[--pointers[masked]] = chrpos - 118;
+ }
+
+ masked = array[64];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 119,chrpos,119));
+ table[--pointers[masked]] = chrpos - 119;
+ }
+
+ masked = array[56];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 120,chrpos,120));
+ table[--pointers[masked]] = chrpos - 120;
+ }
+
+ masked = array[48];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 121,chrpos,121));
+ table[--pointers[masked]] = chrpos - 121;
+ }
+
+ masked = array[40];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 122,chrpos,122));
+ table[--pointers[masked]] = chrpos - 122;
+ }
+
+ masked = array[32];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 123,chrpos,123));
+ table[--pointers[masked]] = chrpos - 123;
+ }
+
+ masked = array[24];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 124,chrpos,124));
+ table[--pointers[masked]] = chrpos - 124;
+ }
+
+ masked = array[16];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 125,chrpos,125));
+ table[--pointers[masked]] = chrpos - 125;
+ }
+
+ masked = array[8];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 126,chrpos,126));
+ table[--pointers[masked]] = chrpos - 126;
+ }
+
+ masked = array[0];
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (%u - %d)\n",masked,chrpos - 127,chrpos,127));
+ table[--pointers[masked]] = chrpos - 127;
+ }
+#endif
+
+ return chrpos - 128;
+}
+
+#endif /* HAVE_AVX2 */
+
+#endif /* USE_SIMD_FOR_COUNTS */
+
+
+
+#if !defined(HAVE_AVX2)
+
+static void
+count_9mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+#ifdef INDIVIDUAL_SHIFTS
+#elif defined(SIMD_MASK_THEN_STORE)
+ UINT4 _masked[4] __attribute__ ((aligned (16)));
+ __m128i _oligo;
+#else
+ __m128i _oligo, _masked;
+#endif
+
+
+ oligo = nexthigh_rev >> 16; /* For 31..24 */
+ oligo |= low_rev << 16;
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = oligo & MASK9; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 2) & MASK9; /* 30 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 4) & MASK9; /* 29 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 6) & MASK9; /* 28 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 8) & MASK9; /* 27 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 10) & MASK9; /* 26 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 12) & MASK9; /* 25 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 14) & MASK9; /* 24 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+#endif
+
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = low_rev & MASK9; /* 23 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = (low_rev >> 2) & MASK9; /* 22 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = (low_rev >> 4) & MASK9; /* 21 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = (low_rev >> 6) & MASK9; /* 20 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = (low_rev >> 8) & MASK9; /* 19 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = (low_rev >> 10) & MASK9; /* 18 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = (low_rev >> 12) & MASK9; /* 17 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = low_rev >> 14; /* 16, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(low_rev, low_rev >> 2, low_rev >> 4, low_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
@@ -10380,19 +12321,19 @@ count_9mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#endif
@@ -10402,35 +12343,35 @@ count_9mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK9; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK9; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK9; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK9; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK9; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK9; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 12) & MASK9; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 14) & MASK9; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
#else
@@ -10442,19 +12383,19 @@ count_9mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
@@ -10466,108 +12407,404 @@ count_9mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
- debug(printf("9 %04X => %d\n",masked,counts[masked]));
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+#endif
+
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = high_rev & MASK9; /* 7 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 2) & MASK9; /* 6 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 4) & MASK9; /* 5 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 6) & MASK9; /* 4 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 8) & MASK9; /* 3 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 10) & MASK9; /* 2 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 12) & MASK9; /* 1 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = high_rev >> 14; /* 0, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_9mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = nexthigh_rev >> 16; /* For 31..24 */
+ oligo |= low_rev << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
- masked = EXTRACT(_masked,3);
- counts[masked] += 1;
- debug(printf("8 %04X => %d\n",masked,counts[masked]));
-#endif
+ oligo = low_rev >> 16; /* For 15..8 */
+ oligo |= high_rev << 16;
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
-#ifdef INDIVIDUAL_SHIFTS
- masked = high_rev & MASK9; /* 7 */
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
- debug(printf("7 %04X => %d\n",masked,counts[masked]));
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 2) & MASK9; /* 6 */
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
- debug(printf("6 %04X => %d\n",masked,counts[masked]));
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 4) & MASK9; /* 5 */
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("5 %04X => %d\n",masked,counts[masked]));
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 6) & MASK9; /* 4 */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("4 %04X => %d\n",masked,counts[masked]));
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 8) & MASK9; /* 3 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
- debug(printf("3 %04X => %d\n",masked,counts[masked]));
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 10) & MASK9; /* 2 */
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
- debug(printf("2 %04X => %d\n",masked,counts[masked]));
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 12) & MASK9; /* 1 */
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
- debug(printf("1 %04X => %d\n",masked,counts[masked]));
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
- masked = high_rev >> 14; /* 0, No mask necessary */
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
- debug(printf("0 %04X => %d\n",masked,counts[masked]));
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
- masked = EXTRACT(_masked,0);
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("7 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("6 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("5 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("4 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("3 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("2 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("1 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("0 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
/* Expecting current to have {high0_rev, low0_rev, high1_rev,
low1_rev}, and next to have {low0_rev, high1_rev, low1_rev, and
@@ -10599,115 +12836,1578 @@ extract_9mers_fwd_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+
+#ifdef HAVE_AVX2
+static void
+extract_9mers_fwd_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,14)); /* No mask necessary */
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask9));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,16), _mm256_slli_epi32(current,16));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,14), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask9));
+
+ return;
+}
+#endif
+
+
static void
-count_9mers_fwd_simd (Count_T *counts, __m128i current, __m128i next) {
+count_9mers_fwd_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,14); /* No mask necessary */
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,14)); /* No mask necessary */
- counts[array[0]] += 1; /* 0 */
- counts[array[1]] += 1; /* 16 */
- counts[array[2]] += 1; /* 32 */
- counts[array[3]] += 1; /* 48 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("16 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("32 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("48 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 0 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 48 */
+#endif
+ debug(printf("0 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask9));
- counts[array[0]] += 1; /* 1 */
- counts[array[1]] += 1; /* 17 */
- counts[array[2]] += 1; /* 33 */
- counts[array[3]] += 1; /* 49 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("17 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("33 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("49 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 1 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 49 */
+#endif
+ debug(printf("1 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask9));
- counts[array[0]] += 1; /* 2 */
- counts[array[1]] += 1; /* 18 */
- counts[array[2]] += 1; /* 34 */
- counts[array[3]] += 1; /* 50 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("18 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("34 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("50 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 2 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 50 */
+#endif
+ debug(printf("2 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask9));
- counts[array[0]] += 1; /* 3 */
- counts[array[1]] += 1; /* 19 */
- counts[array[2]] += 1; /* 35 */
- counts[array[3]] += 1; /* 51 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("19 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("35 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("51 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 3 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 51 */
+#endif
+ debug(printf("3 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask9));
- counts[array[0]] += 1; /* 4 */
- counts[array[1]] += 1; /* 20 */
- counts[array[2]] += 1; /* 36 */
- counts[array[3]] += 1; /* 52 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("20 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("36 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("52 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 4 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 52 */
+#endif
+ debug(printf("4 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask9));
- counts[array[0]] += 1; /* 5 */
- counts[array[1]] += 1; /* 21 */
- counts[array[2]] += 1; /* 37 */
- counts[array[3]] += 1; /* 53 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("21 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("37 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("53 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 5 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 53 */
+#endif
+ debug(printf("5 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask9));
- counts[array[0]] += 1; /* 6 */
- counts[array[1]] += 1; /* 22 */
- counts[array[2]] += 1; /* 38 */
- counts[array[3]] += 1; /* 54 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("22 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("38 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("54 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 6 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 54 */
+#endif
+ debug(printf("6 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( current, mask9));
- counts[array[0]] += 1; /* 7 */
- counts[array[1]] += 1; /* 23 */
- counts[array[2]] += 1; /* 39 */
- counts[array[3]] += 1; /* 55 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("23 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("39 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("55 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 7 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 55 */
+#endif
+ debug(printf("7 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
oligo = _mm_or_si128( _mm_srli_epi32(next,16), _mm_slli_epi32(current,16));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,14), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,14), mask9));
- counts[array[0]] += 1; /* 8 */
- counts[array[1]] += 1; /* 24 */
- counts[array[2]] += 1; /* 40 */
- counts[array[3]] += 1; /* 56 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("24 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("40 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("56 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 8 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 56 */
+#endif
+ debug(printf("8 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,12), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,12), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("25 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("41 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("57 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 9 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 57 */
+#endif
+ debug(printf("9 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,10), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("26 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("42 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("58 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 10 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 58 */
+#endif
+ debug(printf("10 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("27 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("43 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("59 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 11 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 59 */
+#endif
+ debug(printf("11 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("28 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("44 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("60 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 12 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 60 */
+#endif
+ debug(printf("12 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("29 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("45 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("61 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 13 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 61 */
+#endif
+ debug(printf("13 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,12), mask9));
- counts[array[0]] += 1; /* 9 */
- counts[array[1]] += 1; /* 25 */
- counts[array[2]] += 1; /* 41 */
- counts[array[3]] += 1; /* 57 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("30 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("46 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("62 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask9));
- counts[array[0]] += 1; /* 10 */
- counts[array[1]] += 1; /* 26 */
- counts[array[2]] += 1; /* 42 */
- counts[array[3]] += 1; /* 58 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 14 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 62 */
+#endif
+ debug(printf("14 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask9));
- counts[array[0]] += 1; /* 11 */
- counts[array[1]] += 1; /* 27 */
- counts[array[2]] += 1; /* 43 */
- counts[array[3]] += 1; /* 59 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("31 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("47 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("63 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask9));
- counts[array[0]] += 1; /* 12 */
- counts[array[1]] += 1; /* 28 */
- counts[array[2]] += 1; /* 44 */
- counts[array[3]] += 1; /* 60 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 15 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 63 */
+#endif
+ debug(printf("15 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask9));
- counts[array[0]] += 1; /* 13 */
- counts[array[1]] += 1; /* 29 */
- counts[array[2]] += 1; /* 45 */
- counts[array[3]] += 1; /* 61 */
+ return;
+}
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask9));
- counts[array[0]] += 1; /* 14 */
- counts[array[1]] += 1; /* 30 */
- counts[array[2]] += 1; /* 46 */
- counts[array[3]] += 1; /* 62 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask9));
- counts[array[0]] += 1; /* 15 */
- counts[array[1]] += 1; /* 31 */
- counts[array[2]] += 1; /* 47 */
- counts[array[3]] += 1; /* 63 */
+#ifdef HAVE_AVX2
+static void
+count_9mers_fwd_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+ array = _mm256_srli_epi32(current,14); /* No mask necessary */
+ counts[EXTRACT256(array,0)] += 1; /* 0 */
+ counts[EXTRACT256(array,1)] += 1; /* 16 */
+ counts[EXTRACT256(array,2)] += 1; /* 32 */
+ counts[EXTRACT256(array,3)] += 1; /* 48 */
+ counts[EXTRACT256(array,4)] += 1; /* 64 */
+ counts[EXTRACT256(array,5)] += 1; /* 80 */
+ counts[EXTRACT256(array,6)] += 1; /* 96 */
+ counts[EXTRACT256(array,7)] += 1; /* 112 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 1 */
+ counts[EXTRACT256(array,1)] += 1; /* 17 */
+ counts[EXTRACT256(array,2)] += 1; /* 33 */
+ counts[EXTRACT256(array,3)] += 1; /* 49 */
+ counts[EXTRACT256(array,4)] += 1; /* 65 */
+ counts[EXTRACT256(array,5)] += 1; /* 81 */
+ counts[EXTRACT256(array,6)] += 1; /* 97 */
+ counts[EXTRACT256(array,7)] += 1; /* 113 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 2 */
+ counts[EXTRACT256(array,1)] += 1; /* 18 */
+ counts[EXTRACT256(array,2)] += 1; /* 34 */
+ counts[EXTRACT256(array,3)] += 1; /* 50 */
+ counts[EXTRACT256(array,4)] += 1; /* 66 */
+ counts[EXTRACT256(array,5)] += 1; /* 82 */
+ counts[EXTRACT256(array,6)] += 1; /* 98 */
+ counts[EXTRACT256(array,7)] += 1; /* 114 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 3 */
+ counts[EXTRACT256(array,1)] += 1; /* 19 */
+ counts[EXTRACT256(array,2)] += 1; /* 35 */
+ counts[EXTRACT256(array,3)] += 1; /* 51 */
+ counts[EXTRACT256(array,4)] += 1; /* 67 */
+ counts[EXTRACT256(array,5)] += 1; /* 83 */
+ counts[EXTRACT256(array,6)] += 1; /* 99 */
+ counts[EXTRACT256(array,7)] += 1; /* 115 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 4 */
+ counts[EXTRACT256(array,1)] += 1; /* 20 */
+ counts[EXTRACT256(array,2)] += 1; /* 36 */
+ counts[EXTRACT256(array,3)] += 1; /* 52 */
+ counts[EXTRACT256(array,4)] += 1; /* 68 */
+ counts[EXTRACT256(array,5)] += 1; /* 84 */
+ counts[EXTRACT256(array,6)] += 1; /* 100 */
+ counts[EXTRACT256(array,7)] += 1; /* 116 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 5 */
+ counts[EXTRACT256(array,1)] += 1; /* 21 */
+ counts[EXTRACT256(array,2)] += 1; /* 37 */
+ counts[EXTRACT256(array,3)] += 1; /* 53 */
+ counts[EXTRACT256(array,4)] += 1; /* 69 */
+ counts[EXTRACT256(array,5)] += 1; /* 85 */
+ counts[EXTRACT256(array,6)] += 1; /* 101 */
+ counts[EXTRACT256(array,7)] += 1; /* 117 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 6 */
+ counts[EXTRACT256(array,1)] += 1; /* 22 */
+ counts[EXTRACT256(array,2)] += 1; /* 38 */
+ counts[EXTRACT256(array,3)] += 1; /* 54 */
+ counts[EXTRACT256(array,4)] += 1; /* 70 */
+ counts[EXTRACT256(array,5)] += 1; /* 86 */
+ counts[EXTRACT256(array,6)] += 1; /* 102 */
+ counts[EXTRACT256(array,7)] += 1; /* 118 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 7 */
+ counts[EXTRACT256(array,1)] += 1; /* 23 */
+ counts[EXTRACT256(array,2)] += 1; /* 39 */
+ counts[EXTRACT256(array,3)] += 1; /* 55 */
+ counts[EXTRACT256(array,4)] += 1; /* 71 */
+ counts[EXTRACT256(array,5)] += 1; /* 87 */
+ counts[EXTRACT256(array,6)] += 1; /* 103 */
+ counts[EXTRACT256(array,7)] += 1; /* 119 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,16), _mm256_slli_epi32(current,16));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,14), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 8 */
+ counts[EXTRACT256(array,1)] += 1; /* 24 */
+ counts[EXTRACT256(array,2)] += 1; /* 40 */
+ counts[EXTRACT256(array,3)] += 1; /* 56 */
+ counts[EXTRACT256(array,4)] += 1; /* 72 */
+ counts[EXTRACT256(array,5)] += 1; /* 88 */
+ counts[EXTRACT256(array,6)] += 1; /* 104 */
+ counts[EXTRACT256(array,7)] += 1; /* 120 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 9 */
+ counts[EXTRACT256(array,1)] += 1; /* 25 */
+ counts[EXTRACT256(array,2)] += 1; /* 41 */
+ counts[EXTRACT256(array,3)] += 1; /* 57 */
+ counts[EXTRACT256(array,4)] += 1; /* 73 */
+ counts[EXTRACT256(array,5)] += 1; /* 89 */
+ counts[EXTRACT256(array,6)] += 1; /* 105 */
+ counts[EXTRACT256(array,7)] += 1; /* 121 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 10 */
+ counts[EXTRACT256(array,1)] += 1; /* 26 */
+ counts[EXTRACT256(array,2)] += 1; /* 42 */
+ counts[EXTRACT256(array,3)] += 1; /* 58 */
+ counts[EXTRACT256(array,4)] += 1; /* 74 */
+ counts[EXTRACT256(array,5)] += 1; /* 90 */
+ counts[EXTRACT256(array,6)] += 1; /* 106 */
+ counts[EXTRACT256(array,7)] += 1; /* 122 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 11 */
+ counts[EXTRACT256(array,1)] += 1; /* 27 */
+ counts[EXTRACT256(array,2)] += 1; /* 43 */
+ counts[EXTRACT256(array,3)] += 1; /* 59 */
+ counts[EXTRACT256(array,4)] += 1; /* 75 */
+ counts[EXTRACT256(array,5)] += 1; /* 91 */
+ counts[EXTRACT256(array,6)] += 1; /* 107 */
+ counts[EXTRACT256(array,7)] += 1; /* 123 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 12 */
+ counts[EXTRACT256(array,1)] += 1; /* 28 */
+ counts[EXTRACT256(array,2)] += 1; /* 44 */
+ counts[EXTRACT256(array,3)] += 1; /* 60 */
+ counts[EXTRACT256(array,4)] += 1; /* 76 */
+ counts[EXTRACT256(array,5)] += 1; /* 92 */
+ counts[EXTRACT256(array,6)] += 1; /* 108 */
+ counts[EXTRACT256(array,7)] += 1; /* 124 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 13 */
+ counts[EXTRACT256(array,1)] += 1; /* 29 */
+ counts[EXTRACT256(array,2)] += 1; /* 45 */
+ counts[EXTRACT256(array,3)] += 1; /* 61 */
+ counts[EXTRACT256(array,4)] += 1; /* 77 */
+ counts[EXTRACT256(array,5)] += 1; /* 93 */
+ counts[EXTRACT256(array,6)] += 1; /* 109 */
+ counts[EXTRACT256(array,7)] += 1; /* 125 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 14 */
+ counts[EXTRACT256(array,1)] += 1; /* 30 */
+ counts[EXTRACT256(array,2)] += 1; /* 46 */
+ counts[EXTRACT256(array,3)] += 1; /* 62 */
+ counts[EXTRACT256(array,4)] += 1; /* 78 */
+ counts[EXTRACT256(array,5)] += 1; /* 94 */
+ counts[EXTRACT256(array,6)] += 1; /* 110 */
+ counts[EXTRACT256(array,7)] += 1; /* 126 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 15 */
+ counts[EXTRACT256(array,1)] += 1; /* 31 */
+ counts[EXTRACT256(array,2)] += 1; /* 47 */
+ counts[EXTRACT256(array,3)] += 1; /* 63 */
+ counts[EXTRACT256(array,4)] += 1; /* 79 */
+ counts[EXTRACT256(array,5)] += 1; /* 95 */
+ counts[EXTRACT256(array,6)] += 1; /* 111 */
+ counts[EXTRACT256(array,7)] += 1; /* 127 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
#endif
+
+#if !defined(HAVE_AVX2)
+
static int
-store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_9mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -10725,74 +14425,58 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK9; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (oligo >> 2) & MASK9; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (oligo >> 4) & MASK9; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (oligo >> 6) & MASK9; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (oligo >> 8) & MASK9; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (oligo >> 10) & MASK9; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (oligo >> 12) & MASK9; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (oligo >> 14) & MASK9; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
#else
@@ -10805,38 +14489,30 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -10849,38 +14525,30 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
#endif
@@ -10888,74 +14556,58 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK9; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rev >> 2) & MASK9; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (low_rev >> 4) & MASK9; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (low_rev >> 6) & MASK9; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (low_rev >> 8) & MASK9; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (low_rev >> 10) & MASK9; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (low_rev >> 12) & MASK9; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = low_rev >> 14; /* 16, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -10968,38 +14620,30 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
@@ -11012,38 +14656,30 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -11054,74 +14690,58 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK9; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (oligo >> 2) & MASK9; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (oligo >> 4) & MASK9; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (oligo >> 6) & MASK9; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (oligo >> 8) & MASK9; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (oligo >> 10) & MASK9; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (oligo >> 12) & MASK9; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (oligo >> 14) & MASK9; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
#else
@@ -11134,38 +14754,30 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -11178,38 +14790,30 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
#endif
@@ -11217,172 +14821,405 @@ store_9mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK9; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rev >> 2) & MASK9; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (high_rev >> 4) & MASK9; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (high_rev >> 6) & MASK9; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (high_rev >> 8) & MASK9; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (high_rev >> 10) & MASK9; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (high_rev >> 12) & MASK9; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = high_rev >> 14; /* 0, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_9mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ oligo = nexthigh_rev >> 16; /* For 31..24 */
+ oligo |= low_rev << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ oligo = low_rev >> 16; /* For 15..8 */
+ oligo |= high_rev << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+#if !defined(HAVE_AVX2)
+
static void
-count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+count_8mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -11398,31 +15235,31 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 31 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK8; /* 30 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK8; /* 29 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK8; /* 28 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK8; /* 27 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK8; /* 26 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 12) & MASK8; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
#else
@@ -11434,19 +15271,19 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
@@ -11458,54 +15295,54 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK8; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 2) & MASK8; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 4) & MASK8; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 6) & MASK8; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 8) & MASK8; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 10) & MASK8; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 12) & MASK8; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 14) & MASK8; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = low_rev >> 16; /* 16, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#else
@@ -11517,19 +15354,19 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
@@ -11541,24 +15378,24 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = low_rev >> 16; /* 16, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#endif
@@ -11568,31 +15405,31 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK8; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK8; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK8; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK8; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK8; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 12) & MASK8; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
#else
@@ -11604,19 +15441,19 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
@@ -11628,113 +15465,405 @@ count_8mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
#endif
-#ifdef INDIVIDUAL_SHIFTS
- masked = high_rev & MASK8; /* 8 */
- counts[masked] += 1;
- debug(printf("8 %04X => %d\n",masked,counts[masked]));
+#ifdef INDIVIDUAL_SHIFTS
+ masked = high_rev & MASK8; /* 8 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 2) & MASK8; /* 7 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 4) & MASK8; /* 6 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 6) & MASK8; /* 5 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 8) & MASK8; /* 4 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 10) & MASK8; /* 3 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 12) & MASK8; /* 2 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 14) & MASK8; /* 1 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = high_rev >> 16; /* 0, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
+#else
+ _masked = _mm_and_si128(_oligo, mask8);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
+#else
+ _masked = _mm_and_si128(_oligo, mask8);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+
+ masked = high_rev >> 16; /* 0, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_8mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = nexthigh_rev >> 18; /* For 31..25 */
+ oligo |= low_rev << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low7);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ masked = low_rev >> 16; /* 16, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+
+ oligo = low_rev >> 18; /* For 15..9 */
+ oligo |= high_rev << 14;
- masked = (high_rev >> 2) & MASK8; /* 7 */
- counts[masked] += 1;
- debug(printf("7 %04X => %d\n",masked,counts[masked]));
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
- masked = (high_rev >> 4) & MASK8; /* 6 */
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
- debug(printf("6 %04X => %d\n",masked,counts[masked]));
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 6) & MASK8; /* 5 */
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
- debug(printf("5 %04X => %d\n",masked,counts[masked]));
-
- masked = (high_rev >> 8) & MASK8; /* 4 */
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("4 %04X => %d\n",masked,counts[masked]));
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 10) & MASK8; /* 3 */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("3 %04X => %d\n",masked,counts[masked]));
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 12) & MASK8; /* 2 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
- debug(printf("2 %04X => %d\n",masked,counts[masked]));
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 14) & MASK8; /* 1 */
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
- debug(printf("1 %04X => %d\n",masked,counts[masked]));
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
- masked = high_rev >> 16; /* 0, No mask necessary */
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
- debug(printf("0 %04X => %d\n",masked,counts[masked]));
-
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
-#else
- _masked = _mm_and_si128(_oligo, mask8);
-#endif
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,0);
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low7);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("8 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("7 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("6 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("5 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
-#else
- _masked = _mm_and_si128(_oligo, mask8);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("4 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("3 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("2 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("1 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
masked = high_rev >> 16; /* 0, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
-#endif
return;
}
+#endif /* HAVE_AVX2 */
+
+
+
/* Expecting current to have {high0_rev, low0_rev, high1_rev,
low1_rev}, and next to have {low0_rev, high1_rev, low1_rev, and
high2_rev} */
@@ -11765,116 +15894,1577 @@ extract_8mers_fwd_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_8mers_fwd_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,16)); /* No mask necessary */
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask8));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,18), _mm256_slli_epi32(current,14));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask8));
+
+ return;
+}
+#endif
+
+
static void
-count_8mers_fwd_simd (Count_T *counts, __m128i current, __m128i next) {
+count_8mers_fwd_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,16); /* No mask necessary */
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,16)); /* No mask necessary */
- counts[array[0]] += 1; /* 0 */
- counts[array[1]] += 1; /* 16 */
- counts[array[2]] += 1; /* 32 */
- counts[array[3]] += 1; /* 48 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("16 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("32 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("48 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 0 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 48 */
+#endif
+ debug(printf("0 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask8));
- counts[array[0]] += 1; /* 1 */
- counts[array[1]] += 1; /* 17 */
- counts[array[2]] += 1; /* 33 */
- counts[array[3]] += 1; /* 49 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("17 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("33 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("49 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 1 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 49 */
+#endif
+ debug(printf("1 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask8));
- counts[array[0]] += 1; /* 2 */
- counts[array[1]] += 1; /* 18 */
- counts[array[2]] += 1; /* 34 */
- counts[array[3]] += 1; /* 50 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("18 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("34 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("50 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 2 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 50 */
+#endif
+ debug(printf("2 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask8));
- counts[array[0]] += 1; /* 3 */
- counts[array[1]] += 1; /* 19 */
- counts[array[2]] += 1; /* 35 */
- counts[array[3]] += 1; /* 51 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("19 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("35 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("51 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 3 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 51 */
+#endif
+ debug(printf("3 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask8));
- counts[array[0]] += 1; /* 4 */
- counts[array[1]] += 1; /* 20 */
- counts[array[2]] += 1; /* 36 */
- counts[array[3]] += 1; /* 52 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("20 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("36 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("52 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 4 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 52 */
+#endif
+ debug(printf("4 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask8));
- counts[array[0]] += 1; /* 5 */
- counts[array[1]] += 1; /* 21 */
- counts[array[2]] += 1; /* 37 */
- counts[array[3]] += 1; /* 53 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("21 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("37 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("53 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 5 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 53 */
+#endif
+ debug(printf("5 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask8));
- counts[array[0]] += 1; /* 6 */
- counts[array[1]] += 1; /* 22 */
- counts[array[2]] += 1; /* 38 */
- counts[array[3]] += 1; /* 54 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("22 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("38 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("54 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 6 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 54 */
+#endif
+ debug(printf("6 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask8));
- counts[array[0]] += 1; /* 7 */
- counts[array[1]] += 1; /* 23 */
- counts[array[2]] += 1; /* 39 */
- counts[array[3]] += 1; /* 55 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("23 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("39 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("55 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 7 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 55 */
+#endif
+ debug(printf("7 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( current, mask8));
- counts[array[0]] += 1; /* 8 */
- counts[array[1]] += 1; /* 24 */
- counts[array[2]] += 1; /* 40 */
- counts[array[3]] += 1; /* 56 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("24 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("40 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("56 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 8 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 56 */
+#endif
+ debug(printf("8 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+ oligo = _mm_or_si128( _mm_srli_epi32(next,18), _mm_slli_epi32(current,14));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,12), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,12), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("25 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("41 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("57 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 9 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 57 */
+#endif
+ debug(printf("9 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,10), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("26 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("42 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("58 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 10 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 58 */
+#endif
+ debug(printf("10 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("27 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("43 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("59 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 11 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 59 */
+#endif
+ debug(printf("11 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("28 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("44 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("60 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 12 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 60 */
+#endif
+ debug(printf("12 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("29 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("45 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("61 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 13 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 61 */
+#endif
+ debug(printf("13 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- oligo = _mm_or_si128( _mm_srli_epi32(next,18), _mm_slli_epi32(current,14));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,12), mask8));
- counts[array[0]] += 1; /* 9 */
- counts[array[1]] += 1; /* 25 */
- counts[array[2]] += 1; /* 41 */
- counts[array[3]] += 1; /* 57 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("30 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("46 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("62 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask8));
- counts[array[0]] += 1; /* 10 */
- counts[array[1]] += 1; /* 26 */
- counts[array[2]] += 1; /* 42 */
- counts[array[3]] += 1; /* 58 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 14 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 62 */
+#endif
+ debug(printf("14 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask8));
- counts[array[0]] += 1; /* 11 */
- counts[array[1]] += 1; /* 27 */
- counts[array[2]] += 1; /* 43 */
- counts[array[3]] += 1; /* 59 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("31 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("47 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("63 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask8));
- counts[array[0]] += 1; /* 12 */
- counts[array[1]] += 1; /* 28 */
- counts[array[2]] += 1; /* 44 */
- counts[array[3]] += 1; /* 60 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 15 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 63 */
+#endif
+ debug(printf("15 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask8));
- counts[array[0]] += 1; /* 13 */
- counts[array[1]] += 1; /* 29 */
- counts[array[2]] += 1; /* 45 */
- counts[array[3]] += 1; /* 61 */
+ return;
+}
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask8));
- counts[array[0]] += 1; /* 14 */
- counts[array[1]] += 1; /* 30 */
- counts[array[2]] += 1; /* 46 */
- counts[array[3]] += 1; /* 62 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask8));
- counts[array[0]] += 1; /* 15 */
- counts[array[1]] += 1; /* 31 */
- counts[array[2]] += 1; /* 47 */
- counts[array[3]] += 1; /* 63 */
+#ifdef HAVE_AVX2
+static void
+count_8mers_fwd_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+ array = _mm256_srli_epi32(current,16); /* No mask necessary */
+ counts[EXTRACT256(array,0)] += 1; /* 0 */
+ counts[EXTRACT256(array,1)] += 1; /* 16 */
+ counts[EXTRACT256(array,2)] += 1; /* 32 */
+ counts[EXTRACT256(array,3)] += 1; /* 48 */
+ counts[EXTRACT256(array,4)] += 1; /* 64 */
+ counts[EXTRACT256(array,5)] += 1; /* 80 */
+ counts[EXTRACT256(array,6)] += 1; /* 96 */
+ counts[EXTRACT256(array,7)] += 1; /* 112 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 1 */
+ counts[EXTRACT256(array,1)] += 1; /* 17 */
+ counts[EXTRACT256(array,2)] += 1; /* 33 */
+ counts[EXTRACT256(array,3)] += 1; /* 49 */
+ counts[EXTRACT256(array,4)] += 1; /* 65 */
+ counts[EXTRACT256(array,5)] += 1; /* 81 */
+ counts[EXTRACT256(array,6)] += 1; /* 97 */
+ counts[EXTRACT256(array,7)] += 1; /* 113 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 2 */
+ counts[EXTRACT256(array,1)] += 1; /* 18 */
+ counts[EXTRACT256(array,2)] += 1; /* 34 */
+ counts[EXTRACT256(array,3)] += 1; /* 50 */
+ counts[EXTRACT256(array,4)] += 1; /* 66 */
+ counts[EXTRACT256(array,5)] += 1; /* 82 */
+ counts[EXTRACT256(array,6)] += 1; /* 98 */
+ counts[EXTRACT256(array,7)] += 1; /* 114 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 3 */
+ counts[EXTRACT256(array,1)] += 1; /* 19 */
+ counts[EXTRACT256(array,2)] += 1; /* 35 */
+ counts[EXTRACT256(array,3)] += 1; /* 51 */
+ counts[EXTRACT256(array,4)] += 1; /* 67 */
+ counts[EXTRACT256(array,5)] += 1; /* 83 */
+ counts[EXTRACT256(array,6)] += 1; /* 99 */
+ counts[EXTRACT256(array,7)] += 1; /* 115 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 4 */
+ counts[EXTRACT256(array,1)] += 1; /* 20 */
+ counts[EXTRACT256(array,2)] += 1; /* 36 */
+ counts[EXTRACT256(array,3)] += 1; /* 52 */
+ counts[EXTRACT256(array,4)] += 1; /* 68 */
+ counts[EXTRACT256(array,5)] += 1; /* 84 */
+ counts[EXTRACT256(array,6)] += 1; /* 100 */
+ counts[EXTRACT256(array,7)] += 1; /* 116 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 5 */
+ counts[EXTRACT256(array,1)] += 1; /* 21 */
+ counts[EXTRACT256(array,2)] += 1; /* 37 */
+ counts[EXTRACT256(array,3)] += 1; /* 53 */
+ counts[EXTRACT256(array,4)] += 1; /* 69 */
+ counts[EXTRACT256(array,5)] += 1; /* 85 */
+ counts[EXTRACT256(array,6)] += 1; /* 101 */
+ counts[EXTRACT256(array,7)] += 1; /* 117 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 6 */
+ counts[EXTRACT256(array,1)] += 1; /* 22 */
+ counts[EXTRACT256(array,2)] += 1; /* 38 */
+ counts[EXTRACT256(array,3)] += 1; /* 54 */
+ counts[EXTRACT256(array,4)] += 1; /* 70 */
+ counts[EXTRACT256(array,5)] += 1; /* 86 */
+ counts[EXTRACT256(array,6)] += 1; /* 102 */
+ counts[EXTRACT256(array,7)] += 1; /* 118 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 7 */
+ counts[EXTRACT256(array,1)] += 1; /* 23 */
+ counts[EXTRACT256(array,2)] += 1; /* 39 */
+ counts[EXTRACT256(array,3)] += 1; /* 55 */
+ counts[EXTRACT256(array,4)] += 1; /* 71 */
+ counts[EXTRACT256(array,5)] += 1; /* 87 */
+ counts[EXTRACT256(array,6)] += 1; /* 103 */
+ counts[EXTRACT256(array,7)] += 1; /* 119 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 8 */
+ counts[EXTRACT256(array,1)] += 1; /* 24 */
+ counts[EXTRACT256(array,2)] += 1; /* 40 */
+ counts[EXTRACT256(array,3)] += 1; /* 56 */
+ counts[EXTRACT256(array,4)] += 1; /* 72 */
+ counts[EXTRACT256(array,5)] += 1; /* 88 */
+ counts[EXTRACT256(array,6)] += 1; /* 104 */
+ counts[EXTRACT256(array,7)] += 1; /* 120 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,18), _mm256_slli_epi32(current,14));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 9 */
+ counts[EXTRACT256(array,1)] += 1; /* 25 */
+ counts[EXTRACT256(array,2)] += 1; /* 41 */
+ counts[EXTRACT256(array,3)] += 1; /* 57 */
+ counts[EXTRACT256(array,4)] += 1; /* 73 */
+ counts[EXTRACT256(array,5)] += 1; /* 89 */
+ counts[EXTRACT256(array,6)] += 1; /* 105 */
+ counts[EXTRACT256(array,7)] += 1; /* 121 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 10 */
+ counts[EXTRACT256(array,1)] += 1; /* 26 */
+ counts[EXTRACT256(array,2)] += 1; /* 42 */
+ counts[EXTRACT256(array,3)] += 1; /* 58 */
+ counts[EXTRACT256(array,4)] += 1; /* 74 */
+ counts[EXTRACT256(array,5)] += 1; /* 90 */
+ counts[EXTRACT256(array,6)] += 1; /* 106 */
+ counts[EXTRACT256(array,7)] += 1; /* 122 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 11 */
+ counts[EXTRACT256(array,1)] += 1; /* 27 */
+ counts[EXTRACT256(array,2)] += 1; /* 43 */
+ counts[EXTRACT256(array,3)] += 1; /* 59 */
+ counts[EXTRACT256(array,4)] += 1; /* 75 */
+ counts[EXTRACT256(array,5)] += 1; /* 91 */
+ counts[EXTRACT256(array,6)] += 1; /* 107 */
+ counts[EXTRACT256(array,7)] += 1; /* 123 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 12 */
+ counts[EXTRACT256(array,1)] += 1; /* 28 */
+ counts[EXTRACT256(array,2)] += 1; /* 44 */
+ counts[EXTRACT256(array,3)] += 1; /* 60 */
+ counts[EXTRACT256(array,4)] += 1; /* 76 */
+ counts[EXTRACT256(array,5)] += 1; /* 92 */
+ counts[EXTRACT256(array,6)] += 1; /* 108 */
+ counts[EXTRACT256(array,7)] += 1; /* 124 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 13 */
+ counts[EXTRACT256(array,1)] += 1; /* 29 */
+ counts[EXTRACT256(array,2)] += 1; /* 45 */
+ counts[EXTRACT256(array,3)] += 1; /* 61 */
+ counts[EXTRACT256(array,4)] += 1; /* 77 */
+ counts[EXTRACT256(array,5)] += 1; /* 93 */
+ counts[EXTRACT256(array,6)] += 1; /* 109 */
+ counts[EXTRACT256(array,7)] += 1; /* 125 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 14 */
+ counts[EXTRACT256(array,1)] += 1; /* 30 */
+ counts[EXTRACT256(array,2)] += 1; /* 46 */
+ counts[EXTRACT256(array,3)] += 1; /* 62 */
+ counts[EXTRACT256(array,4)] += 1; /* 78 */
+ counts[EXTRACT256(array,5)] += 1; /* 94 */
+ counts[EXTRACT256(array,6)] += 1; /* 110 */
+ counts[EXTRACT256(array,7)] += 1; /* 126 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 15 */
+ counts[EXTRACT256(array,1)] += 1; /* 31 */
+ counts[EXTRACT256(array,2)] += 1; /* 47 */
+ counts[EXTRACT256(array,3)] += 1; /* 63 */
+ counts[EXTRACT256(array,4)] += 1; /* 79 */
+ counts[EXTRACT256(array,5)] += 1; /* 95 */
+ counts[EXTRACT256(array,6)] += 1; /* 111 */
+ counts[EXTRACT256(array,7)] += 1; /* 127 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_8mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -11892,72 +17482,51 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (oligo >> 2) & MASK8; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (oligo >> 4) & MASK8; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (oligo >> 6) & MASK8; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (oligo >> 8) & MASK8; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (oligo >> 10) & MASK8; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (oligo >> 12) & MASK8; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
#else
@@ -11970,42 +17539,30 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos));
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -12018,32 +17575,23 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
#endif
@@ -12051,92 +17599,65 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK8; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rev >> 2) & MASK8; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rev >> 4) & MASK8; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (low_rev >> 6) & MASK8; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (low_rev >> 8) & MASK8; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (low_rev >> 10) & MASK8; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (low_rev >> 12) & MASK8; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (low_rev >> 14) & MASK8; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = low_rev >> 16; /* 16, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -12149,42 +17670,30 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
@@ -12197,53 +17706,38 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = low_rev >> 16; /* 16, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -12254,72 +17748,51 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (oligo >> 2) & MASK8; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (oligo >> 4) & MASK8; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (oligo >> 6) & MASK8; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (oligo >> 8) & MASK8; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (oligo >> 10) & MASK8; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (oligo >> 12) & MASK8; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
#else
@@ -12332,42 +17805,30 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -12380,32 +17841,23 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
#endif
@@ -12413,92 +17865,65 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK8; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rev >> 2) & MASK8; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rev >> 4) & MASK8; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (high_rev >> 6) & MASK8; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (high_rev >> 8) & MASK8; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (high_rev >> 10) & MASK8; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (high_rev >> 12) & MASK8; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (high_rev >> 14) & MASK8; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = high_rev >> 16; /* 0, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -12509,112 +17934,353 @@ store_8mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
_masked = _mm_and_si128(_oligo, mask8);
#endif
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
- *(--pointers[masked]) = chrpos - 23;
- }
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
+#else
+ _masked = _mm_and_si128(_oligo, mask8);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = high_rev >> 16; /* 0, No mask necessary */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_8mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ oligo = nexthigh_rev >> 18; /* For 31..25 */
+ oligo |= low_rev << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+
+ masked = low_rev >> 16; /* 16, No mask necessary */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+
+ oligo = low_rev >> 18; /* For 9..15 */
+ oligo |= high_rev << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
- *(--pointers[masked]) = chrpos - 24;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
- *(--pointers[masked]) = chrpos - 25;
- }
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
- *(--pointers[masked]) = chrpos - 26;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
-#else
- _masked = _mm_and_si128(_oligo, mask8);
-#endif
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
- *(--pointers[masked]) = chrpos - 27;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = high_rev >> 16; /* 0, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
+#if !defined(HAVE_AVX2)
+
static void
-count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+count_7mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -12630,27 +18296,27 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 31 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK7; /* 30 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK7; /* 29 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK7; /* 28 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK7; /* 27 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK7; /* 26 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
#else
@@ -12662,19 +18328,19 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
@@ -12686,54 +18352,54 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK7; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 2) & MASK7; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 4) & MASK7; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 6) & MASK7; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 8) & MASK7; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 10) & MASK7; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 12) & MASK7; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 14) & MASK7; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 16) & MASK7; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = low_rev >> 18; /* 16, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#else
@@ -12745,19 +18411,19 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
@@ -12769,19 +18435,19 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
@@ -12793,11 +18459,11 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#endif
@@ -12807,27 +18473,27 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK7; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK7; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK7; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK7; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK7; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
#else
@@ -12839,19 +18505,19 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
@@ -12863,124 +18529,418 @@ count_7mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK7; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 2) & MASK7; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 4) & MASK7; /* 7 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 6) & MASK7; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 8) & MASK7; /* 5 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 10) & MASK7; /* 4 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 12) & MASK7; /* 3 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 14) & MASK7; /* 2 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 16) & MASK7; /* 1 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = high_rev >> 18; /* 0, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 8) & MASK7; /* 5 */
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_7mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = nexthigh_rev >> 20; /* For 31..26 */
+ oligo |= low_rev << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low6);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+
+
+ oligo = low_rev >> 20; /* For 15..10 */
+ oligo |= high_rev << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
- debug(printf("5 %04X => %d\n",masked,counts[masked]));
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 10) & MASK7; /* 4 */
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
- debug(printf("4 %04X => %d\n",masked,counts[masked]));
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 12) & MASK7; /* 3 */
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("3 %04X => %d\n",masked,counts[masked]));
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 14) & MASK7; /* 2 */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("2 %04X => %d\n",masked,counts[masked]));
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 16) & MASK7; /* 1 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
- debug(printf("1 %04X => %d\n",masked,counts[masked]));
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
- masked = high_rev >> 18; /* 0, No mask necessary */
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
- debug(printf("0 %04X => %d\n",masked,counts[masked]));
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low6);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
- masked = EXTRACT(_masked,0);
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("9 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("8 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("7 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("6 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("5 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("4 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("3 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("2 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
-#endif
return;
}
+#endif /* HAVE_AVX2 */
+
+
+
/* Expecting current to have {high0_rev, low0_rev, high1_rev,
low1_rev}, and next to have {low0_rev, high1_rev, low1_rev, and
high2_rev} */
@@ -13011,117 +18971,1576 @@ extract_7mers_fwd_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_7mers_fwd_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,18)); /* No mask necessary */
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask7));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,20), _mm256_slli_epi32(current,12));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask7));
+
+ return;
+}
+#endif
+
static void
-count_7mers_fwd_simd (Count_T *counts, __m128i current, __m128i next) {
+count_7mers_fwd_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,18); /* No mask necessary */
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,18)); /* No mask necessary */
- counts[array[0]] += 1; /* 0 */
- counts[array[1]] += 1; /* 16 */
- counts[array[2]] += 1; /* 32 */
- counts[array[3]] += 1; /* 48 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("16 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("32 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("48 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 0 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 48 */
+#endif
+ debug(printf("0 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,16), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,16), mask7));
- counts[array[0]] += 1; /* 1 */
- counts[array[1]] += 1; /* 17 */
- counts[array[2]] += 1; /* 33 */
- counts[array[3]] += 1; /* 49 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("17 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("33 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("49 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 1 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 49 */
+#endif
+ debug(printf("1 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask7));
- counts[array[0]] += 1; /* 2 */
- counts[array[1]] += 1; /* 18 */
- counts[array[2]] += 1; /* 34 */
- counts[array[3]] += 1; /* 50 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("18 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("34 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("50 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 2 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 50 */
+#endif
+ debug(printf("2 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask7));
- counts[array[0]] += 1; /* 3 */
- counts[array[1]] += 1; /* 19 */
- counts[array[2]] += 1; /* 35 */
- counts[array[3]] += 1; /* 51 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("19 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("35 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("51 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 3 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 51 */
+#endif
+ debug(printf("3 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask7));
- counts[array[0]] += 1; /* 4 */
- counts[array[1]] += 1; /* 20 */
- counts[array[2]] += 1; /* 36 */
- counts[array[3]] += 1; /* 52 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("20 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("36 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("52 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 4 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 52 */
+#endif
+ debug(printf("4 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask7));
- counts[array[0]] += 1; /* 5 */
- counts[array[1]] += 1; /* 21 */
- counts[array[2]] += 1; /* 37 */
- counts[array[3]] += 1; /* 53 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("21 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("37 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("53 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 5 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 53 */
+#endif
+ debug(printf("5 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask7));
- counts[array[0]] += 1; /* 6 */
- counts[array[1]] += 1; /* 22 */
- counts[array[2]] += 1; /* 38 */
- counts[array[3]] += 1; /* 54 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("22 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("38 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("54 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 6 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 54 */
+#endif
+ debug(printf("6 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask7));
- counts[array[0]] += 1; /* 7 */
- counts[array[1]] += 1; /* 23 */
- counts[array[2]] += 1; /* 39 */
- counts[array[3]] += 1; /* 55 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("23 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("39 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("55 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 7 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 55 */
+#endif
+ debug(printf("7 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask7));
- counts[array[0]] += 1; /* 8 */
- counts[array[1]] += 1; /* 24 */
- counts[array[2]] += 1; /* 40 */
- counts[array[3]] += 1; /* 56 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("24 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("40 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("56 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 8 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 56 */
+#endif
+ debug(printf("8 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( current, mask7));
- counts[array[0]] += 1; /* 9 */
- counts[array[1]] += 1; /* 25 */
- counts[array[2]] += 1; /* 41 */
- counts[array[3]] += 1; /* 57 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("25 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("41 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("57 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 9 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 57 */
+#endif
+ debug(printf("9 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+
+ oligo = _mm_or_si128( _mm_srli_epi32(next,20), _mm_slli_epi32(current,12));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,10), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("26 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("42 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("58 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 10 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 58 */
+#endif
+ debug(printf("10 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("27 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("43 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("59 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 11 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 59 */
+#endif
+ debug(printf("11 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("28 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("44 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("60 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 12 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 60 */
+#endif
+ debug(printf("12 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("29 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("45 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("61 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 13 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 61 */
+#endif
+ debug(printf("13 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("30 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("46 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("62 %04X => %d\n",array[3],counts[array[3]]));
- oligo = _mm_or_si128( _mm_srli_epi32(next,20), _mm_slli_epi32(current,12));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask7));
- counts[array[0]] += 1; /* 10 */
- counts[array[1]] += 1; /* 26 */
- counts[array[2]] += 1; /* 42 */
- counts[array[3]] += 1; /* 58 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 14 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 62 */
+#endif
+ debug(printf("14 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask7));
- counts[array[0]] += 1; /* 11 */
- counts[array[1]] += 1; /* 27 */
- counts[array[2]] += 1; /* 43 */
- counts[array[3]] += 1; /* 59 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("31 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("47 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("63 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask7));
- counts[array[0]] += 1; /* 12 */
- counts[array[1]] += 1; /* 28 */
- counts[array[2]] += 1; /* 44 */
- counts[array[3]] += 1; /* 60 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 15 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 63 */
+#endif
+ debug(printf("15 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask7));
- counts[array[0]] += 1; /* 13 */
- counts[array[1]] += 1; /* 29 */
- counts[array[2]] += 1; /* 45 */
- counts[array[3]] += 1; /* 61 */
+ return;
+}
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask7));
- counts[array[0]] += 1; /* 14 */
- counts[array[1]] += 1; /* 30 */
- counts[array[2]] += 1; /* 46 */
- counts[array[3]] += 1; /* 62 */
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask7));
- counts[array[0]] += 1; /* 15 */
- counts[array[1]] += 1; /* 31 */
- counts[array[2]] += 1; /* 47 */
- counts[array[3]] += 1; /* 63 */
+#ifdef HAVE_AVX2
+static void
+count_7mers_fwd_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+ array = _mm256_srli_epi32(current,18); /* No mask necessary */
+ counts[EXTRACT256(array,0)] += 1; /* 0 */
+ counts[EXTRACT256(array,1)] += 1; /* 16 */
+ counts[EXTRACT256(array,2)] += 1; /* 32 */
+ counts[EXTRACT256(array,3)] += 1; /* 48 */
+ counts[EXTRACT256(array,4)] += 1; /* 64 */
+ counts[EXTRACT256(array,5)] += 1; /* 80 */
+ counts[EXTRACT256(array,6)] += 1; /* 96 */
+ counts[EXTRACT256(array,7)] += 1; /* 112 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 1 */
+ counts[EXTRACT256(array,1)] += 1; /* 17 */
+ counts[EXTRACT256(array,2)] += 1; /* 33 */
+ counts[EXTRACT256(array,3)] += 1; /* 49 */
+ counts[EXTRACT256(array,4)] += 1; /* 65 */
+ counts[EXTRACT256(array,5)] += 1; /* 81 */
+ counts[EXTRACT256(array,6)] += 1; /* 97 */
+ counts[EXTRACT256(array,7)] += 1; /* 113 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 2 */
+ counts[EXTRACT256(array,1)] += 1; /* 18 */
+ counts[EXTRACT256(array,2)] += 1; /* 34 */
+ counts[EXTRACT256(array,3)] += 1; /* 50 */
+ counts[EXTRACT256(array,4)] += 1; /* 66 */
+ counts[EXTRACT256(array,5)] += 1; /* 82 */
+ counts[EXTRACT256(array,6)] += 1; /* 98 */
+ counts[EXTRACT256(array,7)] += 1; /* 114 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 3 */
+ counts[EXTRACT256(array,1)] += 1; /* 19 */
+ counts[EXTRACT256(array,2)] += 1; /* 35 */
+ counts[EXTRACT256(array,3)] += 1; /* 51 */
+ counts[EXTRACT256(array,4)] += 1; /* 67 */
+ counts[EXTRACT256(array,5)] += 1; /* 83 */
+ counts[EXTRACT256(array,6)] += 1; /* 99 */
+ counts[EXTRACT256(array,7)] += 1; /* 115 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 4 */
+ counts[EXTRACT256(array,1)] += 1; /* 20 */
+ counts[EXTRACT256(array,2)] += 1; /* 36 */
+ counts[EXTRACT256(array,3)] += 1; /* 52 */
+ counts[EXTRACT256(array,4)] += 1; /* 68 */
+ counts[EXTRACT256(array,5)] += 1; /* 84 */
+ counts[EXTRACT256(array,6)] += 1; /* 100 */
+ counts[EXTRACT256(array,7)] += 1; /* 116 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 5 */
+ counts[EXTRACT256(array,1)] += 1; /* 21 */
+ counts[EXTRACT256(array,2)] += 1; /* 37 */
+ counts[EXTRACT256(array,3)] += 1; /* 53 */
+ counts[EXTRACT256(array,4)] += 1; /* 69 */
+ counts[EXTRACT256(array,5)] += 1; /* 85 */
+ counts[EXTRACT256(array,6)] += 1; /* 101 */
+ counts[EXTRACT256(array,7)] += 1; /* 117 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 6 */
+ counts[EXTRACT256(array,1)] += 1; /* 22 */
+ counts[EXTRACT256(array,2)] += 1; /* 38 */
+ counts[EXTRACT256(array,3)] += 1; /* 54 */
+ counts[EXTRACT256(array,4)] += 1; /* 70 */
+ counts[EXTRACT256(array,5)] += 1; /* 86 */
+ counts[EXTRACT256(array,6)] += 1; /* 102 */
+ counts[EXTRACT256(array,7)] += 1; /* 118 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 7 */
+ counts[EXTRACT256(array,1)] += 1; /* 23 */
+ counts[EXTRACT256(array,2)] += 1; /* 39 */
+ counts[EXTRACT256(array,3)] += 1; /* 55 */
+ counts[EXTRACT256(array,4)] += 1; /* 71 */
+ counts[EXTRACT256(array,5)] += 1; /* 87 */
+ counts[EXTRACT256(array,6)] += 1; /* 103 */
+ counts[EXTRACT256(array,7)] += 1; /* 119 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 8 */
+ counts[EXTRACT256(array,1)] += 1; /* 24 */
+ counts[EXTRACT256(array,2)] += 1; /* 40 */
+ counts[EXTRACT256(array,3)] += 1; /* 56 */
+ counts[EXTRACT256(array,4)] += 1; /* 72 */
+ counts[EXTRACT256(array,5)] += 1; /* 88 */
+ counts[EXTRACT256(array,6)] += 1; /* 104 */
+ counts[EXTRACT256(array,7)] += 1; /* 120 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 9 */
+ counts[EXTRACT256(array,1)] += 1; /* 25 */
+ counts[EXTRACT256(array,2)] += 1; /* 41 */
+ counts[EXTRACT256(array,3)] += 1; /* 57 */
+ counts[EXTRACT256(array,4)] += 1; /* 73 */
+ counts[EXTRACT256(array,5)] += 1; /* 89 */
+ counts[EXTRACT256(array,6)] += 1; /* 105 */
+ counts[EXTRACT256(array,7)] += 1; /* 121 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,20), _mm256_slli_epi32(current,12));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 10 */
+ counts[EXTRACT256(array,1)] += 1; /* 26 */
+ counts[EXTRACT256(array,2)] += 1; /* 42 */
+ counts[EXTRACT256(array,3)] += 1; /* 58 */
+ counts[EXTRACT256(array,4)] += 1; /* 74 */
+ counts[EXTRACT256(array,5)] += 1; /* 90 */
+ counts[EXTRACT256(array,6)] += 1; /* 106 */
+ counts[EXTRACT256(array,7)] += 1; /* 122 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 11 */
+ counts[EXTRACT256(array,1)] += 1; /* 27 */
+ counts[EXTRACT256(array,2)] += 1; /* 43 */
+ counts[EXTRACT256(array,3)] += 1; /* 59 */
+ counts[EXTRACT256(array,4)] += 1; /* 75 */
+ counts[EXTRACT256(array,5)] += 1; /* 91 */
+ counts[EXTRACT256(array,6)] += 1; /* 107 */
+ counts[EXTRACT256(array,7)] += 1; /* 123 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 12 */
+ counts[EXTRACT256(array,1)] += 1; /* 28 */
+ counts[EXTRACT256(array,2)] += 1; /* 44 */
+ counts[EXTRACT256(array,3)] += 1; /* 60 */
+ counts[EXTRACT256(array,4)] += 1; /* 76 */
+ counts[EXTRACT256(array,5)] += 1; /* 92 */
+ counts[EXTRACT256(array,6)] += 1; /* 108 */
+ counts[EXTRACT256(array,7)] += 1; /* 124 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 13 */
+ counts[EXTRACT256(array,1)] += 1; /* 29 */
+ counts[EXTRACT256(array,2)] += 1; /* 45 */
+ counts[EXTRACT256(array,3)] += 1; /* 61 */
+ counts[EXTRACT256(array,4)] += 1; /* 77 */
+ counts[EXTRACT256(array,5)] += 1; /* 93 */
+ counts[EXTRACT256(array,6)] += 1; /* 109 */
+ counts[EXTRACT256(array,7)] += 1; /* 125 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 14 */
+ counts[EXTRACT256(array,1)] += 1; /* 30 */
+ counts[EXTRACT256(array,2)] += 1; /* 46 */
+ counts[EXTRACT256(array,3)] += 1; /* 62 */
+ counts[EXTRACT256(array,4)] += 1; /* 78 */
+ counts[EXTRACT256(array,5)] += 1; /* 94 */
+ counts[EXTRACT256(array,6)] += 1; /* 110 */
+ counts[EXTRACT256(array,7)] += 1; /* 126 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 15 */
+ counts[EXTRACT256(array,1)] += 1; /* 31 */
+ counts[EXTRACT256(array,2)] += 1; /* 47 */
+ counts[EXTRACT256(array,3)] += 1; /* 63 */
+ counts[EXTRACT256(array,4)] += 1; /* 79 */
+ counts[EXTRACT256(array,5)] += 1; /* 95 */
+ counts[EXTRACT256(array,6)] += 1; /* 111 */
+ counts[EXTRACT256(array,7)] += 1; /* 127 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
-
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_7mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -13132,63 +20551,51 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
__m128i _oligo, _masked;
#endif
-
+
oligo = nexthigh_rev >> 20; /* For 31..26 */
oligo |= low_rev << 12;
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (oligo >> 2) & MASK7; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (oligo >> 4) & MASK7; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (oligo >> 6) & MASK7; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (oligo >> 8) & MASK7; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (oligo >> 10) & MASK7; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
#else
@@ -13201,38 +20608,30 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -13245,20 +20644,16 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
#endif
@@ -13266,92 +20661,72 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK7; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rev >> 2) & MASK7; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rev >> 4) & MASK7; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rev >> 6) & MASK7; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (low_rev >> 8) & MASK7; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (low_rev >> 10) & MASK7; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (low_rev >> 12) & MASK7; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (low_rev >> 14) & MASK7; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (low_rev >> 16) & MASK7; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = low_rev >> 18; /* 16, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -13364,38 +20739,30 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
@@ -13408,38 +20775,30 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
@@ -13452,20 +20811,16 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -13476,56 +20831,44 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (oligo >> 2) & MASK7; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (oligo >> 4) & MASK7; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (oligo >> 6) & MASK7; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (oligo >> 8) & MASK7; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (oligo >> 10) & MASK7; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
#else
@@ -13538,38 +20881,30 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -13582,20 +20917,16 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
#endif
@@ -13603,92 +20934,72 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK7; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rev >> 2) & MASK7; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rev >> 4) & MASK7; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rev >> 6) & MASK7; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (high_rev >> 8) & MASK7; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (high_rev >> 10) & MASK7; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (high_rev >> 12) & MASK7; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (high_rev >> 14) & MASK7; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (high_rev >> 16) & MASK7; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = high_rev >> 18; /* 0, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -13701,117 +21012,373 @@ store_7mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_7mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ oligo = nexthigh_rev >> 20; /* For 31..26 */
+ oligo |= low_rev << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ oligo = low_rev >> 20; /* For 15..10 */
+ oligo |= high_rev << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
+
+#if !defined(HAVE_AVX2)
static void
-count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+count_6mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -13827,23 +21394,23 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 31 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK6; /* 30 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK6; /* 29 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK6; /* 28 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK6; /* 27 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
#else
@@ -13855,71 +21422,71 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK6; /* 27 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK6; /* 26 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 2) & MASK6; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 4) & MASK6; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 6) & MASK6; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 8) & MASK6; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 10) & MASK6; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 12) & MASK6; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 14) & MASK6; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 16) & MASK6; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 18) & MASK6; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = low_rev >> 20; /* 16, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#else
@@ -13931,19 +21498,19 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
@@ -13955,19 +21522,19 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
@@ -13979,15 +21546,15 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#endif
@@ -13997,23 +21564,23 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK6; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK6; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK6; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK6; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
#else
@@ -14025,145 +21592,430 @@ count_6mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK6; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK6; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 2) & MASK6; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 4) & MASK6; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 6) & MASK6; /* 7 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 8) & MASK6; /* 6 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 10) & MASK6; /* 5 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 12) & MASK6; /* 4 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 14) & MASK6; /* 3 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 16) & MASK6; /* 2 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 18) & MASK6; /* 1 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = high_rev >> 20; /* 0, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 6) & MASK6; /* 7 */
- counts[masked] += 1;
- debug(printf("7 %04X => %d\n",masked,counts[masked]));
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_6mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = nexthigh_rev >> 22; /* For 31..27 */
+ oligo |= low_rev << 10;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low5);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+
+ oligo = low_rev >> 22; /* For 15..11 */
+ oligo |= high_rev << 10;
- masked = (high_rev >> 8) & MASK6; /* 6 */
- counts[masked] += 1;
- debug(printf("6 %04X => %d\n",masked,counts[masked]));
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
- masked = (high_rev >> 10) & MASK6; /* 5 */
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
- debug(printf("5 %04X => %d\n",masked,counts[masked]));
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 12) & MASK6; /* 4 */
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
- debug(printf("4 %04X => %d\n",masked,counts[masked]));
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 14) & MASK6; /* 3 */
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("3 %04X => %d\n",masked,counts[masked]));
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 16) & MASK6; /* 2 */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("2 %04X => %d\n",masked,counts[masked]));
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 18) & MASK6; /* 1 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
- debug(printf("1 %04X => %d\n",masked,counts[masked]));
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
- masked = high_rev >> 20; /* 0, No mask necessary */
- counts[masked] += 1;
- debug(printf("0 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low5);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
- masked = EXTRACT(_masked,0);
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("10 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("9 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("8 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("7 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("6 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("5 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("4 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("3 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
-#endif
return;
}
+#endif /* HAVE_AVX2 */
+
+
/* Expecting current to have {high0_rev, low0_rev, high1_rev,
low1_rev}, and next to have {low0_rev, high1_rev, low1_rev, and
@@ -14195,117 +22047,1578 @@ extract_6mers_fwd_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
static void
-count_6mers_fwd_simd (Count_T *counts, __m128i current, __m128i next) {
+extract_6mers_fwd_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,20)); /* No mask necessary */;
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask6));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,22), _mm256_slli_epi32(current,10));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask6));
+
+ return;
+}
+#endif
+
+
+static void
+count_6mers_fwd_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,20); /* No mask necessary */;
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,20)); /* No mask necessary */;
- counts[array[0]] += 1; /* 0 */
- counts[array[1]] += 1; /* 16 */
- counts[array[2]] += 1; /* 32 */
- counts[array[3]] += 1; /* 48 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("16 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("32 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("48 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 0 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 48 */
+#endif
+ debug(printf("0 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,18), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,18), mask6));
- counts[array[0]] += 1; /* 1 */
- counts[array[1]] += 1; /* 17 */
- counts[array[2]] += 1; /* 33 */
- counts[array[3]] += 1; /* 49 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("17 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("33 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("49 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 1 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 49 */
+#endif
+ debug(printf("1 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,16), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,16), mask6));
- counts[array[0]] += 1; /* 2 */
- counts[array[1]] += 1; /* 18 */
- counts[array[2]] += 1; /* 34 */
- counts[array[3]] += 1; /* 50 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("18 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("34 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("50 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 2 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 50 */
+#endif
+ debug(printf("2 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask6));
- counts[array[0]] += 1; /* 3 */
- counts[array[1]] += 1; /* 19 */
- counts[array[2]] += 1; /* 35 */
- counts[array[3]] += 1; /* 51 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("19 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("35 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("51 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 3 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 51 */
+#endif
+ debug(printf("3 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask6));
- counts[array[0]] += 1; /* 4 */
- counts[array[1]] += 1; /* 20 */
- counts[array[2]] += 1; /* 36 */
- counts[array[3]] += 1; /* 52 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("20 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("36 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("52 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 4 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 52 */
+#endif
+ debug(printf("4 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask6));
- counts[array[0]] += 1; /* 5 */
- counts[array[1]] += 1; /* 21 */
- counts[array[2]] += 1; /* 37 */
- counts[array[3]] += 1; /* 53 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("21 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("37 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("53 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 5 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 53 */
+#endif
+ debug(printf("5 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask6));
- counts[array[0]] += 1; /* 6 */
- counts[array[1]] += 1; /* 22 */
- counts[array[2]] += 1; /* 38 */
- counts[array[3]] += 1; /* 54 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("22 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("38 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("54 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 6 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 54 */
+#endif
+ debug(printf("6 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask6));
- counts[array[0]] += 1; /* 7 */
- counts[array[1]] += 1; /* 23 */
- counts[array[2]] += 1; /* 39 */
- counts[array[3]] += 1; /* 55 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("23 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("39 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("55 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 7 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 55 */
+#endif
+ debug(printf("7 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask6));
- counts[array[0]] += 1; /* 8 */
- counts[array[1]] += 1; /* 24 */
- counts[array[2]] += 1; /* 40 */
- counts[array[3]] += 1; /* 56 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("24 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("40 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("56 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 8 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 56 */
+#endif
+ debug(printf("8 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask6));
- counts[array[0]] += 1; /* 9 */
- counts[array[1]] += 1; /* 25 */
- counts[array[2]] += 1; /* 41 */
- counts[array[3]] += 1; /* 57 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("25 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("41 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("57 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 9 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 57 */
+#endif
+ debug(printf("9 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("26 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("42 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("58 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 10 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 58 */
+#endif
+ debug(printf("10 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+
+ oligo = _mm_or_si128( _mm_srli_epi32(next,22), _mm_slli_epi32(current,10));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("27 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("43 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("59 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 11 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 59 */
+#endif
+ debug(printf("11 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("28 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("44 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("60 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 12 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 60 */
+#endif
+ debug(printf("12 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("29 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("45 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("61 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 13 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 61 */
+#endif
+ debug(printf("13 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("30 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("46 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("62 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask6));
- counts[array[0]] += 1; /* 10 */
- counts[array[1]] += 1; /* 26 */
- counts[array[2]] += 1; /* 42 */
- counts[array[3]] += 1; /* 58 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 14 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 62 */
+#endif
+ debug(printf("14 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("31 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("47 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("63 %04X => %d\n",array[3],counts[array[3]]));
- oligo = _mm_or_si128( _mm_srli_epi32(next,22), _mm_slli_epi32(current,10));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask6));
- counts[array[0]] += 1; /* 11 */
- counts[array[1]] += 1; /* 27 */
- counts[array[2]] += 1; /* 43 */
- counts[array[3]] += 1; /* 59 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 15 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 63 */
+#endif
+ debug(printf("15 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask6));
- counts[array[0]] += 1; /* 12 */
- counts[array[1]] += 1; /* 28 */
- counts[array[2]] += 1; /* 44 */
- counts[array[3]] += 1; /* 60 */
+ return;
+}
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask6));
- counts[array[0]] += 1; /* 13 */
- counts[array[1]] += 1; /* 29 */
- counts[array[2]] += 1; /* 45 */
- counts[array[3]] += 1; /* 61 */
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask6));
- counts[array[0]] += 1; /* 14 */
- counts[array[1]] += 1; /* 30 */
- counts[array[2]] += 1; /* 46 */
- counts[array[3]] += 1; /* 62 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask6));
- counts[array[0]] += 1; /* 15 */
- counts[array[1]] += 1; /* 31 */
- counts[array[2]] += 1; /* 47 */
- counts[array[3]] += 1; /* 63 */
+#ifdef HAVE_AVX2
+static void
+count_6mers_fwd_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+ array = _mm256_srli_epi32(current,20); /* No mask necessary */;
+ counts[EXTRACT256(array,0)] += 1; /* 0 */
+ counts[EXTRACT256(array,1)] += 1; /* 16 */
+ counts[EXTRACT256(array,2)] += 1; /* 32 */
+ counts[EXTRACT256(array,3)] += 1; /* 48 */
+ counts[EXTRACT256(array,4)] += 1; /* 64 */
+ counts[EXTRACT256(array,5)] += 1; /* 80 */
+ counts[EXTRACT256(array,6)] += 1; /* 96 */
+ counts[EXTRACT256(array,7)] += 1; /* 112 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 1 */
+ counts[EXTRACT256(array,1)] += 1; /* 17 */
+ counts[EXTRACT256(array,2)] += 1; /* 33 */
+ counts[EXTRACT256(array,3)] += 1; /* 49 */
+ counts[EXTRACT256(array,4)] += 1; /* 65 */
+ counts[EXTRACT256(array,5)] += 1; /* 81 */
+ counts[EXTRACT256(array,6)] += 1; /* 97 */
+ counts[EXTRACT256(array,7)] += 1; /* 113 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 2 */
+ counts[EXTRACT256(array,1)] += 1; /* 18 */
+ counts[EXTRACT256(array,2)] += 1; /* 34 */
+ counts[EXTRACT256(array,3)] += 1; /* 50 */
+ counts[EXTRACT256(array,4)] += 1; /* 66 */
+ counts[EXTRACT256(array,5)] += 1; /* 82 */
+ counts[EXTRACT256(array,6)] += 1; /* 98 */
+ counts[EXTRACT256(array,7)] += 1; /* 114 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 3 */
+ counts[EXTRACT256(array,1)] += 1; /* 19 */
+ counts[EXTRACT256(array,2)] += 1; /* 35 */
+ counts[EXTRACT256(array,3)] += 1; /* 51 */
+ counts[EXTRACT256(array,4)] += 1; /* 67 */
+ counts[EXTRACT256(array,5)] += 1; /* 83 */
+ counts[EXTRACT256(array,6)] += 1; /* 99 */
+ counts[EXTRACT256(array,7)] += 1; /* 115 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 4 */
+ counts[EXTRACT256(array,1)] += 1; /* 20 */
+ counts[EXTRACT256(array,2)] += 1; /* 36 */
+ counts[EXTRACT256(array,3)] += 1; /* 52 */
+ counts[EXTRACT256(array,4)] += 1; /* 68 */
+ counts[EXTRACT256(array,5)] += 1; /* 84 */
+ counts[EXTRACT256(array,6)] += 1; /* 100 */
+ counts[EXTRACT256(array,7)] += 1; /* 116 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 5 */
+ counts[EXTRACT256(array,1)] += 1; /* 21 */
+ counts[EXTRACT256(array,2)] += 1; /* 37 */
+ counts[EXTRACT256(array,3)] += 1; /* 53 */
+ counts[EXTRACT256(array,4)] += 1; /* 69 */
+ counts[EXTRACT256(array,5)] += 1; /* 85 */
+ counts[EXTRACT256(array,6)] += 1; /* 101 */
+ counts[EXTRACT256(array,7)] += 1; /* 117 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 6 */
+ counts[EXTRACT256(array,1)] += 1; /* 22 */
+ counts[EXTRACT256(array,2)] += 1; /* 38 */
+ counts[EXTRACT256(array,3)] += 1; /* 54 */
+ counts[EXTRACT256(array,4)] += 1; /* 70 */
+ counts[EXTRACT256(array,5)] += 1; /* 86 */
+ counts[EXTRACT256(array,6)] += 1; /* 102 */
+ counts[EXTRACT256(array,7)] += 1; /* 118 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 7 */
+ counts[EXTRACT256(array,1)] += 1; /* 23 */
+ counts[EXTRACT256(array,2)] += 1; /* 39 */
+ counts[EXTRACT256(array,3)] += 1; /* 55 */
+ counts[EXTRACT256(array,4)] += 1; /* 71 */
+ counts[EXTRACT256(array,5)] += 1; /* 87 */
+ counts[EXTRACT256(array,6)] += 1; /* 103 */
+ counts[EXTRACT256(array,7)] += 1; /* 119 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 8 */
+ counts[EXTRACT256(array,1)] += 1; /* 24 */
+ counts[EXTRACT256(array,2)] += 1; /* 40 */
+ counts[EXTRACT256(array,3)] += 1; /* 56 */
+ counts[EXTRACT256(array,4)] += 1; /* 72 */
+ counts[EXTRACT256(array,5)] += 1; /* 88 */
+ counts[EXTRACT256(array,6)] += 1; /* 104 */
+ counts[EXTRACT256(array,7)] += 1; /* 120 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 9 */
+ counts[EXTRACT256(array,1)] += 1; /* 25 */
+ counts[EXTRACT256(array,2)] += 1; /* 41 */
+ counts[EXTRACT256(array,3)] += 1; /* 57 */
+ counts[EXTRACT256(array,4)] += 1; /* 73 */
+ counts[EXTRACT256(array,5)] += 1; /* 89 */
+ counts[EXTRACT256(array,6)] += 1; /* 105 */
+ counts[EXTRACT256(array,7)] += 1; /* 121 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 10 */
+ counts[EXTRACT256(array,1)] += 1; /* 26 */
+ counts[EXTRACT256(array,2)] += 1; /* 42 */
+ counts[EXTRACT256(array,3)] += 1; /* 58 */
+ counts[EXTRACT256(array,4)] += 1; /* 74 */
+ counts[EXTRACT256(array,5)] += 1; /* 90 */
+ counts[EXTRACT256(array,6)] += 1; /* 106 */
+ counts[EXTRACT256(array,7)] += 1; /* 122 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,22), _mm256_slli_epi32(current,10));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 11 */
+ counts[EXTRACT256(array,1)] += 1; /* 27 */
+ counts[EXTRACT256(array,2)] += 1; /* 43 */
+ counts[EXTRACT256(array,3)] += 1; /* 59 */
+ counts[EXTRACT256(array,4)] += 1; /* 75 */
+ counts[EXTRACT256(array,5)] += 1; /* 91 */
+ counts[EXTRACT256(array,6)] += 1; /* 107 */
+ counts[EXTRACT256(array,7)] += 1; /* 123 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 12 */
+ counts[EXTRACT256(array,1)] += 1; /* 28 */
+ counts[EXTRACT256(array,2)] += 1; /* 44 */
+ counts[EXTRACT256(array,3)] += 1; /* 60 */
+ counts[EXTRACT256(array,4)] += 1; /* 76 */
+ counts[EXTRACT256(array,5)] += 1; /* 92 */
+ counts[EXTRACT256(array,6)] += 1; /* 108 */
+ counts[EXTRACT256(array,7)] += 1; /* 124 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 13 */
+ counts[EXTRACT256(array,1)] += 1; /* 29 */
+ counts[EXTRACT256(array,2)] += 1; /* 45 */
+ counts[EXTRACT256(array,3)] += 1; /* 61 */
+ counts[EXTRACT256(array,4)] += 1; /* 77 */
+ counts[EXTRACT256(array,5)] += 1; /* 93 */
+ counts[EXTRACT256(array,6)] += 1; /* 109 */
+ counts[EXTRACT256(array,7)] += 1; /* 125 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 14 */
+ counts[EXTRACT256(array,1)] += 1; /* 30 */
+ counts[EXTRACT256(array,2)] += 1; /* 46 */
+ counts[EXTRACT256(array,3)] += 1; /* 62 */
+ counts[EXTRACT256(array,4)] += 1; /* 78 */
+ counts[EXTRACT256(array,5)] += 1; /* 94 */
+ counts[EXTRACT256(array,6)] += 1; /* 110 */
+ counts[EXTRACT256(array,7)] += 1; /* 126 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 15 */
+ counts[EXTRACT256(array,1)] += 1; /* 31 */
+ counts[EXTRACT256(array,2)] += 1; /* 47 */
+ counts[EXTRACT256(array,3)] += 1; /* 63 */
+ counts[EXTRACT256(array,4)] += 1; /* 79 */
+ counts[EXTRACT256(array,5)] += 1; /* 95 */
+ counts[EXTRACT256(array,6)] += 1; /* 111 */
+ counts[EXTRACT256(array,7)] += 1; /* 127 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
-
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_6mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -14323,47 +23636,37 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (oligo >> 2) & MASK6; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (oligo >> 4) & MASK6; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (oligo >> 6) & MASK6; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (oligo >> 8) & MASK6; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
#else
@@ -14376,48 +23679,38 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (oligo >> 8) & MASK6; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
#endif
@@ -14425,101 +23718,79 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK6; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rev >> 2) & MASK6; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rev >> 4) & MASK6; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rev >> 6) & MASK6; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rev >> 8) & MASK6; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (low_rev >> 10) & MASK6; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (low_rev >> 12) & MASK6; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (low_rev >> 14) & MASK6; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (low_rev >> 16) & MASK6; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (low_rev >> 18) & MASK6; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = low_rev >> 20; /* 16, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -14532,38 +23803,30 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
@@ -14576,38 +23839,30 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
@@ -14620,29 +23875,23 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -14653,47 +23902,37 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (oligo >> 2) & MASK6; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (oligo >> 4) & MASK6; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (oligo >> 6) & MASK6; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (oligo >> 8) & MASK6; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
#else
@@ -14706,48 +23945,38 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (oligo >> 8) & MASK6; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
#endif
@@ -14755,101 +23984,79 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK6; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rev >> 2) & MASK6; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rev >> 4) & MASK6; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rev >> 6) & MASK6; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rev >> 8) & MASK6; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (high_rev >> 10) & MASK6; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (high_rev >> 12) & MASK6; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (high_rev >> 14) & MASK6; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (high_rev >> 16) & MASK6; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (high_rev >> 18) & MASK6; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = high_rev >> 20; /* 0, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -14862,38 +24069,66 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
@@ -14904,85 +24139,313 @@ store_6mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
_masked = _mm_and_si128(_oligo, mask6);
#endif
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_6mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ oligo = nexthigh_rev >> 22; /* For 27..31 */
+ oligo |= low_rev << 10;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ oligo = low_rev >> 22; /* For 15..11 */
+ oligo |= high_rev << 10;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
-#endif
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
+#if !defined(HAVE_AVX2)
static void
-count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+count_5mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -14998,19 +24461,19 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 31 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK5; /* 30 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK5; /* 29 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK5; /* 28 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
#else
@@ -15022,70 +24485,70 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("31 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("30 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("29 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("28 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK5; /* 27 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 2) & MASK5; /* 26 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 4) & MASK5; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 6) & MASK5; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 8) & MASK5; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 10) & MASK5; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 12) & MASK5; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 14) & MASK5; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 16) & MASK5; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 18) & MASK5; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (low_rev >> 20) & MASK5; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = low_rev >> 22; /* 16, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#else
@@ -15097,19 +24560,19 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
@@ -15121,19 +24584,19 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
@@ -15145,19 +24608,19 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
#endif
@@ -15167,19 +24630,19 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK5; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK5; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK5; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
#else
@@ -15191,148 +24654,471 @@ count_5mers_fwd (Count_T *counts, Genomecomp_T high_rev, Genomecomp_T low_rev, G
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK5; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 2) & MASK5; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 4) & MASK5; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 6) & MASK5; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 8) & MASK5; /* 7 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 10) & MASK5; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 12) & MASK5; /* 5 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = (high_rev >> 14) & MASK5; /* 4 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 16) & MASK5; /* 3 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 18) & MASK5; /* 2 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = (high_rev >> 20) & MASK5; /* 1 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = high_rev >> 22; /* 0, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 16) & MASK5; /* 3 */
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_5mers_fwd (Count_T *counts, Inquery_T *inquery, Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = nexthigh_rev >> 24; /* For 31..28 */
+ oligo |= low_rev << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ oligo = low_rev >> 24; /* For 15..12 */
+ oligo |= high_rev << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
- debug(printf("3 %04X => %d\n",masked,counts[masked]));
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 18) & MASK5; /* 2 */
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
- debug(printf("2 %04X => %d\n",masked,counts[masked]));
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
- masked = (high_rev >> 20) & MASK5; /* 1 */
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("1 %04X => %d\n",masked,counts[masked]));
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
- masked = high_rev >> 22; /* 0, No mask necessary */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("0 %04X => %d\n",masked,counts[masked]));
-
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,0);
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("11 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("10 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("9 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("8 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("7 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("6 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("5 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("4 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("3 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("2 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("1 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("0 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
+
#ifdef USE_SIMD_FOR_COUNTS
static void
@@ -15361,117 +25147,1579 @@ extract_5mers_fwd_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_5mers_fwd_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,22)); /* No mask necessary */
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,20), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask5));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,24), _mm256_slli_epi32(current,8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask5));
+
+ return;
+}
+#endif
+
+
static void
-count_5mers_fwd_simd (Count_T *counts, __m128i current, __m128i next) {
+count_5mers_fwd_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,22); /* No mask necessary */
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,22)); /* No mask necessary */
- counts[array[0]] += 1; /* 0 */
- counts[array[1]] += 1; /* 16 */
- counts[array[2]] += 1; /* 32 */
- counts[array[3]] += 1; /* 48 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("16 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("32 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("48 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 0 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 48 */
+#endif
+ debug(printf("0 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,20), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,20), mask5));
- counts[array[0]] += 1; /* 1 */
- counts[array[1]] += 1; /* 17 */
- counts[array[2]] += 1; /* 33 */
- counts[array[3]] += 1; /* 49 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("17 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("33 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("49 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 1 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 49 */
+#endif
+ debug(printf("1 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,18), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,18), mask5));
- counts[array[0]] += 1; /* 2 */
- counts[array[1]] += 1; /* 18 */
- counts[array[2]] += 1; /* 34 */
- counts[array[3]] += 1; /* 50 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("18 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("34 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("50 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 2 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 50 */
+#endif
+ debug(printf("2 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,16), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,16), mask5));
- counts[array[0]] += 1; /* 3 */
- counts[array[1]] += 1; /* 19 */
- counts[array[2]] += 1; /* 35 */
- counts[array[3]] += 1; /* 51 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("19 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("35 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("51 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 3 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 51 */
+#endif
+ debug(printf("3 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask5));
- counts[array[0]] += 1; /* 4 */
- counts[array[1]] += 1; /* 20 */
- counts[array[2]] += 1; /* 36 */
- counts[array[3]] += 1; /* 52 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("20 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("36 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("52 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 4 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 52 */
+#endif
+ debug(printf("4 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask5));
- counts[array[0]] += 1; /* 5 */
- counts[array[1]] += 1; /* 21 */
- counts[array[2]] += 1; /* 37 */
- counts[array[3]] += 1; /* 53 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("21 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("37 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("53 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 5 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 53 */
+#endif
+ debug(printf("5 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask5));
- counts[array[0]] += 1; /* 6 */
- counts[array[1]] += 1; /* 22 */
- counts[array[2]] += 1; /* 38 */
- counts[array[3]] += 1; /* 54 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("22 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("38 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("54 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 6 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 54 */
+#endif
+ debug(printf("6 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask5));
- counts[array[0]] += 1; /* 7 */
- counts[array[1]] += 1; /* 23 */
- counts[array[2]] += 1; /* 39 */
- counts[array[3]] += 1; /* 55 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("23 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("39 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("55 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 7 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 55 */
+#endif
+ debug(printf("7 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask5));
- counts[array[0]] += 1; /* 8 */
- counts[array[1]] += 1; /* 24 */
- counts[array[2]] += 1; /* 40 */
- counts[array[3]] += 1; /* 56 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("24 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("40 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("56 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 8 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 56 */
+#endif
+ debug(printf("8 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask5));
- counts[array[0]] += 1; /* 9 */
- counts[array[1]] += 1; /* 25 */
- counts[array[2]] += 1; /* 41 */
- counts[array[3]] += 1; /* 57 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("25 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("41 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("57 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 9 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 57 */
+#endif
+ debug(printf("9 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask5);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask5));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("26 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("42 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("58 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 10 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 58 */
+#endif
+ debug(printf("10 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask5);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask5));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("27 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("43 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("59 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 11 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 59 */
+#endif
+ debug(printf("11 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+
+ oligo = _mm_or_si128( _mm_srli_epi32(next,24), _mm_slli_epi32(current,8));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask5);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask5));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("28 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("44 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("60 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 12 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 60 */
+#endif
+ debug(printf("12 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask5);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask5));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("29 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("45 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("61 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 13 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 61 */
+#endif
+ debug(printf("13 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask5);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask5));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("30 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("46 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("62 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask5));
- counts[array[0]] += 1; /* 10 */
- counts[array[1]] += 1; /* 26 */
- counts[array[2]] += 1; /* 42 */
- counts[array[3]] += 1; /* 58 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 14 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 62 */
+#endif
+ debug(printf("14 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask5));
- counts[array[0]] += 1; /* 11 */
- counts[array[1]] += 1; /* 27 */
- counts[array[2]] += 1; /* 43 */
- counts[array[3]] += 1; /* 59 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask5);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask5));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("31 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("47 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("63 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 15 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 63 */
+#endif
+ debug(printf("15 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- oligo = _mm_or_si128( _mm_srli_epi32(next,24), _mm_slli_epi32(current,8));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask5));
- counts[array[0]] += 1; /* 12 */
- counts[array[1]] += 1; /* 28 */
- counts[array[2]] += 1; /* 44 */
- counts[array[3]] += 1; /* 60 */
+ return;
+}
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask5));
- counts[array[0]] += 1; /* 13 */
- counts[array[1]] += 1; /* 29 */
- counts[array[2]] += 1; /* 45 */
- counts[array[3]] += 1; /* 61 */
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask5));
- counts[array[0]] += 1; /* 14 */
- counts[array[1]] += 1; /* 30 */
- counts[array[2]] += 1; /* 46 */
- counts[array[3]] += 1; /* 62 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask5));
- counts[array[0]] += 1; /* 15 */
- counts[array[1]] += 1; /* 31 */
- counts[array[2]] += 1; /* 47 */
- counts[array[3]] += 1; /* 63 */
+#ifdef HAVE_AVX2
+static void
+count_5mers_fwd_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ array = _mm256_srli_epi32(current,22); /* No mask necessary */
+ counts[EXTRACT256(array,0)] += 1; /* 0 */
+ counts[EXTRACT256(array,1)] += 1; /* 16 */
+ counts[EXTRACT256(array,2)] += 1; /* 32 */
+ counts[EXTRACT256(array,3)] += 1; /* 48 */
+ counts[EXTRACT256(array,4)] += 1; /* 64 */
+ counts[EXTRACT256(array,5)] += 1; /* 80 */
+ counts[EXTRACT256(array,6)] += 1; /* 96 */
+ counts[EXTRACT256(array,7)] += 1; /* 112 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,20), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 1 */
+ counts[EXTRACT256(array,1)] += 1; /* 17 */
+ counts[EXTRACT256(array,2)] += 1; /* 33 */
+ counts[EXTRACT256(array,3)] += 1; /* 49 */
+ counts[EXTRACT256(array,4)] += 1; /* 65 */
+ counts[EXTRACT256(array,5)] += 1; /* 81 */
+ counts[EXTRACT256(array,6)] += 1; /* 97 */
+ counts[EXTRACT256(array,7)] += 1; /* 113 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 2 */
+ counts[EXTRACT256(array,1)] += 1; /* 18 */
+ counts[EXTRACT256(array,2)] += 1; /* 34 */
+ counts[EXTRACT256(array,3)] += 1; /* 50 */
+ counts[EXTRACT256(array,4)] += 1; /* 66 */
+ counts[EXTRACT256(array,5)] += 1; /* 82 */
+ counts[EXTRACT256(array,6)] += 1; /* 98 */
+ counts[EXTRACT256(array,7)] += 1; /* 114 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 3 */
+ counts[EXTRACT256(array,1)] += 1; /* 19 */
+ counts[EXTRACT256(array,2)] += 1; /* 35 */
+ counts[EXTRACT256(array,3)] += 1; /* 51 */
+ counts[EXTRACT256(array,4)] += 1; /* 67 */
+ counts[EXTRACT256(array,5)] += 1; /* 83 */
+ counts[EXTRACT256(array,6)] += 1; /* 99 */
+ counts[EXTRACT256(array,7)] += 1; /* 115 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 4 */
+ counts[EXTRACT256(array,1)] += 1; /* 20 */
+ counts[EXTRACT256(array,2)] += 1; /* 36 */
+ counts[EXTRACT256(array,3)] += 1; /* 52 */
+ counts[EXTRACT256(array,4)] += 1; /* 68 */
+ counts[EXTRACT256(array,5)] += 1; /* 84 */
+ counts[EXTRACT256(array,6)] += 1; /* 100 */
+ counts[EXTRACT256(array,7)] += 1; /* 116 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 5 */
+ counts[EXTRACT256(array,1)] += 1; /* 21 */
+ counts[EXTRACT256(array,2)] += 1; /* 37 */
+ counts[EXTRACT256(array,3)] += 1; /* 53 */
+ counts[EXTRACT256(array,4)] += 1; /* 69 */
+ counts[EXTRACT256(array,5)] += 1; /* 85 */
+ counts[EXTRACT256(array,6)] += 1; /* 101 */
+ counts[EXTRACT256(array,7)] += 1; /* 117 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 6 */
+ counts[EXTRACT256(array,1)] += 1; /* 22 */
+ counts[EXTRACT256(array,2)] += 1; /* 38 */
+ counts[EXTRACT256(array,3)] += 1; /* 54 */
+ counts[EXTRACT256(array,4)] += 1; /* 70 */
+ counts[EXTRACT256(array,5)] += 1; /* 86 */
+ counts[EXTRACT256(array,6)] += 1; /* 102 */
+ counts[EXTRACT256(array,7)] += 1; /* 118 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 7 */
+ counts[EXTRACT256(array,1)] += 1; /* 23 */
+ counts[EXTRACT256(array,2)] += 1; /* 39 */
+ counts[EXTRACT256(array,3)] += 1; /* 55 */
+ counts[EXTRACT256(array,4)] += 1; /* 71 */
+ counts[EXTRACT256(array,5)] += 1; /* 87 */
+ counts[EXTRACT256(array,6)] += 1; /* 103 */
+ counts[EXTRACT256(array,7)] += 1; /* 119 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 8 */
+ counts[EXTRACT256(array,1)] += 1; /* 24 */
+ counts[EXTRACT256(array,2)] += 1; /* 40 */
+ counts[EXTRACT256(array,3)] += 1; /* 56 */
+ counts[EXTRACT256(array,4)] += 1; /* 72 */
+ counts[EXTRACT256(array,5)] += 1; /* 88 */
+ counts[EXTRACT256(array,6)] += 1; /* 104 */
+ counts[EXTRACT256(array,7)] += 1; /* 120 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 9 */
+ counts[EXTRACT256(array,1)] += 1; /* 25 */
+ counts[EXTRACT256(array,2)] += 1; /* 41 */
+ counts[EXTRACT256(array,3)] += 1; /* 57 */
+ counts[EXTRACT256(array,4)] += 1; /* 73 */
+ counts[EXTRACT256(array,5)] += 1; /* 89 */
+ counts[EXTRACT256(array,6)] += 1; /* 105 */
+ counts[EXTRACT256(array,7)] += 1; /* 121 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 10 */
+ counts[EXTRACT256(array,1)] += 1; /* 26 */
+ counts[EXTRACT256(array,2)] += 1; /* 42 */
+ counts[EXTRACT256(array,3)] += 1; /* 58 */
+ counts[EXTRACT256(array,4)] += 1; /* 74 */
+ counts[EXTRACT256(array,5)] += 1; /* 90 */
+ counts[EXTRACT256(array,6)] += 1; /* 106 */
+ counts[EXTRACT256(array,7)] += 1; /* 122 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 11 */
+ counts[EXTRACT256(array,1)] += 1; /* 27 */
+ counts[EXTRACT256(array,2)] += 1; /* 43 */
+ counts[EXTRACT256(array,3)] += 1; /* 59 */
+ counts[EXTRACT256(array,4)] += 1; /* 75 */
+ counts[EXTRACT256(array,5)] += 1; /* 91 */
+ counts[EXTRACT256(array,6)] += 1; /* 107 */
+ counts[EXTRACT256(array,7)] += 1; /* 123 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(next,24), _mm256_slli_epi32(current,8));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 12 */
+ counts[EXTRACT256(array,1)] += 1; /* 28 */
+ counts[EXTRACT256(array,2)] += 1; /* 44 */
+ counts[EXTRACT256(array,3)] += 1; /* 60 */
+ counts[EXTRACT256(array,4)] += 1; /* 76 */
+ counts[EXTRACT256(array,5)] += 1; /* 92 */
+ counts[EXTRACT256(array,6)] += 1; /* 108 */
+ counts[EXTRACT256(array,7)] += 1; /* 124 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 13 */
+ counts[EXTRACT256(array,1)] += 1; /* 29 */
+ counts[EXTRACT256(array,2)] += 1; /* 45 */
+ counts[EXTRACT256(array,3)] += 1; /* 61 */
+ counts[EXTRACT256(array,4)] += 1; /* 77 */
+ counts[EXTRACT256(array,5)] += 1; /* 93 */
+ counts[EXTRACT256(array,6)] += 1; /* 109 */
+ counts[EXTRACT256(array,7)] += 1; /* 125 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 14 */
+ counts[EXTRACT256(array,1)] += 1; /* 30 */
+ counts[EXTRACT256(array,2)] += 1; /* 46 */
+ counts[EXTRACT256(array,3)] += 1; /* 62 */
+ counts[EXTRACT256(array,4)] += 1; /* 78 */
+ counts[EXTRACT256(array,5)] += 1; /* 94 */
+ counts[EXTRACT256(array,6)] += 1; /* 110 */
+ counts[EXTRACT256(array,7)] += 1; /* 126 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 15 */
+ counts[EXTRACT256(array,1)] += 1; /* 31 */
+ counts[EXTRACT256(array,2)] += 1; /* 47 */
+ counts[EXTRACT256(array,3)] += 1; /* 63 */
+ counts[EXTRACT256(array,4)] += 1; /* 79 */
+ counts[EXTRACT256(array,5)] += 1; /* 95 */
+ counts[EXTRACT256(array,6)] += 1; /* 111 */
+ counts[EXTRACT256(array,7)] += 1; /* 127 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
-
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_5mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -15489,38 +26737,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (oligo >> 2) & MASK5; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (oligo >> 4) & MASK5; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (oligo >> 6) & MASK5; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
#else
@@ -15533,38 +26773,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
#endif
@@ -15572,110 +26804,86 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rev & MASK5; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (low_rev >> 2) & MASK5; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rev >> 4) & MASK5; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rev >> 6) & MASK5; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rev >> 8) & MASK5; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rev >> 10) & MASK5; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (low_rev >> 12) & MASK5; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (low_rev >> 14) & MASK5; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (low_rev >> 16) & MASK5; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (low_rev >> 18) & MASK5; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (low_rev >> 20) & MASK5; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = low_rev >> 22; /* 16, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -15688,38 +26896,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
@@ -15732,38 +26932,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
@@ -15776,38 +26968,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -15818,38 +27002,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (oligo >> 2) & MASK5; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (oligo >> 4) & MASK5; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (oligo >> 6) & MASK5; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
#else
@@ -15862,38 +27038,30 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
#endif
@@ -15901,252 +27069,479 @@ store_5mers_fwd (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rev & MASK5; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (high_rev >> 2) & MASK5; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rev >> 4) & MASK5; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rev >> 6) & MASK5; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rev >> 8) & MASK5; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rev >> 10) & MASK5; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (high_rev >> 12) & MASK5; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (high_rev >> 14) & MASK5; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (high_rev >> 16) & MASK5; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = (high_rev >> 18) & MASK5; /* 2 */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = (high_rev >> 20) & MASK5; /* 1 */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = high_rev >> 22; /* 0, No mask necessary */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+
+#else
+ _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_5mers_fwd (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T high_rev, Genomecomp_T low_rev, Genomecomp_T nexthigh_rev) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ oligo = nexthigh_rev >> 24; /* For 31..28 */
+ oligo |= low_rev << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
- masked = (high_rev >> 18) & MASK5; /* 2 */
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
- masked = (high_rev >> 20) & MASK5; /* 1 */
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
- masked = high_rev >> 22; /* 0, No mask necessary */
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+
+ oligo = low_rev >> 24; /* For 15..12 */
+ oligo |= high_rev << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
-
-#else
- _oligo = _mm_setr_epi32(high_rev, high_rev >> 2, high_rev >> 4, high_rev >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rev),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
#ifndef USE_SIMD_FOR_COUNTS
+
static void
-count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univcoord_T left_plus_length,
+count_positions_fwd_std (Count_T *counts, Inquery_T *inquery, int indexsize, Univcoord_T left, Univcoord_T left_plus_length,
int genestrand) {
int startdiscard, enddiscard;
Genomecomp_T ptr, startptr, endptr, high_rev, low_rev, nexthigh_rev,
@@ -16154,7 +27549,7 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
debug(printf("Starting count_positions_fwd_std\n"));
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -16196,15 +27591,15 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
if (indexsize == 9) {
- count_9mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_9mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 8) {
- count_8mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_8mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 7) {
- count_7mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_7mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 6) {
- count_6mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_6mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 5) {
- count_5mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_5mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -16241,15 +27636,15 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
if (indexsize == 9) {
- count_9mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_9mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- count_8mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_8mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- count_7mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_7mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- count_6mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_6mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- count_5mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_5mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else {
abort();
}
@@ -16285,7 +27680,7 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- count_9mers_fwd(counts,high_rev,low_rev,nexthigh_rev);
+ count_9mers_fwd(counts,inquery,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 8) {
@@ -16318,7 +27713,7 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- count_8mers_fwd(counts,high_rev,low_rev,nexthigh_rev);
+ count_8mers_fwd(counts,inquery,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 7) {
@@ -16351,7 +27746,7 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- count_7mers_fwd(counts,high_rev,low_rev,nexthigh_rev);
+ count_7mers_fwd(counts,inquery,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 6) {
@@ -16384,7 +27779,7 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- count_6mers_fwd(counts,high_rev,low_rev,nexthigh_rev);
+ count_6mers_fwd(counts,inquery,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 5) {
@@ -16417,7 +27812,7 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- count_5mers_fwd(counts,high_rev,low_rev,nexthigh_rev);
+ count_5mers_fwd(counts,inquery,high_rev,low_rev,nexthigh_rev);
}
} else {
@@ -16456,15 +27851,15 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
if (indexsize == 9) {
- count_9mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_9mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- count_8mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_8mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- count_7mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_7mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- count_6mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_6mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- count_5mers_fwd_partial(counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_5mers_fwd_partial(counts,inquery,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -16479,8 +27874,9 @@ count_positions_fwd_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
#ifdef USE_SIMD_FOR_COUNTS
+
static void
-count_positions_fwd_simd (Count_T *counts, int indexsize,
+count_positions_fwd_simd (Count_T *counts, Inquery_T *inquery, int indexsize,
Univcoord_T left, Univcoord_T left_plus_length, int genestrand) {
int startdiscard, enddiscard;
Genomecomp_T ptr, startptr, endptr, nexthigh_rev, nextlow;
@@ -16497,11 +27893,16 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#else
Genomecomp_T high1_rev, low1_rev;
#endif
+#ifdef HAVE_AVX2
+ Genomecomp_T low2, high2, low3, high3;
+ __m256i current256, next256, temp256, bigmask2, bigmask4, bigreverse8;
+ __m256i shift256;
+#endif
debug(printf("Starting count_positions_fwd_simd\n"));
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -16519,6 +27920,13 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#else
mask8 = _mm_set1_epi32(0x00FF00FF);
#endif
+#ifdef HAVE_AVX2
+ bigmask2 = _mm256_set1_epi32(0x33333333);
+ bigmask4 = _mm256_set1_epi32(0x0F0F0F0F);
+ bigreverse8 = _mm256_set_epi8(0x0C,0x0D,0x0E,0x0F, 0x08,0x09,0x0A,0x0B, 0x04,0x05,0x06,0x07, 0x00,0x01,0x02,0x03,
+ 0x0C,0x0D,0x0E,0x0F, 0x08,0x09,0x0A,0x0B, 0x04,0x05,0x06,0x07, 0x00,0x01,0x02,0x03);
+ shift256 = _mm256_setr_epi32(1,2,3,4,5,6,7,0);
+#endif
if (left_plus_length <= left) {
/* Skip */
@@ -16564,15 +27972,15 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#endif
if (indexsize == 9) {
- count_9mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_9mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 8) {
- count_8mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_8mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 7) {
- count_7mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_7mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 6) {
- count_6mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_6mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 5) {
- count_5mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ count_5mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -16622,21 +28030,87 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#endif
if (indexsize == 9) {
- count_9mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_9mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- count_8mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_8mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- count_7mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_7mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- count_6mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_6mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- count_5mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ count_5mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else {
abort();
}
/* Middle blocks */
if (indexsize == 9) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes*/
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_9mers_fwd_simd_128(counts,inquery,current256,next256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -16700,9 +28174,9 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#if 0
extract_9mers_fwd_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_9mers_fwd_simd(counts,current,next);
+ count_9mers_fwd_simd(counts,inquery,current,next);
#endif
}
@@ -16747,10 +28221,76 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- count_9mers_fwd(counts,high0_rev,low0_rev,nexthigh_rev);
+ count_9mers_fwd(counts,inquery,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 8) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_8mers_fwd_simd_128(counts,inquery,current256,next256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -16814,9 +28354,9 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#if 0
extract_8mers_fwd_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_8mers_fwd_simd(counts,current,next);
+ count_8mers_fwd_simd(counts,inquery,current,next);
#endif
}
@@ -16861,10 +28401,76 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- count_8mers_fwd(counts,high0_rev,low0_rev,nexthigh_rev);
+ count_8mers_fwd(counts,inquery,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 7) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_7mers_fwd_simd_128(counts,inquery,current256,next256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -16928,9 +28534,9 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#if 0
extract_7mers_fwd_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_7mers_fwd_simd(counts,current,next);
+ count_7mers_fwd_simd(counts,inquery,current,next);
#endif
}
@@ -16967,18 +28573,84 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#endif
nexthigh_rev = high0_rev;
-#ifdef HAVE_SSE4_1
- high0_rev = (unsigned int) _mm_extract_epi32(current,0);
- low0_rev = (unsigned int) _mm_extract_epi32(current,1);
-#else
- high0_rev = (reverse_nt[low0 >> 16] | reverse_nt[low0 & 0x0000FFFF] << 16);
- low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
-#endif
+#ifdef HAVE_SSE4_1
+ high0_rev = (unsigned int) _mm_extract_epi32(current,0);
+ low0_rev = (unsigned int) _mm_extract_epi32(current,1);
+#else
+ high0_rev = (reverse_nt[low0 >> 16] | reverse_nt[low0 & 0x0000FFFF] << 16);
+ low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
+#endif
+
+ count_7mers_fwd(counts,inquery,high0_rev,low0_rev,nexthigh_rev);
+ }
+
+ } else if (indexsize == 6) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
- count_7mers_fwd(counts,high0_rev,low0_rev,nexthigh_rev);
+ count_6mers_fwd_simd_128(counts,inquery,current256,next256);
}
+#endif
- } else if (indexsize == 6) {
while (ptr > startptr + 6) {
ptr -= 6;
@@ -17042,9 +28714,9 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#if 0
extract_6mers_fwd_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_6mers_fwd_simd(counts,current,next);
+ count_6mers_fwd_simd(counts,inquery,current,next);
#endif
}
@@ -17089,10 +28761,76 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- count_6mers_fwd(counts,high0_rev,low0_rev,nexthigh_rev);
+ count_6mers_fwd(counts,inquery,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 5) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_5mers_fwd_simd_128(counts,inquery,current256,next256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -17155,9 +28893,9 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#if 0
extract_5mers_fwd_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_5mers_fwd_simd(counts,current,next);
+ count_5mers_fwd_simd(counts,inquery,current,next);
#endif
}
@@ -17202,7 +28940,7 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- count_5mers_fwd(counts,high0_rev,low0_rev,nexthigh_rev);
+ count_5mers_fwd(counts,inquery,high0_rev,low0_rev,nexthigh_rev);
}
} else {
@@ -17253,15 +28991,15 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
#endif
if (indexsize == 9) {
- count_9mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_9mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- count_8mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_8mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- count_7mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_7mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- count_6mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_6mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- count_5mers_fwd_partial(counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ count_5mers_fwd_partial(counts,inquery,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -17270,12 +29008,13 @@ count_positions_fwd_simd (Count_T *counts, int indexsize,
return;
}
+
#endif
#ifndef USE_SIMD_FOR_COUNTS
static void
-store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts, int indexsize,
+store_positions_fwd_std (Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts, int indexsize,
Univcoord_T left, Univcoord_T left_plus_length, Chrpos_T chrpos,
int genestrand) {
int startdiscard, enddiscard;
@@ -17283,7 +29022,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
low, high, nextlow;
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -17326,15 +29065,15 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
if (indexsize == 9) {
- chrpos = store_9mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_9mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_8mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_7mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_6mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_5mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -17371,15 +29110,15 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
if (indexsize == 9) {
- chrpos = store_9mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_9mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_8mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_7mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_6mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_5mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else {
abort();
}
@@ -17414,7 +29153,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- chrpos = store_9mers_fwd(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
+ chrpos = store_9mers_fwd(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 8) {
@@ -17447,7 +29186,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- chrpos = store_8mers_fwd(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
+ chrpos = store_8mers_fwd(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 7) {
@@ -17480,7 +29219,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- chrpos = store_7mers_fwd(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
+ chrpos = store_7mers_fwd(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 6) {
@@ -17513,7 +29252,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- chrpos = store_6mers_fwd(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
+ chrpos = store_6mers_fwd(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
}
} else if (indexsize == 5) {
@@ -17546,7 +29285,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev = reverse_nt[nextlow >> 16];
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
- chrpos = store_5mers_fwd(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
+ chrpos = store_5mers_fwd(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev);
}
} else {
abort();
@@ -17584,15 +29323,15 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nexthigh_rev |= (reverse_nt[nextlow & 0x0000FFFF] << 16);
if (indexsize == 9) {
- chrpos = store_9mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_9mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- chrpos = store_8mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_8mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- chrpos = store_7mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_7mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- chrpos = store_6mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_6mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- chrpos = store_5mers_fwd_partial(chrpos,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_5mers_fwd_partial(chrpos,table,pointers,positions,counts,high_rev,low_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -17607,7 +29346,7 @@ store_positions_fwd_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
#ifdef USE_SIMD_FOR_COUNTS
static void
-store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts, int indexsize,
+store_positions_fwd_simd (Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts, int indexsize,
Univcoord_T left, Univcoord_T left_plus_length, Chrpos_T chrpos,
int genestrand) {
int startdiscard, enddiscard;
@@ -17625,11 +29364,17 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#else
Genomecomp_T high1_rev, low1_rev;
#endif
+#ifdef HAVE_AVX2
+ __m256i array256[16];
+ Genomecomp_T low2, high2, low3, high3;
+ __m256i current256, next256, temp256, bigmask2, bigmask4, bigreverse8;
+ __m256i shift256;
+#endif
debug(printf("Starting store_positions_fwd_simd\n"));
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -17648,6 +29393,13 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#else
mask8 = _mm_set1_epi32(0x00FF00FF);
#endif
+#ifdef HAVE_AVX2
+ bigmask2 = _mm256_set1_epi32(0x33333333);
+ bigmask4 = _mm256_set1_epi32(0x0F0F0F0F);
+ bigreverse8 = _mm256_set_epi8(0x0C,0x0D,0x0E,0x0F, 0x08,0x09,0x0A,0x0B, 0x04,0x05,0x06,0x07, 0x00,0x01,0x02,0x03,
+ 0x0C,0x0D,0x0E,0x0F, 0x08,0x09,0x0A,0x0B, 0x04,0x05,0x06,0x07, 0x00,0x01,0x02,0x03);
+ shift256 = _mm256_setr_epi32(1,2,3,4,5,6,7,0);
+#endif
if (left_plus_length <= left) {
/* Skip */
@@ -17693,15 +29445,15 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
if (indexsize == 9) {
- chrpos = store_9mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_9mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_8mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_7mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_6mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
+ chrpos = store_5mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -17751,21 +29503,88 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
if (indexsize == 9) {
- chrpos = store_9mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_9mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_8mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_7mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_6mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
+ chrpos = store_5mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,/*startdiscard*/0,enddiscard);
} else {
abort();
}
/* Middle blocks */
if (indexsize == 9) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_9mers_fwd_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -17827,7 +29646,7 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_9mers_fwd_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
}
if (ptr > startptr + 3) {
@@ -17871,10 +29690,77 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- chrpos = store_9mers_fwd(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
+ chrpos = store_9mers_fwd(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 8) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_8mers_fwd_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -17936,7 +29822,7 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_8mers_fwd_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
}
if (ptr > startptr + 3) {
@@ -17980,10 +29866,77 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- chrpos = store_8mers_fwd(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
+ chrpos = store_8mers_fwd(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 7) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_7mers_fwd_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -18045,7 +29998,7 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_7mers_fwd_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
}
if (ptr > startptr + 3) {
@@ -18089,10 +30042,77 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- chrpos = store_7mers_fwd(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
+ chrpos = store_7mers_fwd(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 6) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_6mers_fwd_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -18154,7 +30174,7 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_6mers_fwd_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
}
if (ptr > startptr + 3) {
@@ -18198,10 +30218,77 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- chrpos = store_6mers_fwd(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
+ chrpos = store_6mers_fwd(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
}
} else if (indexsize == 5) {
+#ifdef HAVE_AVX2
+ while (ptr > startptr + 12) {
+ ptr -= 12;
+
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ low0 = Bigendian_convert_uint(ref_blocks[ptr+1]);
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ /* nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]); */
+#else
+ high0 = ref_blocks[ptr];
+ low0 = ref_blocks[ptr+1];
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ /* nextlow = ref_blocks[ptr+13]; */
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); low0 = Cmet_reduce_ct(low0);
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ /* nextlow = Cmet_reduce_ct(nextlow); */
+ } else {
+ high0 = Cmet_reduce_ga(high0); low0 = Cmet_reduce_ga(low0);
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ /* nextlow = Cmet_reduce_ga(nextlow); */
+ }
+ }
+
+ current256 = _mm256_set_epi32(high3,low3,high2,low2,high1,low1,high0,low0);
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,2),bigmask2),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask2),2)); /* Swap pairs */
+ current256 = _mm256_or_si256(_mm256_and_si256(_mm256_srli_epi32(current256,4),bigmask4),_mm256_slli_epi32(_mm256_and_si256(current256,bigmask4),4)); /* Swap nibbles */
+ current256 = _mm256_shuffle_epi8(current256,bigreverse8); /* Reverse bytes within 128-bit lanes */
+
+ nexthigh_rev = high0_rev;
+
+ high0_rev = (unsigned int) _mm256_extract_epi32(current256,0);
+ /* low0_rev = (unsigned int) _mm_extract_epi32(current,1); */
+ /* high1_rev = (unsigned int) _mm_extract_epi32(current,2); */
+ /* low1_rev = (unsigned int) _mm_extract_epi32(current,3); */
+
+ temp256 = _mm256_insert_epi32(current256,nexthigh_rev,0x00);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_5mers_fwd_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ }
+#endif
+
while (ptr > startptr + 6) {
ptr -= 6;
@@ -18263,7 +30350,7 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_5mers_fwd_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
}
if (ptr > startptr + 3) {
@@ -18307,7 +30394,7 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
low0_rev = (reverse_nt[high0 >> 16] | reverse_nt[high0 & 0x0000FFFF] << 16);
#endif
- chrpos = store_5mers_fwd(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
+ chrpos = store_5mers_fwd(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev);
}
} else {
@@ -18358,15 +30445,15 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
if (indexsize == 9) {
- chrpos = store_9mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_9mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- chrpos = store_8mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_8mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- chrpos = store_7mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_7mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- chrpos = store_6mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_6mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- chrpos = store_5mers_fwd_partial(chrpos,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
+ chrpos = store_5mers_fwd_partial(chrpos,table,pointers,positions,counts,high0_rev,low0_rev,nexthigh_rev,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -18383,8 +30470,8 @@ store_positions_fwd_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
************************************************************************/
static void
-count_9mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
- int startdiscard, int enddiscard) {
+count_9mers_rev_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc,
+ Genomecomp_T nextlow_rc, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
@@ -18393,8 +30480,8 @@ count_9mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
while (pos <= enddiscard && pos <= 7) {
masked = low_rc >> 2*pos;
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18402,16 +30489,16 @@ count_9mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = low_rc >> 2*pos;
masked |= high_rc << (32 - 2*pos);
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
while (pos <= enddiscard && pos <= 23) {
masked = high_rc >> (2*pos - 32);
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18419,8 +30506,8 @@ count_9mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = high_rc >> (2*pos - 32);
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK9;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18428,7 +30515,7 @@ count_9mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
}
static int
-store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
@@ -18440,11 +30527,9 @@ store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = low_rc >> 2*pos;
masked &= MASK9;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18455,11 +30540,9 @@ store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= high_rc << (32 - 2*pos);
masked &= MASK9;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18469,11 +30552,9 @@ store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = high_rc >> (2*pos - 32);
masked &= MASK9;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18484,11 +30565,9 @@ store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK9;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18499,8 +30578,8 @@ store_9mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
static void
-count_8mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
- int startdiscard, int enddiscard) {
+count_8mers_rev_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc,
+ Genomecomp_T nextlow_rc, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
@@ -18509,8 +30588,8 @@ count_8mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
while (pos <= enddiscard && pos <= 8) {
masked = low_rc >> 2*pos;
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18518,16 +30597,16 @@ count_8mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = low_rc >> 2*pos;
masked |= high_rc << (32 - 2*pos);
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
while (pos <= enddiscard && pos <= 24) {
masked = high_rc >> (2*pos - 32);
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18535,17 +30614,16 @@ count_8mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = high_rc >> (2*pos - 32);
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK8;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
return;
}
-
static int
-store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
@@ -18557,11 +30635,9 @@ store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = low_rc >> 2*pos;
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18572,11 +30648,9 @@ store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= high_rc << (32 - 2*pos);
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18586,11 +30660,9 @@ store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = high_rc >> (2*pos - 32);
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18601,11 +30673,9 @@ store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK8;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18614,10 +30684,9 @@ store_8mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
return chrpos;
}
-
static void
-count_7mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
- int startdiscard, int enddiscard) {
+count_7mers_rev_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc,
+ Genomecomp_T nextlow_rc, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
@@ -18626,8 +30695,8 @@ count_7mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
while (pos <= enddiscard && pos <= 9) {
masked = low_rc >> 2*pos;
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18635,16 +30704,16 @@ count_7mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = low_rc >> 2*pos;
masked |= high_rc << (32 - 2*pos);
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
while (pos <= enddiscard && pos <= 25) {
masked = high_rc >> (2*pos - 32);
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18652,17 +30721,16 @@ count_7mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = high_rc >> (2*pos - 32);
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK7;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
return;
}
-
static int
-store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
@@ -18674,11 +30742,9 @@ store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = low_rc >> 2*pos;
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18689,11 +30755,9 @@ store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= high_rc << (32 - 2*pos);
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18703,11 +30767,9 @@ store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = high_rc >> (2*pos - 32);
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18718,11 +30780,9 @@ store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK7;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18733,8 +30793,8 @@ store_7mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
static void
-count_6mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
- int startdiscard, int enddiscard) {
+count_6mers_rev_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc,
+ Genomecomp_T nextlow_rc, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
@@ -18743,8 +30803,8 @@ count_6mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
while (pos <= enddiscard && pos <= 10) {
masked = low_rc >> 2*pos;
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18752,16 +30812,16 @@ count_6mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = low_rc >> 2*pos;
masked |= high_rc << (32 - 2*pos);
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
while (pos <= enddiscard && pos <= 26) {
masked = high_rc >> (2*pos - 32);
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18769,17 +30829,16 @@ count_6mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = high_rc >> (2*pos - 32);
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK6;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
return;
}
-
static int
-store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
@@ -18791,11 +30850,9 @@ store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = low_rc >> 2*pos;
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18806,11 +30863,9 @@ store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= high_rc << (32 - 2*pos);
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18820,11 +30875,9 @@ store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = high_rc >> (2*pos - 32);
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18835,11 +30888,9 @@ store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK6;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18848,10 +30899,9 @@ store_6mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
return chrpos;
}
-
static void
-count_5mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
- int startdiscard, int enddiscard) {
+count_5mers_rev_partial (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc,
+ Genomecomp_T nextlow_rc, int startdiscard, int enddiscard) {
Genomecomp_T masked;
int pos;
@@ -18860,8 +30910,8 @@ count_5mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
while (pos <= enddiscard && pos <= 11) {
masked = low_rc >> 2*pos;
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18869,16 +30919,16 @@ count_5mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = low_rc >> 2*pos;
masked |= high_rc << (32 - 2*pos);
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
while (pos <= enddiscard && pos <= 27) {
masked = high_rc >> (2*pos - 32);
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
@@ -18886,17 +30936,16 @@ count_5mers_rev_partial (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high
masked = high_rc >> (2*pos - 32);
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK5;
- counts[masked] += 1;
- debug(printf("%d %04X => %d\n",pos,masked,counts[masked]));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("%d partial %04X => %d\n",pos,masked,counts[masked]));
pos++;
}
return;
}
-
static int
-store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc,
int startdiscard, int enddiscard) {
Genomecomp_T masked;
@@ -18908,11 +30957,9 @@ store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = low_rc >> 2*pos;
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18923,11 +30970,9 @@ store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= high_rc << (32 - 2*pos);
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18937,11 +30982,9 @@ store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked = high_rc >> (2*pos - 32);
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18952,11 +30995,9 @@ store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
masked |= nextlow_rc << (64 - 2*pos);
masked &= MASK5;
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u (partial)\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
chrpos--;
pos++;
@@ -18966,8 +31007,11 @@ store_5mers_rev_partial (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positi
}
+
+#if !defined(HAVE_AVX2)
+
static void
-count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+count_9mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -18980,35 +31024,35 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK9; /* 0 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 2) & MASK9; /* 1 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 4) & MASK9; /* 2 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 6) & MASK9; /* 3 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 8) & MASK9; /* 4 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 10) & MASK9; /* 5 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 12) & MASK9; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = low_rc >> 14; /* 7, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
#else
@@ -19020,19 +31064,19 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
@@ -19044,19 +31088,19 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
#endif
@@ -19066,35 +31110,35 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK9; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK9; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK9; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK9; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK9; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK9; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 12) & MASK9; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 14) & MASK9; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#else
@@ -19106,19 +31150,19 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
@@ -19130,54 +31174,54 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK9; /* 16 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 2) & MASK9; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 4) & MASK9; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 6) & MASK9; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 8) & MASK9; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 10) & MASK9; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 12) & MASK9; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = high_rc >> 14; /* 23, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
#else
@@ -19189,19 +31233,19 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
@@ -19213,111 +31257,410 @@ count_9mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
- debug(printf("21 %04X => %d\n",masked,counts[masked]));
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+#endif
+
+
+ oligo = high_rc >> 16; /* For 31..24 */
+ oligo |= nextlow_rc << 16;
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = oligo & MASK9; /* 24 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 2) & MASK9; /* 25 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 4) & MASK9; /* 26 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 6) & MASK9; /* 27 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 8) & MASK9; /* 28 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 10) & MASK9; /* 29 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 12) & MASK9; /* 30 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 14) & MASK9; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_9mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ oligo = low_rc >> 16; /* For 15..8 */
+ oligo |= high_rc << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
- debug(printf("22 %04X => %d\n",masked,counts[masked]));
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
- debug(printf("23 %04X => %d\n",masked,counts[masked]));
-#endif
-
-
- oligo = high_rc >> 16; /* For 31..24 */
- oligo |= nextlow_rc << 16;
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
-#ifdef INDIVIDUAL_SHIFTS
- masked = oligo & MASK9; /* 24 */
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
- debug(printf("24 %04X => %d\n",masked,counts[masked]));
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 2) & MASK9; /* 25 */
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("25 %04X => %d\n",masked,counts[masked]));
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 4) & MASK9; /* 26 */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("26 %04X => %d\n",masked,counts[masked]));
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 6) & MASK9; /* 27 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
- debug(printf("27 %04X => %d\n",masked,counts[masked]));
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 8) & MASK9; /* 28 */
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 10) & MASK9; /* 29 */
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 12) & MASK9; /* 30 */
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 14) & MASK9; /* 31 */
- counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
-#else
- _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
- masked = EXTRACT(_masked,0);
+ oligo = high_rc >> 16; /* For 31..24 */
+ oligo |= nextlow_rc << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("24 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("25 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("26 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("27 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("28 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("29 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("30 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("31 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
+
+
/* Expecting current to have {low0_rc, high0_rc, low1_rc, high1_rc},
and next to have {high0_rc, low1_rc, high1_rc, nextlow_rc} */
#ifdef USE_SIMD_FOR_COUNTS
@@ -19347,116 +31690,1578 @@ extract_9mers_rev_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_9mers_rev_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,16), _mm256_slli_epi32(next,16));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,14), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask9));
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,14)); /* No mask necessary */;
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask9));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask9));
+
+ return;
+}
+#endif
+
+
static void
-count_9mers_rev_simd (Count_T *counts, __m128i current, __m128i next) {
+count_9mers_rev_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
oligo = _mm_or_si128( _mm_srli_epi32(current,16), _mm_slli_epi32(next,16));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,14), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,14), mask9));
- counts[array[0]] += 1; /* 63 */
- counts[array[1]] += 1; /* 47 */
- counts[array[2]] += 1; /* 31 */
- counts[array[3]] += 1; /* 15 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("47 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("31 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("15 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 63 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 15 */
+#endif
+ debug(printf("63 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,12), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,12), mask9));
- counts[array[0]] += 1; /* 62 */
- counts[array[1]] += 1; /* 46 */
- counts[array[2]] += 1; /* 30 */
- counts[array[3]] += 1; /* 14 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("46 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("30 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("14 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 62 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 14 */
+#endif
+ debug(printf("62 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,10), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask9));
- counts[array[0]] += 1; /* 61 */
- counts[array[1]] += 1; /* 45 */
- counts[array[2]] += 1; /* 29 */
- counts[array[3]] += 1; /* 13 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("45 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("29 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("13 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 61 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 13 */
+#endif
+ debug(printf("61 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask9));
- counts[array[0]] += 1; /* 60 */
- counts[array[1]] += 1; /* 44 */
- counts[array[2]] += 1; /* 28 */
- counts[array[3]] += 1; /* 12 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("44 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("28 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("12 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 60 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 12 */
+#endif
+ debug(printf("60 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask9));
- counts[array[0]] += 1; /* 59 */
- counts[array[1]] += 1; /* 43 */
- counts[array[2]] += 1; /* 27 */
- counts[array[3]] += 1; /* 11 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("43 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("27 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("11 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 59 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 11 */
+#endif
+ debug(printf("59 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask9));
- counts[array[0]] += 1; /* 58 */
- counts[array[1]] += 1; /* 42 */
- counts[array[2]] += 1; /* 26 */
- counts[array[3]] += 1; /* 10 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("42 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("26 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("10 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 58 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 10 */
+#endif
+ debug(printf("58 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask9));
- counts[array[0]] += 1; /* 57 */
- counts[array[1]] += 1; /* 41 */
- counts[array[2]] += 1; /* 25 */
- counts[array[3]] += 1; /* 9 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("41 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("25 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("9 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 57 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 9 */
+#endif
+ debug(printf("57 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask9);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask9));
- counts[array[0]] += 1; /* 56 */
- counts[array[1]] += 1; /* 50 */
- counts[array[2]] += 1; /* 24 */
- counts[array[3]] += 1; /* 8 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("40 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("24 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("8 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 56 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 8 */
+#endif
+ debug(printf("56 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,14); /* No mask necessary */;
+#else
+ _mm_store_si128((__m128i *) array, _mm_srli_epi32(current,14)); /* No mask necessary */;
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("39 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("23 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("7 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 55 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 7 */
+#endif
+ debug(printf("55 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("38 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("22 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("6 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 54 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 6 */
+#endif
+ debug(printf("54 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("37 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("21 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("5 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 53 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 5 */
+#endif
+ debug(printf("53 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("36 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("20 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("4 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 52 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 4 */
+#endif
+ debug(printf("52 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("35 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("19 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("3 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 51 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 3 */
+#endif
+ debug(printf("51 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("34 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("18 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("2 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_srli_epi32(current,14)); /* No mask necessary */;
- counts[array[0]] += 1; /* 55 */
- counts[array[1]] += 1; /* 39 */
- counts[array[2]] += 1; /* 23 */
- counts[array[3]] += 1; /* 7 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 50 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 2 */
+#endif
+ debug(printf("50 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask9));
- counts[array[0]] += 1; /* 54 */
- counts[array[1]] += 1; /* 38 */
- counts[array[2]] += 1; /* 22 */
- counts[array[3]] += 1; /* 6 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("33 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("17 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("1 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask9));
- counts[array[0]] += 1; /* 53 */
- counts[array[1]] += 1; /* 37 */
- counts[array[2]] += 1; /* 21 */
- counts[array[3]] += 1; /* 5 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 49 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 1 */
+#endif
+ debug(printf("49 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask9));
- counts[array[0]] += 1; /* 52 */
- counts[array[1]] += 1; /* 36 */
- counts[array[2]] += 1; /* 20 */
- counts[array[3]] += 1; /* 4 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask9);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask9));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("32 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("16 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("0 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask9));
- counts[array[0]] += 1; /* 51 */
- counts[array[1]] += 1; /* 35 */
- counts[array[2]] += 1; /* 19 */
- counts[array[3]] += 1; /* 3 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 48 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 0 */
+#endif
+ debug(printf("48 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask9));
- counts[array[0]] += 1; /* 50 */
- counts[array[1]] += 1; /* 34 */
- counts[array[2]] += 1; /* 18 */
- counts[array[3]] += 1; /* 2 */
+ return;
+}
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask9));
- counts[array[0]] += 1; /* 49 */
- counts[array[1]] += 1; /* 33 */
- counts[array[2]] += 1; /* 17 */
- counts[array[3]] += 1; /* 1 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask9));
- counts[array[0]] += 1; /* 48 */
- counts[array[1]] += 1; /* 32 */
- counts[array[2]] += 1; /* 16 */
- counts[array[3]] += 1; /* 0 */
+#ifdef HAVE_AVX2
+static void
+count_9mers_rev_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,16), _mm256_slli_epi32(next,16));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,14), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 127 */
+ counts[EXTRACT256(array,1)] += 1; /* 111 */
+ counts[EXTRACT256(array,2)] += 1; /* 95 */
+ counts[EXTRACT256(array,3)] += 1; /* 79 */
+ counts[EXTRACT256(array,4)] += 1; /* 63 */
+ counts[EXTRACT256(array,5)] += 1; /* 47 */
+ counts[EXTRACT256(array,6)] += 1; /* 31 */
+ counts[EXTRACT256(array,7)] += 1; /* 15 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 126 */
+ counts[EXTRACT256(array,1)] += 1; /* 110 */
+ counts[EXTRACT256(array,2)] += 1; /* 94 */
+ counts[EXTRACT256(array,3)] += 1; /* 78 */
+ counts[EXTRACT256(array,4)] += 1; /* 62 */
+ counts[EXTRACT256(array,5)] += 1; /* 46 */
+ counts[EXTRACT256(array,6)] += 1; /* 30 */
+ counts[EXTRACT256(array,7)] += 1; /* 14 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 125 */
+ counts[EXTRACT256(array,1)] += 1; /* 109 */
+ counts[EXTRACT256(array,2)] += 1; /* 93 */
+ counts[EXTRACT256(array,3)] += 1; /* 77 */
+ counts[EXTRACT256(array,4)] += 1; /* 61 */
+ counts[EXTRACT256(array,5)] += 1; /* 45 */
+ counts[EXTRACT256(array,6)] += 1; /* 29 */
+ counts[EXTRACT256(array,7)] += 1; /* 13 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 124 */
+ counts[EXTRACT256(array,1)] += 1; /* 108 */
+ counts[EXTRACT256(array,2)] += 1; /* 92 */
+ counts[EXTRACT256(array,3)] += 1; /* 76 */
+ counts[EXTRACT256(array,4)] += 1; /* 60 */
+ counts[EXTRACT256(array,5)] += 1; /* 44 */
+ counts[EXTRACT256(array,6)] += 1; /* 28 */
+ counts[EXTRACT256(array,7)] += 1; /* 12 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 123 */
+ counts[EXTRACT256(array,1)] += 1; /* 107 */
+ counts[EXTRACT256(array,2)] += 1; /* 91 */
+ counts[EXTRACT256(array,3)] += 1; /* 75 */
+ counts[EXTRACT256(array,4)] += 1; /* 59 */
+ counts[EXTRACT256(array,5)] += 1; /* 43 */
+ counts[EXTRACT256(array,6)] += 1; /* 27 */
+ counts[EXTRACT256(array,7)] += 1; /* 11 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 122 */
+ counts[EXTRACT256(array,1)] += 1; /* 106 */
+ counts[EXTRACT256(array,2)] += 1; /* 90 */
+ counts[EXTRACT256(array,3)] += 1; /* 74 */
+ counts[EXTRACT256(array,4)] += 1; /* 58 */
+ counts[EXTRACT256(array,5)] += 1; /* 42 */
+ counts[EXTRACT256(array,6)] += 1; /* 26 */
+ counts[EXTRACT256(array,7)] += 1; /* 10 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 121 */
+ counts[EXTRACT256(array,1)] += 1; /* 105 */
+ counts[EXTRACT256(array,2)] += 1; /* 89 */
+ counts[EXTRACT256(array,3)] += 1; /* 73 */
+ counts[EXTRACT256(array,4)] += 1; /* 57 */
+ counts[EXTRACT256(array,5)] += 1; /* 41 */
+ counts[EXTRACT256(array,6)] += 1; /* 25 */
+ counts[EXTRACT256(array,7)] += 1; /* 9 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 120 */
+ counts[EXTRACT256(array,1)] += 1; /* 104 */
+ counts[EXTRACT256(array,2)] += 1; /* 88 */
+ counts[EXTRACT256(array,3)] += 1; /* 72 */
+ counts[EXTRACT256(array,4)] += 1; /* 56 */
+ counts[EXTRACT256(array,5)] += 1; /* 40 */
+ counts[EXTRACT256(array,6)] += 1; /* 24 */
+ counts[EXTRACT256(array,7)] += 1; /* 8 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_srli_epi32(current,14); /* No mask necessary */;
+ counts[EXTRACT256(array,0)] += 1; /* 119 */
+ counts[EXTRACT256(array,1)] += 1; /* 103 */
+ counts[EXTRACT256(array,2)] += 1; /* 87 */
+ counts[EXTRACT256(array,3)] += 1; /* 71 */
+ counts[EXTRACT256(array,4)] += 1; /* 55 */
+ counts[EXTRACT256(array,5)] += 1; /* 39 */
+ counts[EXTRACT256(array,6)] += 1; /* 23 */
+ counts[EXTRACT256(array,7)] += 1; /* 7 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 118 */
+ counts[EXTRACT256(array,1)] += 1; /* 102 */
+ counts[EXTRACT256(array,2)] += 1; /* 86 */
+ counts[EXTRACT256(array,3)] += 1; /* 70 */
+ counts[EXTRACT256(array,4)] += 1; /* 54 */
+ counts[EXTRACT256(array,5)] += 1; /* 38 */
+ counts[EXTRACT256(array,6)] += 1; /* 22 */
+ counts[EXTRACT256(array,7)] += 1; /* 6 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 117 */
+ counts[EXTRACT256(array,1)] += 1; /* 101 */
+ counts[EXTRACT256(array,2)] += 1; /* 85 */
+ counts[EXTRACT256(array,3)] += 1; /* 69 */
+ counts[EXTRACT256(array,4)] += 1; /* 53 */
+ counts[EXTRACT256(array,5)] += 1; /* 37 */
+ counts[EXTRACT256(array,6)] += 1; /* 21 */
+ counts[EXTRACT256(array,7)] += 1; /* 5 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 116 */
+ counts[EXTRACT256(array,1)] += 1; /* 100 */
+ counts[EXTRACT256(array,2)] += 1; /* 84 */
+ counts[EXTRACT256(array,3)] += 1; /* 68 */
+ counts[EXTRACT256(array,4)] += 1; /* 52 */
+ counts[EXTRACT256(array,5)] += 1; /* 36 */
+ counts[EXTRACT256(array,6)] += 1; /* 20 */
+ counts[EXTRACT256(array,7)] += 1; /* 4 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 115 */
+ counts[EXTRACT256(array,1)] += 1; /* 99 */
+ counts[EXTRACT256(array,2)] += 1; /* 83 */
+ counts[EXTRACT256(array,3)] += 1; /* 67 */
+ counts[EXTRACT256(array,4)] += 1; /* 51 */
+ counts[EXTRACT256(array,5)] += 1; /* 35 */
+ counts[EXTRACT256(array,6)] += 1; /* 19 */
+ counts[EXTRACT256(array,7)] += 1; /* 3 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 114 */
+ counts[EXTRACT256(array,1)] += 1; /* 98 */
+ counts[EXTRACT256(array,2)] += 1; /* 82 */
+ counts[EXTRACT256(array,3)] += 1; /* 66 */
+ counts[EXTRACT256(array,4)] += 1; /* 50 */
+ counts[EXTRACT256(array,5)] += 1; /* 34 */
+ counts[EXTRACT256(array,6)] += 1; /* 18 */
+ counts[EXTRACT256(array,7)] += 1; /* 2 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 113 */
+ counts[EXTRACT256(array,1)] += 1; /* 97 */
+ counts[EXTRACT256(array,2)] += 1; /* 81 */
+ counts[EXTRACT256(array,3)] += 1; /* 65 */
+ counts[EXTRACT256(array,4)] += 1; /* 49 */
+ counts[EXTRACT256(array,5)] += 1; /* 33 */
+ counts[EXTRACT256(array,6)] += 1; /* 17 */
+ counts[EXTRACT256(array,7)] += 1; /* 1 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask9);
+ counts[EXTRACT256(array,0)] += 1; /* 112 */
+ counts[EXTRACT256(array,1)] += 1; /* 96 */
+ counts[EXTRACT256(array,2)] += 1; /* 80 */
+ counts[EXTRACT256(array,3)] += 1; /* 64 */
+ counts[EXTRACT256(array,4)] += 1; /* 48 */
+ counts[EXTRACT256(array,5)] += 1; /* 32 */
+ counts[EXTRACT256(array,6)] += 1; /* 16 */
+ counts[EXTRACT256(array,7)] += 1; /* 0 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_9mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -19471,74 +33276,58 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK9; /* 0 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (low_rc >> 2) & MASK9; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (low_rc >> 4) & MASK9; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (low_rc >> 6) & MASK9; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (low_rc >> 8) & MASK9; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (low_rc >> 10) & MASK9; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rc >> 12) & MASK9; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = low_rc >> 14; /* 7, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
#else
@@ -19551,38 +33340,30 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -19595,38 +33376,30 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
#endif
@@ -19637,74 +33410,58 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK9; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (oligo >> 2) & MASK9; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (oligo >> 4) & MASK9; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (oligo >> 6) & MASK9; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (oligo >> 8) & MASK9; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (oligo >> 10) & MASK9; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (oligo >> 12) & MASK9; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = (oligo >> 14) & MASK9; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -19717,38 +33474,30 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
@@ -19761,38 +33510,30 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -19800,74 +33541,58 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK9; /* 16 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (high_rc >> 2) & MASK9; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (high_rc >> 4) & MASK9; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (high_rc >> 6) & MASK9; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (high_rc >> 8) & MASK9; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (high_rc >> 10) & MASK9; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rc >> 12) & MASK9; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = high_rc >> 14; /* 23, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
#else
@@ -19880,38 +33605,30 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -19924,38 +33641,30 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
#endif
@@ -19966,74 +33675,58 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK9; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (oligo >> 2) & MASK9; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (oligo >> 4) & MASK9; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (oligo >> 6) & MASK9; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (oligo >> 8) & MASK9; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (oligo >> 10) & MASK9; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (oligo >> 12) & MASK9; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = (oligo >> 14) & MASK9; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -20044,93 +33737,344 @@ store_9mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
_masked = _mm_and_si128(_oligo, mask9);
#endif
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
+#else
+ _masked = _mm_and_si128(_oligo, mask9);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_9mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+
+ oligo = low_rc >> 16; /* For 15..8 */
+ oligo |= high_rc << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+
+ oligo = high_rc >> 16; /* For 31..24 */
+ oligo |= nextlow_rc << 16;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask9);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask9));
-#else
- _masked = _mm_and_si128(_oligo, mask9);
-#endif
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
+
+#if !defined(HAVE_AVX2)
+
static void
-count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+count_8mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -20143,39 +34087,39 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK8; /* 0 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 2) & MASK8; /* 1 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 4) & MASK8; /* 2 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 6) & MASK8; /* 3 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 8) & MASK8; /* 4 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 10) & MASK8; /* 5 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 12) & MASK8; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 14) & MASK8; /* 7 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = low_rc >> 16; /* 8, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
#else
@@ -20188,22 +34132,22 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
masked = EXTRACT(_masked,0);
assert(masked == (low_rc & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
assert(masked == ((low_rc >> 2) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
assert(masked == ((low_rc >> 4) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
assert(masked == ((low_rc >> 6) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
@@ -20216,27 +34160,27 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
masked = EXTRACT(_masked,0);
assert(masked == ((low_rc >> 8) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
assert(masked == ((low_rc >> 10) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
assert(masked == ((low_rc >> 12) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
assert(masked == ((low_rc >> 14) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = low_rc >> 16; /* 8, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
#endif
@@ -20246,31 +34190,31 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK8; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK8; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK8; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK8; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK8; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 12) & MASK8; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#else
@@ -20283,22 +34227,22 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
masked = EXTRACT(_masked,0);
assert(masked == (oligo & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
assert(masked == ((oligo >> 2) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
assert(masked == ((oligo >> 4) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
assert(masked == ((oligo >> 6) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
@@ -20311,56 +34255,56 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
masked = EXTRACT(_masked,0);
assert(masked == ((oligo >> 8) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
assert(masked == ((oligo >> 10) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
assert(masked == ((oligo >> 12) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK8; /* 16 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 2) & MASK8; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 4) & MASK8; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 6) & MASK8; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 8) & MASK8; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 10) & MASK8; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 12) & MASK8; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 14) & MASK8; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = high_rc >> 16; /* 24, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
#else
@@ -20373,22 +34317,22 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
masked = EXTRACT(_masked,0);
assert(masked == (high_rc & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
assert(masked == ((high_rc >> 2) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
assert(masked == ((high_rc >> 4) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
assert(masked == ((high_rc >> 6) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
@@ -20401,27 +34345,27 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
masked = EXTRACT(_masked,0);
assert(masked == ((high_rc >> 8) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
assert(masked == ((high_rc >> 10) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
assert(masked == ((high_rc >> 12) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
assert(masked == ((high_rc >> 14) & MASK8));
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = high_rc >> 16; /* 24, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
#endif
@@ -20431,88 +34375,380 @@ count_8mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 2) & MASK8; /* 26 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 4) & MASK8; /* 27 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 6) & MASK8; /* 28 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 8) & MASK8; /* 29 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 10) & MASK8; /* 30 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 12) & MASK8; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
+#else
+ _masked = _mm_and_si128(_oligo, mask8);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ assert(masked == (oligo & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 2) & MASK8; /* 26 */
+ masked = EXTRACT(_masked,1);
+ assert(masked == ((oligo >> 2) & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ assert(masked == ((oligo >> 4) & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ assert(masked == ((oligo >> 6) & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
+#else
+ _masked = _mm_and_si128(_oligo, mask8);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ assert(masked == ((oligo >> 8) & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ assert(masked == ((oligo >> 10) & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ assert(masked == ((oligo >> 12) & MASK8));
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_8mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+ masked = low_rc >> 16; /* 8, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+
+ oligo = low_rc >> 18; /* For 15..9 */
+ oligo |= high_rc << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low7);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
- debug(printf("26 %04X => %d\n",masked,counts[masked]));
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 4) & MASK8; /* 27 */
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
- debug(printf("27 %04X => %d\n",masked,counts[masked]));
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 6) & MASK8; /* 28 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 8) & MASK8; /* 29 */
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 10) & MASK8; /* 30 */
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
- masked = (oligo >> 12) & MASK8; /* 31 */
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
-#else
- _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
-#else
- _masked = _mm_and_si128(_oligo, mask8);
-#endif
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
- masked = EXTRACT(_masked,0);
- assert(masked == (oligo & MASK8));
+ masked = high_rc >> 16; /* 24, No mask necessary */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+
+ oligo = high_rc >> 18; /* For 31..25 */
+ oligo |= nextlow_rc << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("25 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- assert(masked == ((oligo >> 2) & MASK8));
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("26 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
- assert(masked == ((oligo >> 4) & MASK8));
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("27 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
- assert(masked == ((oligo >> 6) & MASK8));
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("28 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
-#else
- _masked = _mm_and_si128(_oligo, mask8);
-#endif
-
- masked = EXTRACT(_masked,0);
- assert(masked == ((oligo >> 8) & MASK8));
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("29 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- assert(masked == ((oligo >> 10) & MASK8));
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("30 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
- assert(masked == ((oligo >> 12) & MASK8));
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("31 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low7);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
+
/* Expecting current to have {low0_rc, high0_rc, low1_rc, high1_rc},
and next to have {high0_rc, low1_rc, high1_rc, nextlow_rc} */
@@ -20543,118 +34779,1578 @@ extract_8mers_rev_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_8mers_rev_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,18), _mm256_slli_epi32(next,14));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask8));
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,16)); /* No mask necessary */;
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask8));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask8));
+
+ return;
+}
+#endif
+
+
static void
-count_8mers_rev_simd (Count_T *counts, __m128i current, __m128i next) {
+count_8mers_rev_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
oligo = _mm_or_si128( _mm_srli_epi32(current,18), _mm_slli_epi32(next,14));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,12), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,12), mask8));
- counts[array[0]] += 1; /* 63 */
- counts[array[1]] += 1; /* 47 */
- counts[array[2]] += 1; /* 31 */
- counts[array[3]] += 1; /* 15 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("47 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("31 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("15 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 63 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 15 */
+#endif
+ debug(printf("63 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,10), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask8));
- counts[array[0]] += 1; /* 62 */
- counts[array[1]] += 1; /* 46 */
- counts[array[2]] += 1; /* 30 */
- counts[array[3]] += 1; /* 14 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("46 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("30 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("14 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 62 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 14 */
+#endif
+ debug(printf("62 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask8));
- counts[array[0]] += 1; /* 61 */
- counts[array[1]] += 1; /* 45 */
- counts[array[2]] += 1; /* 29 */
- counts[array[3]] += 1; /* 13 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("45 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("29 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("13 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 61 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 13 */
+#endif
+ debug(printf("61 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask8));
- counts[array[0]] += 1; /* 60 */
- counts[array[1]] += 1; /* 44 */
- counts[array[2]] += 1; /* 28 */
- counts[array[3]] += 1; /* 12 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("44 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("28 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("12 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 60 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 12 */
+#endif
+ debug(printf("60 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask8));
- counts[array[0]] += 1; /* 59 */
- counts[array[1]] += 1; /* 43 */
- counts[array[2]] += 1; /* 27 */
- counts[array[3]] += 1; /* 11 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("43 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("27 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("11 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 59 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 11 */
+#endif
+ debug(printf("59 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask8));
- counts[array[0]] += 1; /* 58 */
- counts[array[1]] += 1; /* 42 */
- counts[array[2]] += 1; /* 26 */
- counts[array[3]] += 1; /* 10 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("42 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("26 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("10 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 58 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 10 */
+#endif
+ debug(printf("58 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask8));
- counts[array[0]] += 1; /* 57 */
- counts[array[1]] += 1; /* 41 */
- counts[array[2]] += 1; /* 25 */
- counts[array[3]] += 1; /* 9 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("41 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("25 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("9 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 57 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 9 */
+#endif
+ debug(printf("57 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,16); /* No mask necessary */;
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,16)); /* No mask necessary */;
- counts[array[0]] += 1; /* 56 */
- counts[array[1]] += 1; /* 50 */
- counts[array[2]] += 1; /* 24 */
- counts[array[3]] += 1; /* 8 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("40 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("24 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("8 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 56 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 8 */
+#endif
+ debug(printf("56 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask8);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask8));
- counts[array[0]] += 1; /* 55 */
- counts[array[1]] += 1; /* 39 */
- counts[array[2]] += 1; /* 23 */
- counts[array[3]] += 1; /* 7 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("39 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("23 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("7 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 55 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 7 */
+#endif
+ debug(printf("55 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("38 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("22 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("6 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 54 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 6 */
+#endif
+ debug(printf("54 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("37 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("21 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("5 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 53 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 5 */
+#endif
+ debug(printf("53 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("36 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("20 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("4 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 52 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 4 */
+#endif
+ debug(printf("52 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("35 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("19 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("3 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 51 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 3 */
+#endif
+ debug(printf("51 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("34 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("18 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("2 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 50 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 2 */
+#endif
+ debug(printf("50 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("33 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("17 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("1 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask8));
- counts[array[0]] += 1; /* 54 */
- counts[array[1]] += 1; /* 38 */
- counts[array[2]] += 1; /* 22 */
- counts[array[3]] += 1; /* 6 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 49 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 1 */
+#endif
+ debug(printf("49 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask8));
- counts[array[0]] += 1; /* 53 */
- counts[array[1]] += 1; /* 37 */
- counts[array[2]] += 1; /* 21 */
- counts[array[3]] += 1; /* 5 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask8);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask8));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("32 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("16 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("0 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask8));
- counts[array[0]] += 1; /* 52 */
- counts[array[1]] += 1; /* 36 */
- counts[array[2]] += 1; /* 20 */
- counts[array[3]] += 1; /* 4 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 48 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 0 */
+#endif
+ debug(printf("48 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask8));
- counts[array[0]] += 1; /* 51 */
- counts[array[1]] += 1; /* 35 */
- counts[array[2]] += 1; /* 19 */
- counts[array[3]] += 1; /* 3 */
+ return;
+}
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask8));
- counts[array[0]] += 1; /* 50 */
- counts[array[1]] += 1; /* 34 */
- counts[array[2]] += 1; /* 18 */
- counts[array[3]] += 1; /* 2 */
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask8));
- counts[array[0]] += 1; /* 49 */
- counts[array[1]] += 1; /* 33 */
- counts[array[2]] += 1; /* 17 */
- counts[array[3]] += 1; /* 1 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask8));
- counts[array[0]] += 1; /* 48 */
- counts[array[1]] += 1; /* 32 */
- counts[array[2]] += 1; /* 16 */
- counts[array[3]] += 1; /* 0 */
+#ifdef HAVE_AVX2
+static void
+count_8mers_rev_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,18), _mm256_slli_epi32(next,14));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,12), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 127 */
+ counts[EXTRACT256(array,1)] += 1; /* 111 */
+ counts[EXTRACT256(array,2)] += 1; /* 95 */
+ counts[EXTRACT256(array,3)] += 1; /* 79 */
+ counts[EXTRACT256(array,4)] += 1; /* 63 */
+ counts[EXTRACT256(array,5)] += 1; /* 47 */
+ counts[EXTRACT256(array,6)] += 1; /* 31 */
+ counts[EXTRACT256(array,7)] += 1; /* 15 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 126 */
+ counts[EXTRACT256(array,1)] += 1; /* 110 */
+ counts[EXTRACT256(array,2)] += 1; /* 94 */
+ counts[EXTRACT256(array,3)] += 1; /* 78 */
+ counts[EXTRACT256(array,4)] += 1; /* 62 */
+ counts[EXTRACT256(array,5)] += 1; /* 46 */
+ counts[EXTRACT256(array,6)] += 1; /* 30 */
+ counts[EXTRACT256(array,7)] += 1; /* 14 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 125 */
+ counts[EXTRACT256(array,1)] += 1; /* 109 */
+ counts[EXTRACT256(array,2)] += 1; /* 93 */
+ counts[EXTRACT256(array,3)] += 1; /* 77 */
+ counts[EXTRACT256(array,4)] += 1; /* 61 */
+ counts[EXTRACT256(array,5)] += 1; /* 45 */
+ counts[EXTRACT256(array,6)] += 1; /* 29 */
+ counts[EXTRACT256(array,7)] += 1; /* 13 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 124 */
+ counts[EXTRACT256(array,1)] += 1; /* 108 */
+ counts[EXTRACT256(array,2)] += 1; /* 92 */
+ counts[EXTRACT256(array,3)] += 1; /* 76 */
+ counts[EXTRACT256(array,4)] += 1; /* 60 */
+ counts[EXTRACT256(array,5)] += 1; /* 44 */
+ counts[EXTRACT256(array,6)] += 1; /* 28 */
+ counts[EXTRACT256(array,7)] += 1; /* 12 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 123 */
+ counts[EXTRACT256(array,1)] += 1; /* 107 */
+ counts[EXTRACT256(array,2)] += 1; /* 91 */
+ counts[EXTRACT256(array,3)] += 1; /* 75 */
+ counts[EXTRACT256(array,4)] += 1; /* 59 */
+ counts[EXTRACT256(array,5)] += 1; /* 43 */
+ counts[EXTRACT256(array,6)] += 1; /* 27 */
+ counts[EXTRACT256(array,7)] += 1; /* 11 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 122 */
+ counts[EXTRACT256(array,1)] += 1; /* 106 */
+ counts[EXTRACT256(array,2)] += 1; /* 90 */
+ counts[EXTRACT256(array,3)] += 1; /* 74 */
+ counts[EXTRACT256(array,4)] += 1; /* 58 */
+ counts[EXTRACT256(array,5)] += 1; /* 42 */
+ counts[EXTRACT256(array,6)] += 1; /* 26 */
+ counts[EXTRACT256(array,7)] += 1; /* 10 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 121 */
+ counts[EXTRACT256(array,1)] += 1; /* 105 */
+ counts[EXTRACT256(array,2)] += 1; /* 89 */
+ counts[EXTRACT256(array,3)] += 1; /* 73 */
+ counts[EXTRACT256(array,4)] += 1; /* 57 */
+ counts[EXTRACT256(array,5)] += 1; /* 41 */
+ counts[EXTRACT256(array,6)] += 1; /* 25 */
+ counts[EXTRACT256(array,7)] += 1; /* 9 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_srli_epi32(current,16); /* No mask necessary */;
+ counts[EXTRACT256(array,0)] += 1; /* 120 */
+ counts[EXTRACT256(array,1)] += 1; /* 104 */
+ counts[EXTRACT256(array,2)] += 1; /* 88 */
+ counts[EXTRACT256(array,3)] += 1; /* 72 */
+ counts[EXTRACT256(array,4)] += 1; /* 56 */
+ counts[EXTRACT256(array,5)] += 1; /* 40 */
+ counts[EXTRACT256(array,6)] += 1; /* 24 */
+ counts[EXTRACT256(array,7)] += 1; /* 8 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 119 */
+ counts[EXTRACT256(array,1)] += 1; /* 103 */
+ counts[EXTRACT256(array,2)] += 1; /* 87 */
+ counts[EXTRACT256(array,3)] += 1; /* 71 */
+ counts[EXTRACT256(array,4)] += 1; /* 55 */
+ counts[EXTRACT256(array,5)] += 1; /* 39 */
+ counts[EXTRACT256(array,6)] += 1; /* 23 */
+ counts[EXTRACT256(array,7)] += 1; /* 7 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 118 */
+ counts[EXTRACT256(array,1)] += 1; /* 102 */
+ counts[EXTRACT256(array,2)] += 1; /* 86 */
+ counts[EXTRACT256(array,3)] += 1; /* 70 */
+ counts[EXTRACT256(array,4)] += 1; /* 54 */
+ counts[EXTRACT256(array,5)] += 1; /* 38 */
+ counts[EXTRACT256(array,6)] += 1; /* 22 */
+ counts[EXTRACT256(array,7)] += 1; /* 6 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 117 */
+ counts[EXTRACT256(array,1)] += 1; /* 101 */
+ counts[EXTRACT256(array,2)] += 1; /* 85 */
+ counts[EXTRACT256(array,3)] += 1; /* 69 */
+ counts[EXTRACT256(array,4)] += 1; /* 53 */
+ counts[EXTRACT256(array,5)] += 1; /* 37 */
+ counts[EXTRACT256(array,6)] += 1; /* 21 */
+ counts[EXTRACT256(array,7)] += 1; /* 5 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 116 */
+ counts[EXTRACT256(array,1)] += 1; /* 100 */
+ counts[EXTRACT256(array,2)] += 1; /* 84 */
+ counts[EXTRACT256(array,3)] += 1; /* 68 */
+ counts[EXTRACT256(array,4)] += 1; /* 52 */
+ counts[EXTRACT256(array,5)] += 1; /* 36 */
+ counts[EXTRACT256(array,6)] += 1; /* 20 */
+ counts[EXTRACT256(array,7)] += 1; /* 4 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 115 */
+ counts[EXTRACT256(array,1)] += 1; /* 99 */
+ counts[EXTRACT256(array,2)] += 1; /* 83 */
+ counts[EXTRACT256(array,3)] += 1; /* 67 */
+ counts[EXTRACT256(array,4)] += 1; /* 51 */
+ counts[EXTRACT256(array,5)] += 1; /* 35 */
+ counts[EXTRACT256(array,6)] += 1; /* 19 */
+ counts[EXTRACT256(array,7)] += 1; /* 3 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 114 */
+ counts[EXTRACT256(array,1)] += 1; /* 98 */
+ counts[EXTRACT256(array,2)] += 1; /* 82 */
+ counts[EXTRACT256(array,3)] += 1; /* 66 */
+ counts[EXTRACT256(array,4)] += 1; /* 50 */
+ counts[EXTRACT256(array,5)] += 1; /* 34 */
+ counts[EXTRACT256(array,6)] += 1; /* 18 */
+ counts[EXTRACT256(array,7)] += 1; /* 2 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 113 */
+ counts[EXTRACT256(array,1)] += 1; /* 97 */
+ counts[EXTRACT256(array,2)] += 1; /* 81 */
+ counts[EXTRACT256(array,3)] += 1; /* 65 */
+ counts[EXTRACT256(array,4)] += 1; /* 49 */
+ counts[EXTRACT256(array,5)] += 1; /* 33 */
+ counts[EXTRACT256(array,6)] += 1; /* 17 */
+ counts[EXTRACT256(array,7)] += 1; /* 1 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask8);
+ counts[EXTRACT256(array,0)] += 1; /* 112 */
+ counts[EXTRACT256(array,1)] += 1; /* 96 */
+ counts[EXTRACT256(array,2)] += 1; /* 80 */
+ counts[EXTRACT256(array,3)] += 1; /* 64 */
+ counts[EXTRACT256(array,4)] += 1; /* 48 */
+ counts[EXTRACT256(array,5)] += 1; /* 32 */
+ counts[EXTRACT256(array,6)] += 1; /* 16 */
+ counts[EXTRACT256(array,7)] += 1; /* 0 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
-
#endif
+#if !defined(HAVE_AVX2)
static int
-store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_8mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -20669,83 +36365,65 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK8; /* 0 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (low_rc >> 2) & MASK8; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (low_rc >> 4) & MASK8; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (low_rc >> 6) & MASK8; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (low_rc >> 8) & MASK8; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (low_rc >> 10) & MASK8; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rc >> 12) & MASK8; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rc >> 14) & MASK8; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = low_rc >> 16; /* 8, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
#else
@@ -20759,41 +36437,33 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == (low_rc & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
assert(masked == ((low_rc >> 2) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
assert(masked == ((low_rc >> 4) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
assert(masked == ((low_rc >> 6) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -20807,51 +36477,41 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == ((low_rc >> 8) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
assert(masked == ((low_rc >> 10) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
assert(masked == ((low_rc >> 12) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
assert(masked == ((low_rc >> 14) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = low_rc >> 16; /* 8, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
#endif
@@ -20862,65 +36522,51 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (oligo >> 2) & MASK8; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (oligo >> 4) & MASK8; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (oligo >> 6) & MASK8; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (oligo >> 8) & MASK8; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (oligo >> 10) & MASK8; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = (oligo >> 12) & MASK8; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -20934,41 +36580,33 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == (oligo & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,1);
assert(masked == ((oligo >> 2) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,2);
assert(masked == ((oligo >> 4) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = EXTRACT(_masked,3);
assert(masked == ((oligo >> 6) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
@@ -20982,31 +36620,25 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == ((oligo >> 8) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,1);
assert(masked == ((oligo >> 10) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,2);
assert(masked == ((oligo >> 12) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -21014,83 +36646,65 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK8; /* 16 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (high_rc >> 2) & MASK8; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (high_rc >> 4) & MASK8; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (high_rc >> 6) & MASK8; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (high_rc >> 8) & MASK8; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (high_rc >> 10) & MASK8; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rc >> 12) & MASK8; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rc >> 14) & MASK8; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = high_rc >> 16; /* 24, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
#else
@@ -21104,41 +36718,33 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == (high_rc & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
assert(masked == ((high_rc >> 2) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
assert(masked == ((high_rc >> 4) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
assert(masked == ((high_rc >> 6) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -21152,51 +36758,41 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == ((high_rc >> 8) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
assert(masked == ((high_rc >> 10) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
assert(masked == ((high_rc >> 12) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,3);
assert(masked == ((high_rc >> 14) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = high_rc >> 16; /* 24, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
#endif
@@ -21207,65 +36803,51 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK8; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (oligo >> 2) & MASK8; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (oligo >> 4) & MASK8; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (oligo >> 6) & MASK8; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (oligo >> 8) & MASK8; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (oligo >> 10) & MASK8; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = (oligo >> 12) & MASK8; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -21279,89 +36861,342 @@ store_8mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
assert(masked == (oligo & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = EXTRACT(_masked,1);
assert(masked == ((oligo >> 2) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = EXTRACT(_masked,2);
assert(masked == ((oligo >> 4) & MASK8));
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = EXTRACT(_masked,3);
+ assert(masked == ((oligo >> 6) & MASK8));
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
+#else
+ _masked = _mm_and_si128(_oligo, mask8);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ assert(masked == ((oligo >> 8) & MASK8));
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,1);
+ assert(masked == ((oligo >> 10) & MASK8));
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,2);
+ assert(masked == ((oligo >> 12) & MASK8));
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_8mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+
+ masked = low_rc >> 16; /* 8, No mask necessary */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+
+ oligo = low_rc >> 18; /* For 15..9 */
+ oligo |= high_rc << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+
+ masked = high_rc >> 16; /* 24, No mask necessary */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+
+ oligo = high_rc >> 18; /* For 31..25 */
+ oligo |= nextlow_rc << 14;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask8);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
- masked = EXTRACT(_masked,3);
- assert(masked == ((oligo >> 6) & MASK8));
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask8));
-#else
- _masked = _mm_and_si128(_oligo, mask8);
-#endif
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
- masked = EXTRACT(_masked,0);
- assert(masked == ((oligo >> 8) & MASK8));
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- masked = EXTRACT(_masked,1);
- assert(masked == ((oligo >> 10) & MASK8));
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
- masked = EXTRACT(_masked,2);
- assert(masked == ((oligo >> 12) & MASK8));
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+#if !defined(HAVE_AVX2)
+
static void
-count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+count_7mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -21374,43 +37209,43 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK7; /* 0 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 2) & MASK7; /* 1 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 4) & MASK7; /* 2 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 6) & MASK7; /* 3 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 8) & MASK7; /* 4 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 10) & MASK7; /* 5 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 12) & MASK7; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 14) & MASK7; /* 7 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 16) & MASK7; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = low_rc >> 18; /* 9, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
#else
@@ -21422,19 +37257,19 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
@@ -21446,19 +37281,19 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
@@ -21470,11 +37305,11 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
#endif
@@ -21484,27 +37319,27 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK7; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK7; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK7; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK7; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 10) & MASK7; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#else
@@ -21516,19 +37351,19 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
@@ -21540,54 +37375,54 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK7; /* 16 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 2) & MASK7; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 4) & MASK7; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 6) & MASK7; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 8) & MASK7; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 10) & MASK7; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 12) & MASK7; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 14) & MASK7; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 16) & MASK7; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = high_rc >> 18; /* 25, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
#else
@@ -21599,19 +37434,19 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
@@ -21622,112 +37457,406 @@ count_7mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
_masked = _mm_and_si128(_oligo, mask7);
#endif
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+#endif
+
+
+ oligo = high_rc >> 20; /* For 31..26 */
+ oligo |= nextlow_rc << 12;
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = oligo & MASK7; /* 26 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 2) & MASK7; /* 27 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 4) & MASK7; /* 28 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 6) & MASK7; /* 29 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 8) & MASK7; /* 30 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 10) & MASK7; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_7mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+
+ oligo = low_rc >> 20; /* For 15..10 */
+ oligo |= high_rc << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low6);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("20 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("21 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("22 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("23 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
-#endif
oligo = high_rc >> 20; /* For 31..26 */
oligo |= nextlow_rc << 12;
-#ifdef INDIVIDUAL_SHIFTS
- masked = oligo & MASK7; /* 26 */
- counts[masked] += 1;
- debug(printf("26 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 2) & MASK7; /* 27 */
- counts[masked] += 1;
- debug(printf("27 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 4) & MASK7; /* 28 */
- counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 6) & MASK7; /* 29 */
- counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 8) & MASK7; /* 30 */
- counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 10) & MASK7; /* 31 */
- counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
-
-#else
- _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("26 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("27 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("28 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("29 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("30 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("31 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low6);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
+
/* Expecting current to have {low0_rc, high0_rc, low1_rc, high1_rc},
and next to have {high0_rc, low1_rc, high1_rc, nextlow_rc} */
@@ -21758,116 +37887,1578 @@ extract_7mers_rev_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_7mers_rev_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,20), _mm256_slli_epi32(next,12));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask7));
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,18)); /* No mask necessary */
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask7));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask7));
+
+ return;
+}
+#endif
+
+
static void
-count_7mers_rev_simd (Count_T *counts, __m128i current, __m128i next) {
+count_7mers_rev_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
oligo = _mm_or_si128( _mm_srli_epi32(current,20), _mm_slli_epi32(next,12));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,10), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,10), mask7));
- counts[array[0]] += 1; /* 63 */
- counts[array[1]] += 1; /* 47 */
- counts[array[2]] += 1; /* 31 */
- counts[array[3]] += 1; /* 15 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("47 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("31 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("15 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 63 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 15 */
+#endif
+ debug(printf("63 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask7));
- counts[array[0]] += 1; /* 62 */
- counts[array[1]] += 1; /* 46 */
- counts[array[2]] += 1; /* 30 */
- counts[array[3]] += 1; /* 14 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("46 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("30 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("14 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 62 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 14 */
+#endif
+ debug(printf("62 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask7));
- counts[array[0]] += 1; /* 61 */
- counts[array[1]] += 1; /* 45 */
- counts[array[2]] += 1; /* 29 */
- counts[array[3]] += 1; /* 13 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("45 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("29 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("13 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 61 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 13 */
+#endif
+ debug(printf("61 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask7));
- counts[array[0]] += 1; /* 60 */
- counts[array[1]] += 1; /* 44 */
- counts[array[2]] += 1; /* 28 */
- counts[array[3]] += 1; /* 12 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("44 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("28 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("12 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 60 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 12 */
+#endif
+ debug(printf("60 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask7));
- counts[array[0]] += 1; /* 59 */
- counts[array[1]] += 1; /* 43 */
- counts[array[2]] += 1; /* 27 */
- counts[array[3]] += 1; /* 11 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("43 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("27 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("11 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 59 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 11 */
+#endif
+ debug(printf("59 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask7));
- counts[array[0]] += 1; /* 58 */
- counts[array[1]] += 1; /* 42 */
- counts[array[2]] += 1; /* 26 */
- counts[array[3]] += 1; /* 10 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("42 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("26 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("10 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 58 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 10 */
+#endif
+ debug(printf("58 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,18); /* No mask necessary */
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,18)); /* No mask necessary */
- counts[array[0]] += 1; /* 57 */
- counts[array[1]] += 1; /* 41 */
- counts[array[2]] += 1; /* 25 */
- counts[array[3]] += 1; /* 9 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("41 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("25 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("9 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 57 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 9 */
+#endif
+ debug(printf("57 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,16), mask7);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,16), mask7));
- counts[array[0]] += 1; /* 56 */
- counts[array[1]] += 1; /* 50 */
- counts[array[2]] += 1; /* 24 */
- counts[array[3]] += 1; /* 8 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("40 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("24 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("8 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 56 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 8 */
+#endif
+ debug(printf("56 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("39 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("23 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("7 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 55 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 7 */
+#endif
+ debug(printf("55 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("38 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("22 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("6 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 54 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 6 */
+#endif
+ debug(printf("54 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("37 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("21 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("5 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 53 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 5 */
+#endif
+ debug(printf("53 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("36 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("20 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("4 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 52 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 4 */
+#endif
+ debug(printf("52 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("35 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("19 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("3 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 51 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 3 */
+#endif
+ debug(printf("51 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("34 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("18 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("2 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask7));
- counts[array[0]] += 1; /* 55 */
- counts[array[1]] += 1; /* 39 */
- counts[array[2]] += 1; /* 23 */
- counts[array[3]] += 1; /* 7 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 50 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 2 */
+#endif
+ debug(printf("50 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask7));
- counts[array[0]] += 1; /* 54 */
- counts[array[1]] += 1; /* 38 */
- counts[array[2]] += 1; /* 22 */
- counts[array[3]] += 1; /* 6 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("33 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("17 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("1 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask7));
- counts[array[0]] += 1; /* 53 */
- counts[array[1]] += 1; /* 37 */
- counts[array[2]] += 1; /* 21 */
- counts[array[3]] += 1; /* 5 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 49 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 1 */
+#endif
+ debug(printf("49 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask7));
- counts[array[0]] += 1; /* 52 */
- counts[array[1]] += 1; /* 36 */
- counts[array[2]] += 1; /* 20 */
- counts[array[3]] += 1; /* 4 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask7);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask7));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("32 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("16 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("0 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask7));
- counts[array[0]] += 1; /* 51 */
- counts[array[1]] += 1; /* 35 */
- counts[array[2]] += 1; /* 19 */
- counts[array[3]] += 1; /* 3 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 48 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 0 */
+#endif
+ debug(printf("48 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask7));
- counts[array[0]] += 1; /* 50 */
- counts[array[1]] += 1; /* 34 */
- counts[array[2]] += 1; /* 18 */
- counts[array[3]] += 1; /* 2 */
+ return;
+}
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask7));
- counts[array[0]] += 1; /* 49 */
- counts[array[1]] += 1; /* 33 */
- counts[array[2]] += 1; /* 17 */
- counts[array[3]] += 1; /* 1 */
- _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask7));
- counts[array[0]] += 1; /* 48 */
- counts[array[1]] += 1; /* 32 */
- counts[array[2]] += 1; /* 16 */
- counts[array[3]] += 1; /* 0 */
+#ifdef HAVE_AVX2
+static void
+count_7mers_rev_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,20), _mm256_slli_epi32(next,12));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,10), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 127 */
+ counts[EXTRACT256(array,1)] += 1; /* 111 */
+ counts[EXTRACT256(array,2)] += 1; /* 95 */
+ counts[EXTRACT256(array,3)] += 1; /* 79 */
+ counts[EXTRACT256(array,4)] += 1; /* 63 */
+ counts[EXTRACT256(array,5)] += 1; /* 47 */
+ counts[EXTRACT256(array,6)] += 1; /* 31 */
+ counts[EXTRACT256(array,7)] += 1; /* 15 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 126 */
+ counts[EXTRACT256(array,1)] += 1; /* 110 */
+ counts[EXTRACT256(array,2)] += 1; /* 94 */
+ counts[EXTRACT256(array,3)] += 1; /* 78 */
+ counts[EXTRACT256(array,4)] += 1; /* 62 */
+ counts[EXTRACT256(array,5)] += 1; /* 46 */
+ counts[EXTRACT256(array,6)] += 1; /* 30 */
+ counts[EXTRACT256(array,7)] += 1; /* 14 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 125 */
+ counts[EXTRACT256(array,1)] += 1; /* 109 */
+ counts[EXTRACT256(array,2)] += 1; /* 93 */
+ counts[EXTRACT256(array,3)] += 1; /* 77 */
+ counts[EXTRACT256(array,4)] += 1; /* 61 */
+ counts[EXTRACT256(array,5)] += 1; /* 45 */
+ counts[EXTRACT256(array,6)] += 1; /* 29 */
+ counts[EXTRACT256(array,7)] += 1; /* 13 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 124 */
+ counts[EXTRACT256(array,1)] += 1; /* 108 */
+ counts[EXTRACT256(array,2)] += 1; /* 92 */
+ counts[EXTRACT256(array,3)] += 1; /* 76 */
+ counts[EXTRACT256(array,4)] += 1; /* 60 */
+ counts[EXTRACT256(array,5)] += 1; /* 44 */
+ counts[EXTRACT256(array,6)] += 1; /* 28 */
+ counts[EXTRACT256(array,7)] += 1; /* 12 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 123 */
+ counts[EXTRACT256(array,1)] += 1; /* 107 */
+ counts[EXTRACT256(array,2)] += 1; /* 91 */
+ counts[EXTRACT256(array,3)] += 1; /* 75 */
+ counts[EXTRACT256(array,4)] += 1; /* 59 */
+ counts[EXTRACT256(array,5)] += 1; /* 43 */
+ counts[EXTRACT256(array,6)] += 1; /* 27 */
+ counts[EXTRACT256(array,7)] += 1; /* 11 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 122 */
+ counts[EXTRACT256(array,1)] += 1; /* 106 */
+ counts[EXTRACT256(array,2)] += 1; /* 90 */
+ counts[EXTRACT256(array,3)] += 1; /* 74 */
+ counts[EXTRACT256(array,4)] += 1; /* 58 */
+ counts[EXTRACT256(array,5)] += 1; /* 42 */
+ counts[EXTRACT256(array,6)] += 1; /* 26 */
+ counts[EXTRACT256(array,7)] += 1; /* 10 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_srli_epi32(current,18); /* No mask necessary */
+ counts[EXTRACT256(array,0)] += 1; /* 121 */
+ counts[EXTRACT256(array,1)] += 1; /* 105 */
+ counts[EXTRACT256(array,2)] += 1; /* 89 */
+ counts[EXTRACT256(array,3)] += 1; /* 73 */
+ counts[EXTRACT256(array,4)] += 1; /* 57 */
+ counts[EXTRACT256(array,5)] += 1; /* 41 */
+ counts[EXTRACT256(array,6)] += 1; /* 25 */
+ counts[EXTRACT256(array,7)] += 1; /* 9 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 120 */
+ counts[EXTRACT256(array,1)] += 1; /* 104 */
+ counts[EXTRACT256(array,2)] += 1; /* 88 */
+ counts[EXTRACT256(array,3)] += 1; /* 72 */
+ counts[EXTRACT256(array,4)] += 1; /* 56 */
+ counts[EXTRACT256(array,5)] += 1; /* 40 */
+ counts[EXTRACT256(array,6)] += 1; /* 24 */
+ counts[EXTRACT256(array,7)] += 1; /* 8 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 119 */
+ counts[EXTRACT256(array,1)] += 1; /* 103 */
+ counts[EXTRACT256(array,2)] += 1; /* 87 */
+ counts[EXTRACT256(array,3)] += 1; /* 71 */
+ counts[EXTRACT256(array,4)] += 1; /* 55 */
+ counts[EXTRACT256(array,5)] += 1; /* 39 */
+ counts[EXTRACT256(array,6)] += 1; /* 23 */
+ counts[EXTRACT256(array,7)] += 1; /* 7 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 118 */
+ counts[EXTRACT256(array,1)] += 1; /* 102 */
+ counts[EXTRACT256(array,2)] += 1; /* 86 */
+ counts[EXTRACT256(array,3)] += 1; /* 70 */
+ counts[EXTRACT256(array,4)] += 1; /* 54 */
+ counts[EXTRACT256(array,5)] += 1; /* 38 */
+ counts[EXTRACT256(array,6)] += 1; /* 22 */
+ counts[EXTRACT256(array,7)] += 1; /* 6 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 117 */
+ counts[EXTRACT256(array,1)] += 1; /* 101 */
+ counts[EXTRACT256(array,2)] += 1; /* 85 */
+ counts[EXTRACT256(array,3)] += 1; /* 69 */
+ counts[EXTRACT256(array,4)] += 1; /* 53 */
+ counts[EXTRACT256(array,5)] += 1; /* 37 */
+ counts[EXTRACT256(array,6)] += 1; /* 21 */
+ counts[EXTRACT256(array,7)] += 1; /* 5 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 116 */
+ counts[EXTRACT256(array,1)] += 1; /* 100 */
+ counts[EXTRACT256(array,2)] += 1; /* 84 */
+ counts[EXTRACT256(array,3)] += 1; /* 68 */
+ counts[EXTRACT256(array,4)] += 1; /* 52 */
+ counts[EXTRACT256(array,5)] += 1; /* 36 */
+ counts[EXTRACT256(array,6)] += 1; /* 20 */
+ counts[EXTRACT256(array,7)] += 1; /* 4 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 115 */
+ counts[EXTRACT256(array,1)] += 1; /* 99 */
+ counts[EXTRACT256(array,2)] += 1; /* 83 */
+ counts[EXTRACT256(array,3)] += 1; /* 67 */
+ counts[EXTRACT256(array,4)] += 1; /* 51 */
+ counts[EXTRACT256(array,5)] += 1; /* 35 */
+ counts[EXTRACT256(array,6)] += 1; /* 19 */
+ counts[EXTRACT256(array,7)] += 1; /* 3 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 114 */
+ counts[EXTRACT256(array,1)] += 1; /* 98 */
+ counts[EXTRACT256(array,2)] += 1; /* 82 */
+ counts[EXTRACT256(array,3)] += 1; /* 66 */
+ counts[EXTRACT256(array,4)] += 1; /* 50 */
+ counts[EXTRACT256(array,5)] += 1; /* 34 */
+ counts[EXTRACT256(array,6)] += 1; /* 18 */
+ counts[EXTRACT256(array,7)] += 1; /* 2 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 113 */
+ counts[EXTRACT256(array,1)] += 1; /* 97 */
+ counts[EXTRACT256(array,2)] += 1; /* 81 */
+ counts[EXTRACT256(array,3)] += 1; /* 65 */
+ counts[EXTRACT256(array,4)] += 1; /* 49 */
+ counts[EXTRACT256(array,5)] += 1; /* 33 */
+ counts[EXTRACT256(array,6)] += 1; /* 17 */
+ counts[EXTRACT256(array,7)] += 1; /* 1 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask7);
+ counts[EXTRACT256(array,0)] += 1; /* 112 */
+ counts[EXTRACT256(array,1)] += 1; /* 96 */
+ counts[EXTRACT256(array,2)] += 1; /* 80 */
+ counts[EXTRACT256(array,3)] += 1; /* 64 */
+ counts[EXTRACT256(array,4)] += 1; /* 48 */
+ counts[EXTRACT256(array,5)] += 1; /* 32 */
+ counts[EXTRACT256(array,6)] += 1; /* 16 */
+ counts[EXTRACT256(array,7)] += 1; /* 0 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
#endif
+#if !defined(HAVE_AVX2)
+
static Chrpos_T
-store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_7mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -21882,92 +39473,72 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK7; /* 0 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (low_rc >> 2) & MASK7; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (low_rc >> 4) & MASK7; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (low_rc >> 6) & MASK7; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (low_rc >> 8) & MASK7; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (low_rc >> 10) & MASK7; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rc >> 12) & MASK7; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rc >> 14) & MASK7; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rc >> 16) & MASK7; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = low_rc >> 18; /* 9, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
#else
@@ -21980,38 +39551,30 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -22024,38 +39587,30 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
@@ -22068,20 +39623,16 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
#endif
@@ -22092,56 +39643,44 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = (oligo >> 2) & MASK7; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (oligo >> 4) & MASK7; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (oligo >> 6) & MASK7; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (oligo >> 8) & MASK7; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = (oligo >> 10) & MASK7; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -22154,38 +39693,30 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
@@ -22198,20 +39729,16 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -22220,92 +39747,72 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK7; /* 16 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (high_rc >> 2) & MASK7; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (high_rc >> 4) & MASK7; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (high_rc >> 6) & MASK7; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (high_rc >> 8) & MASK7; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (high_rc >> 10) & MASK7; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rc >> 12) & MASK7; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rc >> 14) & MASK7; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rc >> 16) & MASK7; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = high_rc >> 18; /* 25, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
#else
@@ -22318,38 +39825,30 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -22362,38 +39861,30 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
@@ -22406,20 +39897,16 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
#endif
@@ -22430,56 +39917,44 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK7; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = (oligo >> 2) & MASK7; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (oligo >> 4) & MASK7; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (oligo >> 6) & MASK7; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (oligo >> 8) & MASK7; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = (oligo >> 10) & MASK7; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -22492,73 +39967,343 @@ store_7mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
+#else
+ _masked = _mm_and_si128(_oligo, mask7);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static Chrpos_T
+store_7mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+
+ oligo = low_rc >> 20; /* For 15..10 */
+ oligo |= high_rc << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+
+ oligo = high_rc >> 20; /* For 31..26 */
+ oligo |= nextlow_rc << 12;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask7);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ assert(EXTRACT256(_counts,0) == counts[EXTRACT256(_masked,0)]);
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(EXTRACT256(_counts,1) == counts[EXTRACT256(_masked,1)]);
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
+ assert(EXTRACT256(_counts,2) == counts[EXTRACT256(_masked,2)]);
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask7));
-#else
- _masked = _mm_and_si128(_oligo, mask7);
-#endif
+ assert(EXTRACT256(_counts,3) == counts[EXTRACT256(_masked,3)]);
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(EXTRACT256(_counts,4) == counts[EXTRACT256(_masked,4)]);
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(EXTRACT256(_counts,5) == counts[EXTRACT256(_masked,5)]);
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
+
+#if !defined(HAVE_AVX2)
static void
-count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+count_6mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -22571,47 +40316,47 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK6; /* 0 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 2) & MASK6; /* 1 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 4) & MASK6; /* 2 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 6) & MASK6; /* 3 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 8) & MASK6; /* 4 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 10) & MASK6; /* 5 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 12) & MASK6; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 14) & MASK6; /* 7 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 16) & MASK6; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 18) & MASK6; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = low_rc >> 20; /* 10, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
#else
@@ -22623,19 +40368,19 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
@@ -22647,19 +40392,19 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
@@ -22671,15 +40416,15 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
#endif
@@ -22689,23 +40434,23 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 11 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK6; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK6; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK6; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK6; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#else
@@ -22717,71 +40462,71 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 8) & MASK6; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK6; /* 16 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 2) & MASK6; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 4) & MASK6; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 6) & MASK6; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 8) & MASK6; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 10) & MASK6; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 12) & MASK6; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 14) & MASK6; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 16) & MASK6; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 18) & MASK6; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = high_rc >> 20; /* 26, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
#else
@@ -22792,125 +40537,413 @@ count_6mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
_masked = _mm_and_si128(_oligo, mask6);
#endif
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+
+ _oligo = _mm_srli_epi32(_oligo, 8);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+#endif
+
+
+ oligo = high_rc >> 22; /* For 31..27 */
+ oligo |= nextlow_rc << 10;
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = oligo & MASK6; /* 27 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 2) & MASK6; /* 28 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 4) & MASK6; /* 29 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 6) & MASK6; /* 30 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 8) & MASK6; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
+#else
+ _masked = _mm_and_si128(_oligo, mask6);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+
+ masked = (oligo >> 8) & MASK6; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_6mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+
+ oligo = low_rc >> 22; /* For 15..11 */
+ oligo |= high_rc << 10;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low5);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("16 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("17 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("18 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("19 %04X => %d\n",masked,counts[masked]));
-
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
-
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("20 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,5);
counts[masked] += 1;
debug(printf("21 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,6);
counts[masked] += 1;
debug(printf("22 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,7);
counts[masked] += 1;
debug(printf("23 %04X => %d\n",masked,counts[masked]));
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
- _oligo = _mm_srli_epi32(_oligo, 8);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
- masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+
+ masked = EXTRACT256(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ masked = EXTRACT256(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
-#endif
oligo = high_rc >> 22; /* For 31..27 */
oligo |= nextlow_rc << 10;
-#ifdef INDIVIDUAL_SHIFTS
- masked = oligo & MASK6; /* 27 */
- counts[masked] += 1;
- debug(printf("27 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 2) & MASK6; /* 28 */
- counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 4) & MASK6; /* 29 */
- counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 6) & MASK6; /* 30 */
- counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 8) & MASK6; /* 31 */
- counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
-
-#else
- _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask6));
-#else
- _masked = _mm_and_si128(_oligo, mask6);
-#endif
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("27 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("28 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("29 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("30 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 8) & MASK6; /* 31 */
+ masked = EXTRACT256(_masked,4);
counts[masked] += 1;
debug(printf("31 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low5);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
+
/* Expecting current to have {low0_rc, high0_rc, low1_rc, high1_rc},
and next to have {high0_rc, low1_rc, high1_rc, nextlow_rc} */
#ifdef USE_SIMD_FOR_COUNTS
@@ -22940,117 +40973,1578 @@ extract_6mers_rev_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_6mers_rev_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,22), _mm256_slli_epi32(next,10));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask6));
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,20));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask6));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask6));
+
+ return;
+}
+#endif
+
+
static void
-count_6mers_rev_simd (Count_T *counts, __m128i current, __m128i next) {
+count_6mers_rev_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
oligo = _mm_or_si128( _mm_srli_epi32(current,22), _mm_slli_epi32(next,10));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,8), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,8), mask6));
- counts[array[0]] += 1; /* 63 */
- counts[array[1]] += 1; /* 47 */
- counts[array[2]] += 1; /* 31 */
- counts[array[3]] += 1; /* 15 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("47 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("31 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("15 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 63 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 15 */
+#endif
+ debug(printf("63 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask6));
- counts[array[0]] += 1; /* 62 */
- counts[array[1]] += 1; /* 46 */
- counts[array[2]] += 1; /* 30 */
- counts[array[3]] += 1; /* 14 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("46 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("30 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("14 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 62 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 14 */
+#endif
+ debug(printf("62 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask6));
- counts[array[0]] += 1; /* 61 */
- counts[array[1]] += 1; /* 45 */
- counts[array[2]] += 1; /* 29 */
- counts[array[3]] += 1; /* 13 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("45 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("29 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("13 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 61 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 13 */
+#endif
+ debug(printf("61 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask6));
- counts[array[0]] += 1; /* 60 */
- counts[array[1]] += 1; /* 44 */
- counts[array[2]] += 1; /* 28 */
- counts[array[3]] += 1; /* 12 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("44 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("28 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("12 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 60 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 12 */
+#endif
+ debug(printf("60 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask6));
- counts[array[0]] += 1; /* 59 */
- counts[array[1]] += 1; /* 43 */
- counts[array[2]] += 1; /* 27 */
- counts[array[3]] += 1; /* 11 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("43 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("27 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("11 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 59 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 11 */
+#endif
+ debug(printf("59 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,20);
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,20));
- counts[array[0]] += 1; /* 58 */
- counts[array[1]] += 1; /* 42 */
- counts[array[2]] += 1; /* 26 */
- counts[array[3]] += 1; /* 10 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("42 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("26 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("10 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 58 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 10 */
+#endif
+ debug(printf("58 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,18), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,18), mask6));
- counts[array[0]] += 1; /* 57 */
- counts[array[1]] += 1; /* 41 */
- counts[array[2]] += 1; /* 25 */
- counts[array[3]] += 1; /* 9 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("41 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("25 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("9 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 57 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 9 */
+#endif
+ debug(printf("57 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,16), mask6);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,16), mask6));
- counts[array[0]] += 1; /* 56 */
- counts[array[1]] += 1; /* 50 */
- counts[array[2]] += 1; /* 24 */
- counts[array[3]] += 1; /* 8 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("40 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("24 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("8 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 56 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 8 */
+#endif
+ debug(printf("56 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("39 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("23 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("7 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 55 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 7 */
+#endif
+ debug(printf("55 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("38 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("22 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("6 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 54 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 6 */
+#endif
+ debug(printf("54 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("37 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("21 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("5 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 53 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 5 */
+#endif
+ debug(printf("53 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("36 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("20 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("4 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 52 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 4 */
+#endif
+ debug(printf("52 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("35 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("19 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("3 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 51 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 3 */
+#endif
+ debug(printf("51 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("34 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("18 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("2 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask6));
- counts[array[0]] += 1; /* 55 */
- counts[array[1]] += 1; /* 39 */
- counts[array[2]] += 1; /* 23 */
- counts[array[3]] += 1; /* 7 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 50 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 2 */
+#endif
+ debug(printf("50 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask6));
- counts[array[0]] += 1; /* 54 */
- counts[array[1]] += 1; /* 38 */
- counts[array[2]] += 1; /* 22 */
- counts[array[3]] += 1; /* 6 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("33 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("17 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("1 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask6));
- counts[array[0]] += 1; /* 53 */
- counts[array[1]] += 1; /* 37 */
- counts[array[2]] += 1; /* 21 */
- counts[array[3]] += 1; /* 5 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 49 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 1 */
+#endif
+ debug(printf("49 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask6));
- counts[array[0]] += 1; /* 52 */
- counts[array[1]] += 1; /* 36 */
- counts[array[2]] += 1; /* 20 */
- counts[array[3]] += 1; /* 4 */
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask6);
+#else
+ _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask6));
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("32 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("16 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("0 %04X => %d\n",array[3],counts[array[3]]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask6));
- counts[array[0]] += 1; /* 51 */
- counts[array[1]] += 1; /* 35 */
- counts[array[2]] += 1; /* 19 */
- counts[array[3]] += 1; /* 3 */
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 48 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 0 */
+#endif
+ debug(printf("48 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask6));
- counts[array[0]] += 1; /* 50 */
- counts[array[1]] += 1; /* 34 */
- counts[array[2]] += 1; /* 18 */
- counts[array[3]] += 1; /* 2 */
+ return;
+}
- _mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask6));
- counts[array[0]] += 1; /* 49 */
- counts[array[1]] += 1; /* 33 */
- counts[array[2]] += 1; /* 17 */
- counts[array[3]] += 1; /* 1 */
+#endif
- _mm_store_si128((__m128i *) array, _mm_and_si128( current, mask6));
- counts[array[0]] += 1; /* 48 */
- counts[array[1]] += 1; /* 32 */
- counts[array[2]] += 1; /* 16 */
- counts[array[3]] += 1; /* 0 */
+#ifdef HAVE_AVX2
+static void
+count_6mers_rev_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,22), _mm256_slli_epi32(next,10));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,8), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 127 */
+ counts[EXTRACT256(array,1)] += 1; /* 111 */
+ counts[EXTRACT256(array,2)] += 1; /* 95 */
+ counts[EXTRACT256(array,3)] += 1; /* 79 */
+ counts[EXTRACT256(array,4)] += 1; /* 63 */
+ counts[EXTRACT256(array,5)] += 1; /* 47 */
+ counts[EXTRACT256(array,6)] += 1; /* 31 */
+ counts[EXTRACT256(array,7)] += 1; /* 15 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 126 */
+ counts[EXTRACT256(array,1)] += 1; /* 110 */
+ counts[EXTRACT256(array,2)] += 1; /* 94 */
+ counts[EXTRACT256(array,3)] += 1; /* 78 */
+ counts[EXTRACT256(array,4)] += 1; /* 62 */
+ counts[EXTRACT256(array,5)] += 1; /* 46 */
+ counts[EXTRACT256(array,6)] += 1; /* 30 */
+ counts[EXTRACT256(array,7)] += 1; /* 14 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 125 */
+ counts[EXTRACT256(array,1)] += 1; /* 109 */
+ counts[EXTRACT256(array,2)] += 1; /* 93 */
+ counts[EXTRACT256(array,3)] += 1; /* 77 */
+ counts[EXTRACT256(array,4)] += 1; /* 61 */
+ counts[EXTRACT256(array,5)] += 1; /* 45 */
+ counts[EXTRACT256(array,6)] += 1; /* 29 */
+ counts[EXTRACT256(array,7)] += 1; /* 13 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 124 */
+ counts[EXTRACT256(array,1)] += 1; /* 108 */
+ counts[EXTRACT256(array,2)] += 1; /* 92 */
+ counts[EXTRACT256(array,3)] += 1; /* 76 */
+ counts[EXTRACT256(array,4)] += 1; /* 60 */
+ counts[EXTRACT256(array,5)] += 1; /* 44 */
+ counts[EXTRACT256(array,6)] += 1; /* 28 */
+ counts[EXTRACT256(array,7)] += 1; /* 12 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 123 */
+ counts[EXTRACT256(array,1)] += 1; /* 107 */
+ counts[EXTRACT256(array,2)] += 1; /* 91 */
+ counts[EXTRACT256(array,3)] += 1; /* 75 */
+ counts[EXTRACT256(array,4)] += 1; /* 59 */
+ counts[EXTRACT256(array,5)] += 1; /* 43 */
+ counts[EXTRACT256(array,6)] += 1; /* 27 */
+ counts[EXTRACT256(array,7)] += 1; /* 11 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_srli_epi32(current,20);
+ counts[EXTRACT256(array,0)] += 1; /* 122 */
+ counts[EXTRACT256(array,1)] += 1; /* 106 */
+ counts[EXTRACT256(array,2)] += 1; /* 90 */
+ counts[EXTRACT256(array,3)] += 1; /* 74 */
+ counts[EXTRACT256(array,4)] += 1; /* 58 */
+ counts[EXTRACT256(array,5)] += 1; /* 42 */
+ counts[EXTRACT256(array,6)] += 1; /* 26 */
+ counts[EXTRACT256(array,7)] += 1; /* 10 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 121 */
+ counts[EXTRACT256(array,1)] += 1; /* 105 */
+ counts[EXTRACT256(array,2)] += 1; /* 89 */
+ counts[EXTRACT256(array,3)] += 1; /* 73 */
+ counts[EXTRACT256(array,4)] += 1; /* 57 */
+ counts[EXTRACT256(array,5)] += 1; /* 41 */
+ counts[EXTRACT256(array,6)] += 1; /* 25 */
+ counts[EXTRACT256(array,7)] += 1; /* 9 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 120 */
+ counts[EXTRACT256(array,1)] += 1; /* 104 */
+ counts[EXTRACT256(array,2)] += 1; /* 88 */
+ counts[EXTRACT256(array,3)] += 1; /* 72 */
+ counts[EXTRACT256(array,4)] += 1; /* 56 */
+ counts[EXTRACT256(array,5)] += 1; /* 40 */
+ counts[EXTRACT256(array,6)] += 1; /* 24 */
+ counts[EXTRACT256(array,7)] += 1; /* 8 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 119 */
+ counts[EXTRACT256(array,1)] += 1; /* 103 */
+ counts[EXTRACT256(array,2)] += 1; /* 87 */
+ counts[EXTRACT256(array,3)] += 1; /* 71 */
+ counts[EXTRACT256(array,4)] += 1; /* 55 */
+ counts[EXTRACT256(array,5)] += 1; /* 39 */
+ counts[EXTRACT256(array,6)] += 1; /* 23 */
+ counts[EXTRACT256(array,7)] += 1; /* 7 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 118 */
+ counts[EXTRACT256(array,1)] += 1; /* 102 */
+ counts[EXTRACT256(array,2)] += 1; /* 86 */
+ counts[EXTRACT256(array,3)] += 1; /* 70 */
+ counts[EXTRACT256(array,4)] += 1; /* 54 */
+ counts[EXTRACT256(array,5)] += 1; /* 38 */
+ counts[EXTRACT256(array,6)] += 1; /* 22 */
+ counts[EXTRACT256(array,7)] += 1; /* 6 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 117 */
+ counts[EXTRACT256(array,1)] += 1; /* 101 */
+ counts[EXTRACT256(array,2)] += 1; /* 85 */
+ counts[EXTRACT256(array,3)] += 1; /* 69 */
+ counts[EXTRACT256(array,4)] += 1; /* 53 */
+ counts[EXTRACT256(array,5)] += 1; /* 37 */
+ counts[EXTRACT256(array,6)] += 1; /* 21 */
+ counts[EXTRACT256(array,7)] += 1; /* 5 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 116 */
+ counts[EXTRACT256(array,1)] += 1; /* 100 */
+ counts[EXTRACT256(array,2)] += 1; /* 84 */
+ counts[EXTRACT256(array,3)] += 1; /* 68 */
+ counts[EXTRACT256(array,4)] += 1; /* 52 */
+ counts[EXTRACT256(array,5)] += 1; /* 36 */
+ counts[EXTRACT256(array,6)] += 1; /* 20 */
+ counts[EXTRACT256(array,7)] += 1; /* 4 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 115 */
+ counts[EXTRACT256(array,1)] += 1; /* 99 */
+ counts[EXTRACT256(array,2)] += 1; /* 83 */
+ counts[EXTRACT256(array,3)] += 1; /* 67 */
+ counts[EXTRACT256(array,4)] += 1; /* 51 */
+ counts[EXTRACT256(array,5)] += 1; /* 35 */
+ counts[EXTRACT256(array,6)] += 1; /* 19 */
+ counts[EXTRACT256(array,7)] += 1; /* 3 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 114 */
+ counts[EXTRACT256(array,1)] += 1; /* 98 */
+ counts[EXTRACT256(array,2)] += 1; /* 82 */
+ counts[EXTRACT256(array,3)] += 1; /* 66 */
+ counts[EXTRACT256(array,4)] += 1; /* 50 */
+ counts[EXTRACT256(array,5)] += 1; /* 34 */
+ counts[EXTRACT256(array,6)] += 1; /* 18 */
+ counts[EXTRACT256(array,7)] += 1; /* 2 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 113 */
+ counts[EXTRACT256(array,1)] += 1; /* 97 */
+ counts[EXTRACT256(array,2)] += 1; /* 81 */
+ counts[EXTRACT256(array,3)] += 1; /* 65 */
+ counts[EXTRACT256(array,4)] += 1; /* 49 */
+ counts[EXTRACT256(array,5)] += 1; /* 33 */
+ counts[EXTRACT256(array,6)] += 1; /* 17 */
+ counts[EXTRACT256(array,7)] += 1; /* 1 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask6);
+ counts[EXTRACT256(array,0)] += 1; /* 112 */
+ counts[EXTRACT256(array,1)] += 1; /* 96 */
+ counts[EXTRACT256(array,2)] += 1; /* 80 */
+ counts[EXTRACT256(array,3)] += 1; /* 64 */
+ counts[EXTRACT256(array,4)] += 1; /* 48 */
+ counts[EXTRACT256(array,5)] += 1; /* 32 */
+ counts[EXTRACT256(array,6)] += 1; /* 16 */
+ counts[EXTRACT256(array,7)] += 1; /* 0 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
-
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_6mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -23065,101 +42559,79 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK6; /* 0 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (low_rc >> 2) & MASK6; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (low_rc >> 4) & MASK6; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (low_rc >> 6) & MASK6; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (low_rc >> 8) & MASK6; /* 4 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (low_rc >> 10) & MASK6; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rc >> 12) & MASK6; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rc >> 14) & MASK6; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rc >> 16) & MASK6; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rc >> 18) & MASK6; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = low_rc >> 20; /* 10, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
#else
@@ -23172,38 +42644,30 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -23216,38 +42680,30 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
@@ -23260,29 +42716,23 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
#endif
@@ -23293,47 +42743,37 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 11 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = (oligo >> 2) & MASK6; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (oligo >> 4) & MASK6; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (oligo >> 6) & MASK6; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = (oligo >> 8) & MASK6; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -23346,48 +42786,38 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = (oligo >> 8) & MASK6; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -23395,101 +42825,79 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK6; /* 16 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (high_rc >> 2) & MASK6; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (high_rc >> 4) & MASK6; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (high_rc >> 6) & MASK6; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (high_rc >> 8) & MASK6; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (high_rc >> 10) & MASK6; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rc >> 12) & MASK6; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rc >> 14) & MASK6; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rc >> 16) & MASK6; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rc >> 18) & MASK6; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = high_rc >> 20; /* 26, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
#else
@@ -23502,38 +42910,30 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -23546,38 +42946,30 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
@@ -23590,29 +42982,23 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
#endif
@@ -23623,47 +43009,37 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK6; /* 27 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
masked = (oligo >> 2) & MASK6; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (oligo >> 4) & MASK6; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (oligo >> 6) & MASK6; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = (oligo >> 8) & MASK6; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -23674,59 +43050,326 @@ store_6mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
_masked = _mm_and_si128(_oligo, mask6);
#endif
- masked = EXTRACT(_masked,0);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ masked = EXTRACT(_masked,0);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+ masked = EXTRACT(_masked,1);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ masked = EXTRACT(_masked,2);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ masked = EXTRACT(_masked,3);
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+
+ masked = (oligo >> 8) & MASK6; /* 31 */
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+#endif
+
+ return chrpos - 32;
+}
+
+#else /* HAVE_AVX2 */
+
+static int
+store_6mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+
+ oligo = low_rc >> 22; /* For 15..11 */
+ oligo |= high_rc << 10;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+
+ oligo = high_rc >> 22; /* For 31..27 */
+ oligo |= nextlow_rc << 10;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask6);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
- masked = EXTRACT(_masked,1);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
- masked = EXTRACT(_masked,2);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
- masked = EXTRACT(_masked,3);
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
- masked = (oligo >> 8) & MASK6; /* 31 */
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
-#endif
return chrpos - 32;
}
+#endif /* HAVE_AVX2 */
+
+
+
+#if !defined(HAVE_AVX2)
static void
-count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+count_5mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
#elif defined(SIMD_MASK_THEN_STORE)
@@ -23739,51 +43382,51 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK5; /* 0 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 2) & MASK5; /* 1 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 4) & MASK5; /* 2 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 6) & MASK5; /* 3 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 8) & MASK5; /* 4 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 10) & MASK5; /* 5 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 12) & MASK5; /* 6 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 14) & MASK5; /* 7 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 16) & MASK5; /* 8 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 18) & MASK5; /* 9 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = (low_rc >> 20) & MASK5; /* 10 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = low_rc >> 22; /* 11, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
#else
@@ -23795,19 +43438,19 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("0 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("1 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("2 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("3 %04X => %d\n",masked,counts[masked]));
@@ -23819,19 +43462,19 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("4 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("5 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("6 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("7 %04X => %d\n",masked,counts[masked]));
@@ -23843,19 +43486,19 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("8 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("9 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("10 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("11 %04X => %d\n",masked,counts[masked]));
#endif
@@ -23865,19 +43508,19 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 12 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 2) & MASK5; /* 13 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 4) & MASK5; /* 14 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = (oligo >> 6) & MASK5; /* 15 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#else
@@ -23889,70 +43532,70 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("12 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("13 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("14 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("15 %04X => %d\n",masked,counts[masked]));
#endif
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK5; /* 16 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 2) & MASK5; /* 17 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 4) & MASK5; /* 18 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 6) & MASK5; /* 19 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 8) & MASK5; /* 20 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 10) & MASK5; /* 21 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 12) & MASK5; /* 22 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 14) & MASK5; /* 23 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 16) & MASK5; /* 24 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("24 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 18) & MASK5; /* 25 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("25 %04X => %d\n",masked,counts[masked]));
masked = (high_rc >> 20) & MASK5; /* 26 */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("26 %04X => %d\n",masked,counts[masked]));
masked = high_rc >> 22; /* 27, No mask necessary */
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("27 %04X => %d\n",masked,counts[masked]));
#else
@@ -23964,19 +43607,19 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("16 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("17 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("18 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("19 %04X => %d\n",masked,counts[masked]));
@@ -23988,19 +43631,19 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
#endif
masked = EXTRACT(_masked,0);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("20 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,1);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("21 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,2);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("22 %04X => %d\n",masked,counts[masked]));
masked = EXTRACT(_masked,3);
- counts[masked] += 1;
+ INCR_COUNT(counts[masked],inquery[masked]);
debug(printf("23 %04X => %d\n",masked,counts[masked]));
@@ -24011,72 +43654,396 @@ count_5mers_rev (Count_T *counts, Genomecomp_T low_rc, Genomecomp_T high_rc, Gen
_masked = _mm_and_si128(_oligo, mask5);
#endif
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("24 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("25 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("26 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("27 %04X => %d\n",masked,counts[masked]));
+#endif
+
+
+ oligo = high_rc >> 24; /* For 31..28 */
+ oligo |= nextlow_rc << 8;
+
+#ifdef INDIVIDUAL_SHIFTS
+ masked = oligo & MASK5; /* 28 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 2) & MASK5; /* 29 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 4) & MASK5; /* 30 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = (oligo >> 6) & MASK5; /* 31 */
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+
+#else
+ _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
+#ifdef SIMD_MASK_THEN_STORE
+ _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
+#else
+ _masked = _mm_and_si128(_oligo, mask5);
+#endif
+
+ masked = EXTRACT(_masked,0);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("28 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,1);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("29 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,2);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("30 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT(_masked,3);
+ INCR_COUNT(counts[masked],inquery[masked]);
+ debug(printf("31 %04X => %d\n",masked,counts[masked]));
+#endif
+
+ return;
+}
+
+#else /* HAVE_AVX2 */
+
+static void
+count_5mers_rev (Count_T *counts, Inquery_T *inquery, Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("0 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("1 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("2 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("3 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("4 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("5 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("6 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("7 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("8 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("9 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("10 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("11 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ oligo = low_rc >> 24; /* For 15..12 */
+ oligo |= high_rc << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("12 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("13 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("14 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("15 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
+ counts[masked] += 1;
+ debug(printf("16 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,1);
+ counts[masked] += 1;
+ debug(printf("17 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,2);
+ counts[masked] += 1;
+ debug(printf("18 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,3);
+ counts[masked] += 1;
+ debug(printf("19 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,4);
+ counts[masked] += 1;
+ debug(printf("20 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,5);
+ counts[masked] += 1;
+ debug(printf("21 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,6);
+ counts[masked] += 1;
+ debug(printf("22 %04X => %d\n",masked,counts[masked]));
+
+ masked = EXTRACT256(_masked,7);
+ counts[masked] += 1;
+ debug(printf("23 %04X => %d\n",masked,counts[masked]));
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ /* _counts_after = _mm256_and_si256(_counts_after,low8); */
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(_masked,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(_masked,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(_masked,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(_masked,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("24 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("25 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("26 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("27 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
oligo = high_rc >> 24; /* For 31..28 */
oligo |= nextlow_rc << 8;
-#ifdef INDIVIDUAL_SHIFTS
- masked = oligo & MASK5; /* 28 */
- counts[masked] += 1;
- debug(printf("28 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 2) & MASK5; /* 29 */
- counts[masked] += 1;
- debug(printf("29 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 4) & MASK5; /* 30 */
- counts[masked] += 1;
- debug(printf("30 %04X => %d\n",masked,counts[masked]));
-
- masked = (oligo >> 6) & MASK5; /* 31 */
- counts[masked] += 1;
- debug(printf("31 %04X => %d\n",masked,counts[masked]));
-
-#else
- _oligo = _mm_setr_epi32(oligo, oligo >> 2, oligo >> 4, oligo >> 6);
-#ifdef SIMD_MASK_THEN_STORE
- _mm_store_si128((__m128i *) _masked,_mm_and_si128(_oligo, mask5));
-#else
- _masked = _mm_and_si128(_oligo, mask5);
-#endif
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
- masked = EXTRACT(_masked,0);
+ masked = EXTRACT256(_masked,0);
counts[masked] += 1;
debug(printf("28 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,1);
+ masked = EXTRACT256(_masked,1);
counts[masked] += 1;
debug(printf("29 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,2);
+ masked = EXTRACT256(_masked,2);
counts[masked] += 1;
debug(printf("30 %04X => %d\n",masked,counts[masked]));
- masked = EXTRACT(_masked,3);
+ masked = EXTRACT256(_masked,3);
counts[masked] += 1;
debug(printf("31 %04X => %d\n",masked,counts[masked]));
-#endif
+
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,_masked,/*shift*/4);
+ _counts_after = _mm256_and_si256(_counts_after,low4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(_masked,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(_masked,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(_masked,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(_masked,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
return;
}
+#endif /* HAVE_AVX2 */
+
+
/* Expecting current to have {low0_rc, high0_rc, low1_rc, high1_rc},
and next to have {high0_rc, low1_rc, high1_rc, nextlow_rc} */
@@ -24107,116 +44074,1577 @@ extract_5mers_rev_simd (__m128i *out, __m128i current, __m128i next) {
return;
}
+#ifdef HAVE_AVX2
+static void
+extract_5mers_rev_simd_128 (__m256i *out, __m256i current, __m256i next) {
+ __m256i oligo;
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,24), _mm256_slli_epi32(next,8));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( oligo, bigmask5));
+
+ _mm256_store_si256(out++, _mm256_srli_epi32(current,22));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,20), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask5));
+ _mm256_store_si256(out++, _mm256_and_si256( current, bigmask5));
+
+ return;
+}
+#endif
+
+
static void
-count_5mers_rev_simd (Count_T *counts, __m128i current, __m128i next) {
+count_5mers_rev_simd (Count_T *counts, Inquery_T *inquery, __m128i current, __m128i next) {
__m128i oligo;
+#ifdef HAVE_SSE4_1
+ __m128i array;
+#else
Genomecomp_T array[4];
+#endif
+#if defined(HAVE_AVX2) && defined(CHECK_FOR_OVERFLOW)
+ __m128i _counts_after, _counts_neg;
+#endif
oligo = _mm_or_si128( _mm_srli_epi32(current,24), _mm_slli_epi32(next,8));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,6), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,6), mask5));
- counts[array[0]] += 1; /* 63 */
- counts[array[1]] += 1; /* 47 */
- counts[array[2]] += 1; /* 31 */
- counts[array[3]] += 1; /* 15 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("47 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("31 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("15 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 63 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 47 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 31 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 15 */
+#endif
+ debug(printf("63 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,4), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,4), mask5));
- counts[array[0]] += 1; /* 62 */
- counts[array[1]] += 1; /* 46 */
- counts[array[2]] += 1; /* 30 */
- counts[array[3]] += 1; /* 14 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("46 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("30 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("14 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 62 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 46 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 30 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 14 */
+#endif
+ debug(printf("62 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(oligo,2), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(oligo,2), mask5));
- counts[array[0]] += 1; /* 61 */
- counts[array[1]] += 1; /* 45 */
- counts[array[2]] += 1; /* 29 */
- counts[array[3]] += 1; /* 13 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("45 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("29 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("13 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 61 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 45 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 29 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 13 */
+#endif
+ debug(printf("61 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( oligo, mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( oligo, mask5));
- counts[array[0]] += 1; /* 60 */
- counts[array[1]] += 1; /* 44 */
- counts[array[2]] += 1; /* 28 */
- counts[array[3]] += 1; /* 12 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("44 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("28 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("12 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 60 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 44 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 28 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 12 */
+#endif
+ debug(printf("60 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_srli_epi32(current,22);
+#else
_mm_store_si128((__m128i *) array, _mm_srli_epi32(current,22));
- counts[array[0]] += 1; /* 59 */
- counts[array[1]] += 1; /* 43 */
- counts[array[2]] += 1; /* 27 */
- counts[array[3]] += 1; /* 11 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("43 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("27 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("11 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 59 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 43 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 27 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 11 */
+#endif
+ debug(printf("59 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,20), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,20), mask5));
- counts[array[0]] += 1; /* 58 */
- counts[array[1]] += 1; /* 42 */
- counts[array[2]] += 1; /* 26 */
- counts[array[3]] += 1; /* 10 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("42 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("26 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("10 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 58 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 42 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 26 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 10 */
+#endif
+ debug(printf("58 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,18), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,18), mask5));
- counts[array[0]] += 1; /* 57 */
- counts[array[1]] += 1; /* 41 */
- counts[array[2]] += 1; /* 25 */
- counts[array[3]] += 1; /* 9 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("41 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("25 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("9 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 57 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 41 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 25 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 9 */
+#endif
+ debug(printf("57 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,16), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,16), mask5));
- counts[array[0]] += 1; /* 56 */
- counts[array[1]] += 1; /* 50 */
- counts[array[2]] += 1; /* 24 */
- counts[array[3]] += 1; /* 8 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("40 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("24 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("8 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 56 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 40 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 24 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 8 */
+#endif
+ debug(printf("56 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,14), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,14), mask5));
- counts[array[0]] += 1; /* 55 */
- counts[array[1]] += 1; /* 39 */
- counts[array[2]] += 1; /* 23 */
- counts[array[3]] += 1; /* 7 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("39 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("23 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("7 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 55 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 39 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 23 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 7 */
+#endif
+ debug(printf("55 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,12), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,12), mask5));
- counts[array[0]] += 1; /* 54 */
- counts[array[1]] += 1; /* 38 */
- counts[array[2]] += 1; /* 22 */
- counts[array[3]] += 1; /* 6 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("38 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("22 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("6 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 54 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 38 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 22 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 6 */
+#endif
+ debug(printf("54 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,10), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,10), mask5));
- counts[array[0]] += 1; /* 53 */
- counts[array[1]] += 1; /* 37 */
- counts[array[2]] += 1; /* 21 */
- counts[array[3]] += 1; /* 5 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("37 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("21 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("5 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 53 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 37 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 21 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 5 */
+#endif
+ debug(printf("53 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,8), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,8), mask5));
- counts[array[0]] += 1; /* 52 */
- counts[array[1]] += 1; /* 36 */
- counts[array[2]] += 1; /* 20 */
- counts[array[3]] += 1; /* 4 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("36 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("20 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("4 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 52 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 36 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 20 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 4 */
+#endif
+ debug(printf("52 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,6), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,6), mask5));
- counts[array[0]] += 1; /* 51 */
- counts[array[1]] += 1; /* 35 */
- counts[array[2]] += 1; /* 19 */
- counts[array[3]] += 1; /* 3 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("35 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("19 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("3 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 51 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 35 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 19 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 3 */
+#endif
+ debug(printf("51 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,4), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,4), mask5));
- counts[array[0]] += 1; /* 50 */
- counts[array[1]] += 1; /* 34 */
- counts[array[2]] += 1; /* 18 */
- counts[array[3]] += 1; /* 2 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("34 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("18 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("2 %04X => %d\n",array[3],counts[array[3]]));
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 50 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 34 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 18 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 2 */
+#endif
+ debug(printf("50 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( _mm_srli_epi32(current,2), mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( _mm_srli_epi32(current,2), mask5));
- counts[array[0]] += 1; /* 49 */
- counts[array[1]] += 1; /* 33 */
- counts[array[2]] += 1; /* 17 */
- counts[array[3]] += 1; /* 1 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("33 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("17 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("1 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 49 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 33 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 17 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 1 */
+#endif
+ debug(printf("49 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+#ifdef HAVE_SSE4_1
+ array = _mm_and_si128( current, mask5);
+#else
_mm_store_si128((__m128i *) array, _mm_and_si128( current, mask5));
- counts[array[0]] += 1; /* 48 */
- counts[array[1]] += 1; /* 32 */
- counts[array[2]] += 1; /* 16 */
- counts[array[3]] += 1; /* 0 */
+#endif
+#ifdef HAVE_AVX2
+ counts[EXTRACT(array,0)] += 1;
+ counts[EXTRACT(array,1)] += 1;
+ counts[EXTRACT(array,2)] += 1;
+ counts[EXTRACT(array,3)] += 1;
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm_cmpgt_epi32(_counts_after,maxcount128);
+ if (_mm_testz_si128(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT(_counts_neg,0)) {
+ inquery[EXTRACT(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,1)) {
+ inquery[EXTRACT(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,2)) {
+ inquery[EXTRACT(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT(_counts_neg,3)) {
+ inquery[EXTRACT(array,3)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",array[0],counts[array[0]]));
+ debug(printf("32 %04X => %d\n",array[1],counts[array[1]]));
+ debug(printf("16 %04X => %d\n",array[2],counts[array[2]]));
+ debug(printf("0 %04X => %d\n",array[3],counts[array[3]]));
+
+#else
+ INCR_COUNT(counts[EXTRACT(array,0)],inquery[EXTRACT(array,0)]); /* 48 */
+ INCR_COUNT(counts[EXTRACT(array,1)],inquery[EXTRACT(array,1)]); /* 32 */
+ INCR_COUNT(counts[EXTRACT(array,2)],inquery[EXTRACT(array,2)]); /* 16 */
+ INCR_COUNT(counts[EXTRACT(array,3)],inquery[EXTRACT(array,3)]); /* 0 */
+#endif
+ debug(printf("48 %04X => %d\n",EXTRACT(array,0),counts[EXTRACT(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT(array,1),counts[EXTRACT(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT(array,2),counts[EXTRACT(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT(array,3),counts[EXTRACT(array,3)]));
+
+ return;
+}
+#endif
+
+
+#ifdef HAVE_AVX2
+static void
+count_5mers_rev_simd_128 (Count_T *counts, Inquery_T *inquery, __m256i current, __m256i next) {
+ __m256i oligo;
+ __m256i array;
+#ifdef CHECK_FOR_OVERFLOW
+ __m256i _counts_after, _counts_neg;
+#endif
+
+ oligo = _mm256_or_si256( _mm256_srli_epi32(current,24), _mm256_slli_epi32(next,8));
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,6), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 127 */
+ counts[EXTRACT256(array,1)] += 1; /* 111 */
+ counts[EXTRACT256(array,2)] += 1; /* 95 */
+ counts[EXTRACT256(array,3)] += 1; /* 79 */
+ counts[EXTRACT256(array,4)] += 1; /* 63 */
+ counts[EXTRACT256(array,5)] += 1; /* 47 */
+ counts[EXTRACT256(array,6)] += 1; /* 31 */
+ counts[EXTRACT256(array,7)] += 1; /* 15 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("63 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("47 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("31 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("15 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,4), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 126 */
+ counts[EXTRACT256(array,1)] += 1; /* 110 */
+ counts[EXTRACT256(array,2)] += 1; /* 94 */
+ counts[EXTRACT256(array,3)] += 1; /* 78 */
+ counts[EXTRACT256(array,4)] += 1; /* 62 */
+ counts[EXTRACT256(array,5)] += 1; /* 46 */
+ counts[EXTRACT256(array,6)] += 1; /* 30 */
+ counts[EXTRACT256(array,7)] += 1; /* 14 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("62 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("46 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("30 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("14 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(oligo,2), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 125 */
+ counts[EXTRACT256(array,1)] += 1; /* 109 */
+ counts[EXTRACT256(array,2)] += 1; /* 93 */
+ counts[EXTRACT256(array,3)] += 1; /* 77 */
+ counts[EXTRACT256(array,4)] += 1; /* 61 */
+ counts[EXTRACT256(array,5)] += 1; /* 45 */
+ counts[EXTRACT256(array,6)] += 1; /* 29 */
+ counts[EXTRACT256(array,7)] += 1; /* 13 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("61 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("45 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("29 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("13 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( oligo, bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 124 */
+ counts[EXTRACT256(array,1)] += 1; /* 108 */
+ counts[EXTRACT256(array,2)] += 1; /* 92 */
+ counts[EXTRACT256(array,3)] += 1; /* 76 */
+ counts[EXTRACT256(array,4)] += 1; /* 60 */
+ counts[EXTRACT256(array,5)] += 1; /* 44 */
+ counts[EXTRACT256(array,6)] += 1; /* 28 */
+ counts[EXTRACT256(array,7)] += 1; /* 12 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("60 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("44 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("28 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("12 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_srli_epi32(current,22);
+ counts[EXTRACT256(array,0)] += 1; /* 123 */
+ counts[EXTRACT256(array,1)] += 1; /* 107 */
+ counts[EXTRACT256(array,2)] += 1; /* 91 */
+ counts[EXTRACT256(array,3)] += 1; /* 75 */
+ counts[EXTRACT256(array,4)] += 1; /* 59 */
+ counts[EXTRACT256(array,5)] += 1; /* 43 */
+ counts[EXTRACT256(array,6)] += 1; /* 27 */
+ counts[EXTRACT256(array,7)] += 1; /* 11 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("59 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("43 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("27 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("11 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,20), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 122 */
+ counts[EXTRACT256(array,1)] += 1; /* 106 */
+ counts[EXTRACT256(array,2)] += 1; /* 90 */
+ counts[EXTRACT256(array,3)] += 1; /* 74 */
+ counts[EXTRACT256(array,4)] += 1; /* 58 */
+ counts[EXTRACT256(array,5)] += 1; /* 42 */
+ counts[EXTRACT256(array,6)] += 1; /* 26 */
+ counts[EXTRACT256(array,7)] += 1; /* 10 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("58 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("42 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("26 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("10 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,18), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 121 */
+ counts[EXTRACT256(array,1)] += 1; /* 105 */
+ counts[EXTRACT256(array,2)] += 1; /* 89 */
+ counts[EXTRACT256(array,3)] += 1; /* 73 */
+ counts[EXTRACT256(array,4)] += 1; /* 57 */
+ counts[EXTRACT256(array,5)] += 1; /* 41 */
+ counts[EXTRACT256(array,6)] += 1; /* 25 */
+ counts[EXTRACT256(array,7)] += 1; /* 9 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("57 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("41 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("25 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("9 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,16), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 120 */
+ counts[EXTRACT256(array,1)] += 1; /* 104 */
+ counts[EXTRACT256(array,2)] += 1; /* 88 */
+ counts[EXTRACT256(array,3)] += 1; /* 72 */
+ counts[EXTRACT256(array,4)] += 1; /* 56 */
+ counts[EXTRACT256(array,5)] += 1; /* 40 */
+ counts[EXTRACT256(array,6)] += 1; /* 24 */
+ counts[EXTRACT256(array,7)] += 1; /* 8 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("56 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("40 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("24 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("8 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,14), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 119 */
+ counts[EXTRACT256(array,1)] += 1; /* 103 */
+ counts[EXTRACT256(array,2)] += 1; /* 87 */
+ counts[EXTRACT256(array,3)] += 1; /* 71 */
+ counts[EXTRACT256(array,4)] += 1; /* 55 */
+ counts[EXTRACT256(array,5)] += 1; /* 39 */
+ counts[EXTRACT256(array,6)] += 1; /* 23 */
+ counts[EXTRACT256(array,7)] += 1; /* 7 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("55 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("39 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("23 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("7 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,12), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 118 */
+ counts[EXTRACT256(array,1)] += 1; /* 102 */
+ counts[EXTRACT256(array,2)] += 1; /* 86 */
+ counts[EXTRACT256(array,3)] += 1; /* 70 */
+ counts[EXTRACT256(array,4)] += 1; /* 54 */
+ counts[EXTRACT256(array,5)] += 1; /* 38 */
+ counts[EXTRACT256(array,6)] += 1; /* 22 */
+ counts[EXTRACT256(array,7)] += 1; /* 6 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("54 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("38 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("22 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("6 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,10), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 117 */
+ counts[EXTRACT256(array,1)] += 1; /* 101 */
+ counts[EXTRACT256(array,2)] += 1; /* 85 */
+ counts[EXTRACT256(array,3)] += 1; /* 69 */
+ counts[EXTRACT256(array,4)] += 1; /* 53 */
+ counts[EXTRACT256(array,5)] += 1; /* 37 */
+ counts[EXTRACT256(array,6)] += 1; /* 21 */
+ counts[EXTRACT256(array,7)] += 1; /* 5 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("53 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("37 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("21 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("5 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,8), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 116 */
+ counts[EXTRACT256(array,1)] += 1; /* 100 */
+ counts[EXTRACT256(array,2)] += 1; /* 84 */
+ counts[EXTRACT256(array,3)] += 1; /* 68 */
+ counts[EXTRACT256(array,4)] += 1; /* 52 */
+ counts[EXTRACT256(array,5)] += 1; /* 36 */
+ counts[EXTRACT256(array,6)] += 1; /* 20 */
+ counts[EXTRACT256(array,7)] += 1; /* 4 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("52 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("36 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("20 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("4 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,6), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 115 */
+ counts[EXTRACT256(array,1)] += 1; /* 99 */
+ counts[EXTRACT256(array,2)] += 1; /* 83 */
+ counts[EXTRACT256(array,3)] += 1; /* 67 */
+ counts[EXTRACT256(array,4)] += 1; /* 51 */
+ counts[EXTRACT256(array,5)] += 1; /* 35 */
+ counts[EXTRACT256(array,6)] += 1; /* 19 */
+ counts[EXTRACT256(array,7)] += 1; /* 3 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("51 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("35 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("19 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("3 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,4), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 114 */
+ counts[EXTRACT256(array,1)] += 1; /* 98 */
+ counts[EXTRACT256(array,2)] += 1; /* 82 */
+ counts[EXTRACT256(array,3)] += 1; /* 66 */
+ counts[EXTRACT256(array,4)] += 1; /* 50 */
+ counts[EXTRACT256(array,5)] += 1; /* 34 */
+ counts[EXTRACT256(array,6)] += 1; /* 18 */
+ counts[EXTRACT256(array,7)] += 1; /* 2 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("50 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("34 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("18 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("2 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( _mm256_srli_epi32(current,2), bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 113 */
+ counts[EXTRACT256(array,1)] += 1; /* 97 */
+ counts[EXTRACT256(array,2)] += 1; /* 81 */
+ counts[EXTRACT256(array,3)] += 1; /* 65 */
+ counts[EXTRACT256(array,4)] += 1; /* 49 */
+ counts[EXTRACT256(array,5)] += 1; /* 33 */
+ counts[EXTRACT256(array,6)] += 1; /* 17 */
+ counts[EXTRACT256(array,7)] += 1; /* 1 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("49 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("33 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("17 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("1 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
+
+ array = _mm256_and_si256( current, bigmask5);
+ counts[EXTRACT256(array,0)] += 1; /* 112 */
+ counts[EXTRACT256(array,1)] += 1; /* 96 */
+ counts[EXTRACT256(array,2)] += 1; /* 80 */
+ counts[EXTRACT256(array,3)] += 1; /* 64 */
+ counts[EXTRACT256(array,4)] += 1; /* 48 */
+ counts[EXTRACT256(array,5)] += 1; /* 32 */
+ counts[EXTRACT256(array,6)] += 1; /* 16 */
+ counts[EXTRACT256(array,7)] += 1; /* 0 */
+#ifdef CHECK_FOR_OVERFLOW
+ _counts_after = _mm256_i32gather_epi32(counts,array,/*scale*/4);
+ _counts_neg = _mm256_cmpgt_epi32(_counts_after,maxcount256);
+ if (_mm256_testz_si256(_counts_neg,_counts_neg) == 0) {
+ debug(printf("Exceeded maximum counts\n"));
+ if (EXTRACT256(_counts_neg,0)) {
+ inquery[EXTRACT256(array,0)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,1)) {
+ inquery[EXTRACT256(array,1)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,2)) {
+ inquery[EXTRACT256(array,2)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,3)) {
+ inquery[EXTRACT256(array,3)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,4)) {
+ inquery[EXTRACT256(array,4)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,5)) {
+ inquery[EXTRACT256(array,5)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,6)) {
+ inquery[EXTRACT256(array,6)] = INQUERY_FALSE;
+ }
+ if (EXTRACT256(_counts_neg,7)) {
+ inquery[EXTRACT256(array,7)] = INQUERY_FALSE;
+ }
+ }
+#endif /* CHECK_FOR_OVERFLOW */
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,0),counts[EXTRACT256(array,0)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,1),counts[EXTRACT256(array,1)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,2),counts[EXTRACT256(array,2)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,3),counts[EXTRACT256(array,3)]));
+ debug(printf("48 %04X => %d\n",EXTRACT256(array,4),counts[EXTRACT256(array,4)]));
+ debug(printf("32 %04X => %d\n",EXTRACT256(array,5),counts[EXTRACT256(array,5)]));
+ debug(printf("16 %04X => %d\n",EXTRACT256(array,6),counts[EXTRACT256(array,6)]));
+ debug(printf("0 %04X => %d\n",EXTRACT256(array,7),counts[EXTRACT256(array,7)]));
return;
}
#endif
+#if !defined(HAVE_AVX2)
+
static int
-store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts,
+store_5mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
Genomecomp_T masked, oligo;
#ifdef INDIVIDUAL_SHIFTS
@@ -24231,110 +45659,86 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = low_rc & MASK5; /* 0 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = (low_rc >> 2) & MASK5; /* 1 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = (low_rc >> 4) & MASK5; /* 2 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = (low_rc >> 6) & MASK5; /* 3 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
masked = (low_rc >> 8) & MASK5; /* 4 */
- if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ if (counts[masked]) {
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = (low_rc >> 10) & MASK5; /* 5 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = (low_rc >> 12) & MASK5; /* 6 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = (low_rc >> 14) & MASK5; /* 7 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
masked = (low_rc >> 16) & MASK5; /* 8 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = (low_rc >> 18) & MASK5; /* 9 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = (low_rc >> 20) & MASK5; /* 10 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = low_rc >> 22; /* 11, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
#else
@@ -24347,38 +45751,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 1;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 2;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 3;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
}
@@ -24391,38 +45787,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 4;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 5;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 6;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 7;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
}
@@ -24435,38 +45823,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 8;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 9;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 10;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 11;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
}
#endif
@@ -24477,38 +45857,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 12 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = (oligo >> 2) & MASK5; /* 13 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = (oligo >> 4) & MASK5; /* 14 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = (oligo >> 6) & MASK5; /* 15 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#else
@@ -24521,38 +45893,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 12;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 13;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 14;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 15;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
}
#endif
@@ -24560,110 +45924,86 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = high_rc & MASK5; /* 16 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = (high_rc >> 2) & MASK5; /* 17 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = (high_rc >> 4) & MASK5; /* 18 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = (high_rc >> 6) & MASK5; /* 19 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
masked = (high_rc >> 8) & MASK5; /* 20 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = (high_rc >> 10) & MASK5; /* 21 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = (high_rc >> 12) & MASK5; /* 22 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = (high_rc >> 14) & MASK5; /* 23 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
masked = (high_rc >> 16) & MASK5; /* 24 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = (high_rc >> 18) & MASK5; /* 25 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = (high_rc >> 20) & MASK5; /* 26 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = high_rc >> 22; /* 27, No mask necessary */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
#else
@@ -24676,38 +46016,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 16;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 17;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 18;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 19;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
}
@@ -24720,38 +46052,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 20;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 21;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 22;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 23;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
}
@@ -24764,38 +46088,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 24;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 25;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 26;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 27;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
}
#endif
@@ -24806,38 +46122,30 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
#ifdef INDIVIDUAL_SHIFTS
masked = oligo & MASK5; /* 28 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = (oligo >> 2) & MASK5; /* 29 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = (oligo >> 4) & MASK5; /* 30 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = (oligo >> 6) & MASK5; /* 31 */
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#else
@@ -24850,48 +46158,314 @@ store_5mers_rev (Chrpos_T chrpos, Chrpos_T **pointers, Chrpos_T **positions, Cou
masked = EXTRACT(_masked,0);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 28;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
}
masked = EXTRACT(_masked,1);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 29;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
}
masked = EXTRACT(_masked,2);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 30;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
}
masked = EXTRACT(_masked,3);
if (counts[masked]) {
- if (pointers[masked] == positions[masked]) {
- counts[masked] = 0;
- } else {
- *(--pointers[masked]) = chrpos - 31;
- }
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
}
#endif
return chrpos - 32;
}
+#else /* HAVE_AVX2 */
+
+static int
+store_5mers_rev (Chrpos_T chrpos, Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts,
+ Genomecomp_T low_rc, Genomecomp_T high_rc, Genomecomp_T nextlow_rc) {
+ Genomecomp_T masked, oligo;
+ __m256i _oligo, _masked, _counts;
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(low_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos));
+ table[--pointers[masked]] = chrpos;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 1));
+ table[--pointers[masked]] = chrpos - 1;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 2));
+ table[--pointers[masked]] = chrpos - 2;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 3));
+ table[--pointers[masked]] = chrpos - 3;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 4));
+ table[--pointers[masked]] = chrpos - 4;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 5));
+ table[--pointers[masked]] = chrpos - 5;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 6));
+ table[--pointers[masked]] = chrpos - 6;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 7));
+ table[--pointers[masked]] = chrpos - 7;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 8));
+ table[--pointers[masked]] = chrpos - 8;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 9));
+ table[--pointers[masked]] = chrpos - 9;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 10));
+ table[--pointers[masked]] = chrpos - 10;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 11));
+ table[--pointers[masked]] = chrpos - 11;
+ }
+
+
+ oligo = low_rc >> 24; /* For 15..12 */
+ oligo |= high_rc << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 12));
+ table[--pointers[masked]] = chrpos - 12;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 13));
+ table[--pointers[masked]] = chrpos - 13;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 14));
+ table[--pointers[masked]] = chrpos - 14;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 15));
+ table[--pointers[masked]] = chrpos - 15;
+ }
+
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(high_rc),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 16));
+ table[--pointers[masked]] = chrpos - 16;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 17));
+ table[--pointers[masked]] = chrpos - 17;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 18));
+ table[--pointers[masked]] = chrpos - 18;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 19));
+ table[--pointers[masked]] = chrpos - 19;
+ }
+
+ if (EXTRACT256(_counts,4)) {
+ masked = EXTRACT256(_masked,4);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 20));
+ table[--pointers[masked]] = chrpos - 20;
+ }
+
+ if (EXTRACT256(_counts,5)) {
+ masked = EXTRACT256(_masked,5);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 21));
+ table[--pointers[masked]] = chrpos - 21;
+ }
+
+ if (EXTRACT256(_counts,6)) {
+ masked = EXTRACT256(_masked,6);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 22));
+ table[--pointers[masked]] = chrpos - 22;
+ }
+
+ if (EXTRACT256(_counts,7)) {
+ masked = EXTRACT256(_masked,7);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 23));
+ table[--pointers[masked]] = chrpos - 23;
+ }
+
+
+ _oligo = _mm256_srli_epi32(_oligo, 16);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 24));
+ table[--pointers[masked]] = chrpos - 24;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 25));
+ table[--pointers[masked]] = chrpos - 25;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 26));
+ table[--pointers[masked]] = chrpos - 26;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 27));
+ table[--pointers[masked]] = chrpos - 27;
+ }
+
+
+ oligo = high_rc >> 24; /* For 31..28 */
+ oligo |= nextlow_rc << 8;
+
+ _oligo = _mm256_srlv_epi32(_mm256_set1_epi32(oligo),shift0to14);
+ _masked = _mm256_and_si256(_oligo, bigmask5);
+ _counts = _mm256_i32gather_epi32(counts,_masked,/*scale*/4);
+
+ if (EXTRACT256(_counts,0)) {
+ masked = EXTRACT256(_masked,0);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 28));
+ table[--pointers[masked]] = chrpos - 28;
+ }
+
+ if (EXTRACT256(_counts,1)) {
+ masked = EXTRACT256(_masked,1);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 29));
+ table[--pointers[masked]] = chrpos - 29;
+ }
+
+ if (EXTRACT256(_counts,2)) {
+ masked = EXTRACT256(_masked,2);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 30));
+ table[--pointers[masked]] = chrpos - 30;
+ }
+
+ if (EXTRACT256(_counts,3)) {
+ masked = EXTRACT256(_masked,3);
+ assert(pointers[masked] > positions[masked]);
+ debug(printf("Storing masked %u at %u\n",masked,chrpos - 31));
+ table[--pointers[masked]] = chrpos - 31;
+ }
+
+ return chrpos - 32;
+}
+
+#endif /* HAVE_AVX2 */
+
+
#ifndef USE_SIMD_FOR_COUNTS
static void
-count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univcoord_T left_plus_length,
+count_positions_rev_std (Count_T *counts, Inquery_T *inquery, int indexsize, Univcoord_T left, Univcoord_T left_plus_length,
int genestrand) {
int startdiscard, enddiscard;
Genomecomp_T ptr, startptr, endptr, low_rc, high_rc, nextlow_rc,
@@ -24900,7 +46474,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
debug(printf("Starting count_positions_rev_std\n"));
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -24939,15 +46513,15 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- count_9mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ count_9mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 8) {
- count_8mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ count_8mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 7) {
- count_7mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ count_7mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 6) {
- count_6mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ count_6mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 5) {
- count_5mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ count_5mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -24981,15 +46555,15 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- count_9mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ count_9mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- count_8mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ count_8mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- count_7mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ count_7mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- count_6mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ count_6mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- count_5mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ count_5mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -25023,7 +46597,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
high_rc = ~high;
nextlow_rc = ~nextlow;
- count_9mers_rev(counts,low_rc,high_rc,nextlow_rc);
+ count_9mers_rev(counts,inquery,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -25052,7 +46626,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
high_rc = ~high;
nextlow_rc = ~nextlow;
- count_8mers_rev(counts,low_rc,high_rc,nextlow_rc);
+ count_8mers_rev(counts,inquery,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -25081,7 +46655,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
high_rc = ~high;
nextlow_rc = ~nextlow;
- count_7mers_rev(counts,low_rc,high_rc,nextlow_rc);
+ count_7mers_rev(counts,inquery,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -25110,7 +46684,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
high_rc = ~high;
nextlow_rc = ~nextlow;
- count_6mers_rev(counts,low_rc,high_rc,nextlow_rc);
+ count_6mers_rev(counts,inquery,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -25139,7 +46713,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
high_rc = ~high;
nextlow_rc = ~nextlow;
- count_5mers_rev(counts,low_rc,high_rc,nextlow_rc);
+ count_5mers_rev(counts,inquery,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
} else {
@@ -25174,15 +46748,15 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- count_9mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_9mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- count_8mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_8mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- count_7mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_7mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- count_6mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_6mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- count_5mers_rev_partial(counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_5mers_rev_partial(counts,inquery,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else {
abort();
}
@@ -25196,7 +46770,7 @@ count_positions_rev_std (Count_T *counts, int indexsize, Univcoord_T left, Univc
#ifdef USE_SIMD_FOR_COUNTS
static void
-count_positions_rev_simd (Count_T *counts, int indexsize,
+count_positions_rev_simd (Count_T *counts, Inquery_T *inquery, int indexsize,
Univcoord_T left, Univcoord_T left_plus_length, int genestrand) {
int startdiscard, enddiscard;
Genomecomp_T ptr, startptr, endptr, nextlow_rc, nextlow;
@@ -25208,10 +46782,16 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#else
Genomecomp_T low0_rc, high0_rc;
#endif
+#ifdef HAVE_AVX2
+ Genomecomp_T low2, high2, low3, high3;
+ __m256i current256, next256, temp256, shift256;
+ __m256i biginvert3;
+#endif
+
debug(printf("Starting count_positions_rev_simd\n"));
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -25223,6 +46803,10 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
enddiscard = left_plus_length % 32; /* (left+pos3) % 32 */
invert3 = _mm_set_epi32(0x00000000,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF);
+#ifdef HAVE_AVX2
+ biginvert3 = _mm256_set_epi32(0x00000000,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF);
+ shift256 = _mm256_setr_epi32(7,0,1,2,3,4,5,6);
+#endif
if (left_plus_length <= left) {
/* Skip */
@@ -25252,15 +46836,15 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- count_9mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ count_9mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 8) {
- count_8mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ count_8mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 7) {
- count_7mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ count_7mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 6) {
- count_6mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ count_6mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 5) {
- count_5mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ count_5mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -25293,25 +46877,83 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
low1_rc = ~low1;
high1_rc = ~high1;
- if (indexsize == 9) {
- count_9mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
- } else if (indexsize == 8) {
- count_8mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
- } else if (indexsize == 7) {
- count_7mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
- } else if (indexsize == 6) {
- count_6mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
- } else if (indexsize == 5) {
- count_5mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
- } else {
- fprintf(stderr,"indexsize %d not supported\n",indexsize);
- abort();
- }
+ if (indexsize == 9) {
+ count_9mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ } else if (indexsize == 8) {
+ count_8mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ } else if (indexsize == 7) {
+ count_7mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ } else if (indexsize == 6) {
+ count_6mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ } else if (indexsize == 5) {
+ count_5mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ } else {
+ fprintf(stderr,"indexsize %d not supported\n",indexsize);
+ abort();
+ }
+
+ ptr += 3;
+
+ /* Middle blocks */
+ if (indexsize == 9) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
- ptr += 3;
+ count_9mers_rev_simd_128(counts,inquery,current256,next256);
+
+ ptr += 12;
+ }
+#endif
- /* Middle blocks */
- if (indexsize == 9) {
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -25344,6 +46986,7 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
current = _mm_set_epi32(nextlow_rc,high0,low1,high1);
current = _mm_xor_si128(current,invert3);
+
nextlow_rc = ~nextlow;
#ifdef HAVE_SSE4_1
/* high0_rc = _mm_extract_epi32(current,2); */
@@ -25362,9 +47005,9 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#if 0
extract_9mers_rev_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_9mers_rev_simd(counts,current,next);
+ count_9mers_rev_simd(counts,inquery,current,next);
#endif
ptr += 6;
}
@@ -25395,11 +47038,69 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- count_9mers_rev(counts,low1_rc,high1_rc,nextlow_rc);
+ count_9mers_rev(counts,inquery,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 8) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_8mers_rev_simd_128(counts,inquery,current256,next256);
+
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -25450,9 +47151,9 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#if 0
extract_8mers_rev_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_8mers_rev_simd(counts,current,next);
+ count_8mers_rev_simd(counts,inquery,current,next);
#endif
ptr += 6;
}
@@ -25483,11 +47184,69 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- count_8mers_rev(counts,low1_rc,high1_rc,nextlow_rc);
+ count_8mers_rev(counts,inquery,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 7) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_7mers_rev_simd_128(counts,inquery,current256,next256);
+
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -25538,9 +47297,9 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#if 0
extract_7mers_rev_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_7mers_rev_simd(counts,current,next);
+ count_7mers_rev_simd(counts,inquery,current,next);
#endif
ptr += 6;
}
@@ -25571,11 +47330,69 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- count_7mers_rev(counts,low1_rc,high1_rc,nextlow_rc);
+ count_7mers_rev(counts,inquery,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 6) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_6mers_rev_simd_128(counts,inquery,current256,next256);
+
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -25626,9 +47443,9 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#if 0
extract_6mers_rev_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_6mers_rev_simd(counts,current,next);
+ count_6mers_rev_simd(counts,inquery,current,next);
#endif
ptr += 6;
}
@@ -25659,11 +47476,69 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- count_6mers_rev(counts,low1_rc,high1_rc,nextlow_rc);
+ count_6mers_rev(counts,inquery,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 5) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ count_5mers_rev_simd_128(counts,inquery,current256,next256);
+
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -25714,9 +47589,9 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#if 0
extract_5mers_rev_simd(array,current,next);
- count_fwdrev_simd(counts,(Genomecomp_T *) array);
+ count_fwdrev_simd(counts,inquery,(Genomecomp_T *) array);
#else
- count_5mers_rev_simd(counts,current,next);
+ count_5mers_rev_simd(counts,inquery,current,next);
#endif
ptr += 6;
}
@@ -25747,7 +47622,7 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- count_5mers_rev(counts,low1_rc,high1_rc,nextlow_rc);
+ count_5mers_rev(counts,inquery,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
@@ -25785,15 +47660,15 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
high1_rc = ~high1;
if (indexsize == 9) {
- count_9mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_9mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- count_8mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_8mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- count_7mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_7mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- count_6mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_6mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- count_5mers_rev_partial(counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ count_5mers_rev_partial(counts,inquery,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else {
abort();
}
@@ -25806,7 +47681,7 @@ count_positions_rev_simd (Count_T *counts, int indexsize,
#ifndef USE_SIMD_FOR_COUNTS
static void
-store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts, int indexsize,
+store_positions_rev_std (Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts, int indexsize,
Univcoord_T left, Univcoord_T left_plus_length, Chrpos_T chrpos,
int genestrand) {
int startdiscard, enddiscard;
@@ -25814,7 +47689,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
low, high, nextlow;
- if (left_plus_length < indexsize) {
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -25854,15 +47729,15 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- chrpos = store_9mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_9mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_8mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_7mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_6mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_5mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -25896,15 +47771,15 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- chrpos = store_9mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_9mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- chrpos = store_8mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_8mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- chrpos = store_7mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_7mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- chrpos = store_6mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_6mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- chrpos = store_5mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_5mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -25938,7 +47813,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
high_rc = ~high;
nextlow_rc = ~nextlow;
- chrpos = store_9mers_rev(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
+ chrpos = store_9mers_rev(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -25967,7 +47842,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
high_rc = ~high;
nextlow_rc = ~nextlow;
- chrpos = store_8mers_rev(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
+ chrpos = store_8mers_rev(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -25996,7 +47871,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
high_rc = ~high;
nextlow_rc = ~nextlow;
- chrpos = store_7mers_rev(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
+ chrpos = store_7mers_rev(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -26025,7 +47900,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
high_rc = ~high;
nextlow_rc = ~nextlow;
- chrpos = store_6mers_rev(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
+ chrpos = store_6mers_rev(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -26054,7 +47929,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
high_rc = ~high;
nextlow_rc = ~nextlow;
- chrpos = store_5mers_rev(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
+ chrpos = store_5mers_rev(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc);
ptr += 3;
}
@@ -26090,15 +47965,15 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- chrpos = store_9mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_9mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_8mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_7mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_6mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_rev_partial(chrpos,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_5mers_rev_partial(chrpos,table,pointers,positions,counts,low_rc,high_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else {
abort();
}
@@ -26110,7 +47985,7 @@ store_positions_rev_std (Chrpos_T **pointers, Chrpos_T **positions, Count_T *cou
#ifdef USE_SIMD_FOR_COUNTS
static void
-store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *counts, int indexsize,
+store_positions_rev_simd (Chrpos_T *table, UINT4 *pointers, UINT4 *positions, Count_T *counts, int indexsize,
Univcoord_T left, Univcoord_T left_plus_length, Chrpos_T chrpos,
int genestrand) {
int startdiscard, enddiscard;
@@ -26123,9 +47998,17 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#else
Genomecomp_T low0_rc, high0_rc;
#endif
+#ifdef HAVE_AVX2
+ __m256i array256[16];
+ Genomecomp_T low2, high2, low3, high3;
+ __m256i current256, next256, temp256, shift256;
+ __m256i biginvert3;
+#endif
- if (left_plus_length < indexsize) {
+ debug(printf("Starting store_positions_rev_simd\n"));
+
+ if (left_plus_length < (Univcoord_T) indexsize) {
left_plus_length = 0;
} else {
left_plus_length -= indexsize;
@@ -26138,6 +48021,10 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
enddiscard = left_plus_length % 32; /* (left+pos3) % 32 */
invert3 = _mm_set_epi32(0x00000000,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF);
+#ifdef HAVE_AVX2
+ biginvert3 = _mm256_set_epi32(0x00000000,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF);
+ shift256 = _mm256_setr_epi32(7,0,1,2,3,4,5,6);
+#endif
if (left_plus_length <= left) {
/* Skip */
@@ -26167,15 +48054,15 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
nextlow_rc = ~nextlow;
if (indexsize == 9) {
- chrpos = store_9mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_9mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_8mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_7mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_6mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
+ chrpos = store_5mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,enddiscard);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -26209,15 +48096,15 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
high1_rc = ~high1;
if (indexsize == 9) {
- chrpos = store_9mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_9mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 8) {
- chrpos = store_8mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_8mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 7) {
- chrpos = store_7mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_7mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 6) {
- chrpos = store_6mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_6mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else if (indexsize == 5) {
- chrpos = store_5mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
+ chrpos = store_5mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,startdiscard,/*enddiscard*/31);
} else {
fprintf(stderr,"indexsize %d not supported\n",indexsize);
abort();
@@ -26227,6 +48114,64 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
/* Middle blocks */
if (indexsize == 9) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_9mers_rev_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -26276,7 +48221,7 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_9mers_rev_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
ptr += 6;
}
@@ -26306,11 +48251,69 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- chrpos = store_9mers_rev(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
+ chrpos = store_9mers_rev(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 8) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_8mers_rev_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -26360,7 +48363,7 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_8mers_rev_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
ptr += 6;
}
@@ -26380,21 +48383,79 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
if (genestrand > 0) {
high1 = Cmet_reduce_ct(high1); /* low1 = Cmet_reduce_ct(low1); */ nextlow = Cmet_reduce_ct(nextlow);
} else {
- high1 = Cmet_reduce_ga(high1); /* low1 = Cmet_reduce_ga(low1); */ nextlow = Cmet_reduce_ga(nextlow);
+ high1 = Cmet_reduce_ga(high1); /* low1 = Cmet_reduce_ga(low1); */ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ /* low1_rc = ~low1; */
+ low1_rc = nextlow_rc;
+
+ nextlow_rc = ~nextlow;
+ high1_rc = ~high1;
+
+ chrpos = store_8mers_rev(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
+ ptr += 3;
+ }
+
+ } else if (indexsize == 7) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
}
}
- /* low1_rc = ~low1; */
- low1_rc = nextlow_rc;
-
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
nextlow_rc = ~nextlow;
- high1_rc = ~high1;
- chrpos = store_8mers_rev(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
- ptr += 3;
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_7mers_rev_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ ptr += 12;
}
+#endif
- } else if (indexsize == 7) {
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -26444,7 +48505,7 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_7mers_rev_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
ptr += 6;
}
@@ -26474,11 +48535,69 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- chrpos = store_7mers_rev(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
+ chrpos = store_7mers_rev(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 6) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_6mers_rev_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -26528,7 +48647,7 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_6mers_rev_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
ptr += 6;
}
@@ -26558,11 +48677,69 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- chrpos = store_6mers_rev(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
+ chrpos = store_6mers_rev(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
} else if (indexsize == 5) {
+#ifdef HAVE_AVX2
+ while (ptr + 12 <= endptr) {
+#ifdef WORDS_BIGENDIAN
+ high0 = Bigendian_convert_uint(ref_blocks[ptr]);
+ /* low0 = Bigendian_convert_uint(ref_blocks[ptr+1]); */
+ high1 = Bigendian_convert_uint(ref_blocks[ptr+3]);
+ low1 = Bigendian_convert_uint(ref_blocks[ptr+4]);
+ high2 = Bigendian_convert_uint(ref_blocks[ptr+6]);
+ low2 = Bigendian_convert_uint(ref_blocks[ptr+7]);
+ high3 = Bigendian_convert_uint(ref_blocks[ptr+9]);
+ low3 = Bigendian_convert_uint(ref_blocks[ptr+10]);
+ nextlow = Bigendian_convert_uint(ref_blocks[ptr+13]);
+#else
+ high0 = ref_blocks[ptr];
+ /* low0 = ref_blocks[ptr+1]; */
+ high1 = ref_blocks[ptr+3];
+ low1 = ref_blocks[ptr+4];
+ high2 = ref_blocks[ptr+6];
+ low2 = ref_blocks[ptr+7];
+ high3 = ref_blocks[ptr+9];
+ low3 = ref_blocks[ptr+10];
+ nextlow = ref_blocks[ptr+13];
+#endif
+ if (mode == CMET_STRANDED) {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ } else if (mode == CMET_NONSTRANDED) {
+ if (genestrand > 0) {
+ high0 = Cmet_reduce_ct(high0); /* low0 = Cmet_reduce_ct(low0); */
+ high1 = Cmet_reduce_ct(high1); low1 = Cmet_reduce_ct(low1);
+ high2 = Cmet_reduce_ct(high2); low2 = Cmet_reduce_ct(low2);
+ high3 = Cmet_reduce_ct(high3); low3 = Cmet_reduce_ct(low3);
+ nextlow = Cmet_reduce_ct(nextlow);
+ } else {
+ high0 = Cmet_reduce_ga(high0); /* low0 = Cmet_reduce_ga(low0); */
+ high1 = Cmet_reduce_ga(high1); low1 = Cmet_reduce_ga(low1);
+ high2 = Cmet_reduce_ga(high2); low2 = Cmet_reduce_ga(low2);
+ high3 = Cmet_reduce_ga(high3); low3 = Cmet_reduce_ga(low3);
+ nextlow = Cmet_reduce_ga(nextlow);
+ }
+ }
+
+ current256 = _mm256_set_epi32(nextlow_rc,high0,low1,high1,low2,high2,low3,high3);
+ current256 = _mm256_xor_si256(current256,biginvert3);
+ nextlow_rc = ~nextlow;
+
+ temp256 = _mm256_insert_epi32(current256,nextlow_rc,0x07);
+ next256 = _mm256_permutevar8x32_epi32(temp256,shift256);
+
+ extract_5mers_rev_simd_128(array256,current256,next256);
+ chrpos = store_fwdrev_simd_128(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array256);
+ ptr += 12;
+ }
+#endif
+
while (ptr + 6 <= endptr) {
#ifdef WORDS_BIGENDIAN
high0 = Bigendian_convert_uint(ref_blocks[ptr]);
@@ -26612,7 +48789,7 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#endif
extract_5mers_rev_simd(array,current,next);
- chrpos = store_fwdrev_simd(chrpos,pointers,positions,counts,(Genomecomp_T *) array);
+ chrpos = store_fwdrev_simd(chrpos,table,pointers,positions,counts,(Genomecomp_T *) array);
ptr += 6;
}
@@ -26642,7 +48819,7 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
nextlow_rc = ~nextlow;
high1_rc = ~high1;
- chrpos = store_5mers_rev(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
+ chrpos = store_5mers_rev(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc);
ptr += 3;
}
@@ -26680,15 +48857,15 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
high1_rc = ~high1;
if (indexsize == 9) {
- chrpos = store_9mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_9mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 8) {
- chrpos = store_8mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_8mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 7) {
- chrpos = store_7mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_7mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 6) {
- chrpos = store_6mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_6mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else if (indexsize == 5) {
- chrpos = store_5mers_rev_partial(chrpos,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
+ chrpos = store_5mers_rev_partial(chrpos,table,pointers,positions,counts,low1_rc,high1_rc,nextlow_rc,/*startdiscard*/0,enddiscard);
} else {
abort();
}
@@ -26706,17 +48883,160 @@ store_positions_rev_simd (Chrpos_T **pointers, Chrpos_T **positions, Count_T *co
#define POLY_T 0xFFFF
-#define SIMD_NINTS 4
+#ifdef HAVE_AVX2
+static Chrpos_T *
+allocate_positions (UINT4 *pointers, UINT4 *positions,
+ Inquery_T *inquery, Count_T *counts, int oligospace) {
+ Chrpos_T *table;
+ UINT4 *pointers_end, p;
+ int totalcounts = 0;
+ int i, j, k;
+ __m256i *inquery_ptr, *counts_ptr, *end_ptr, qcounts;
+ __m256i terms_ptr[1];
+ Count_T *terms;
+ int *nskip, *nskip_ptr;
+
+#if 0
+ /* Causes problems with new algorithm */
+ inquery[POLY_A & mask] = INQUERY_FALSE;
+ inquery[POLY_C & mask] = INQUERY_FALSE;
+ inquery[POLY_G & mask] = INQUERY_FALSE;
+ inquery[POLY_T & mask] = INQUERY_FALSE;
+#endif
+ /* nskip is a run-length of zero counts, which allows faster processing the second time through */
+ nskip_ptr = nskip = (int *) MALLOCA((oligospace/SIMD_NELTS + 1) * sizeof(int));
+ *nskip_ptr = 0;
-#ifdef HAVE_SSE2
+ inquery_ptr = (__m256i *) inquery;
+ counts_ptr = (__m256i *) counts;
+ end_ptr = &(counts_ptr[oligospace/SIMD_NELTS]);
+ terms = (Count_T *) terms_ptr;
+
+ i = 0;
+ while (counts_ptr < end_ptr) {
+ debug(printf("%d\n",i));
+ debug(print_counts(*counts_ptr,"counts"));
+ qcounts = _mm256_and_si256(*counts_ptr,*inquery_ptr++); /* counts in query (zeroed if INQUERY_FALSE, which can happen if count > MAXCOUNT) */
+ _mm256_store_si256(counts_ptr++,qcounts); /* and store back, so we don't need inquery or overabundant any more */
+ if (_mm256_testz_si256(qcounts,qcounts)) {
+ /* All counts are zero, so incrementing nskip */
+ (*nskip_ptr) += 1;
+
+ } else {
+ /* A valid count found */
+ _mm256_store_si256(terms_ptr,qcounts);
+ for (k = 0; k < SIMD_NELTS; k++) {
+ totalcounts += terms[k];
+ }
+ *(++nskip_ptr) = 0; /* Advance ptr and initialize */
+ }
+
+ i += SIMD_NELTS;
+ }
+
+#if 0
+ /* For debugging */
+ totalcounts_old = 0;
+ for (i = 0; i < oligospace; i++) {
+ if (inquery[i] == INQUERY_TRUE) {
+ totalcounts_old += counts[i];
+ }
+ }
+
+ fprintf(stderr,"Old method %d, new method %d\n",totalcounts_old,totalcounts);
+ if (totalcounts != totalcounts_old) {
+ abort();
+ }
+#endif
+
+ debug(printf("totalcounts is %d\n",totalcounts));
+ if (totalcounts == 0) {
+ table = (Chrpos_T *) NULL;
+ } else {
+ /* Need to assign positions[0] so we can free the space */
+ pointers_end = &(pointers[-1]); /* or pointers_allocated[0] */
+ table = (Chrpos_T *) MALLOC(totalcounts * sizeof(Chrpos_T));
+ p = 0;
+
+ i = 0;
+ nskip_ptr = nskip;
+ j = *nskip_ptr++;
+ while (i + j*SIMD_NELTS < oligospace) {
+#if 0
+ while (--j >= 0) {
+ positions[i++] = p; positions[i++] = p; positions[i++] = p; positions[i++] = p;
+ positions[i++] = p; positions[i++] = p; positions[i++] = p; positions[i++] = p;
+ }
+#else
+ /* Not necessary to assign since we check for counts[i] == 0 */
+ pointers_end[i] = /* positions[i] = */ p;
+ i += j*SIMD_NELTS;
+#endif
+
+ pointers_end[i] = positions[i] = p; /* 0 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 1 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 2 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 3 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 4 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 5 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 6 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 7 */
+ p += counts[i++];
+
+ j = *nskip_ptr++;
+ }
+
+#if 0
+ while (--j >= 0) {
+ /* Not necessary to assign since we check for counts[i] == 0 */
+ positions[i++] = p; positions[i++] = p; positions[i++] = p; positions[i++] = p;
+ positions[i++] = p; positions[i++] = p; positions[i++] = p; positions[i++] = p;
+ }
+#else
+ if (j > 0) {
+ pointers_end[i] = /* positions[i] = */ p;
+ /* i += j*SIMD_NELTS; */
+ }
+#endif
+ }
+
+#if 0
+ /* Faster to assign each individual pointer above */
+ memcpy((void *) pointers,&(positions[1]),(oligospace-1)*sizeof(Chrpos_T *));
+#endif
+ pointers[oligospace-1] = p; /* or pointers_end[oligospace] or pointers_allocated[oligospace+1] */
+
+ /* dump_allocations(positions,counts,oligospace,indexsize,positions_space); */
+
+ FREEA(nskip);
+
+ return table;
+}
+
+
+#elif defined(HAVE_SSE2)
static Chrpos_T *
-allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
- Count_T *inquery, Count_T *counts, int oligospace,
- Shortoligomer_T mask, int indexsize) {
- Chrpos_T *positions_space, **pointers_end, *p;
+allocate_positions (UINT4 *pointers, UINT4 *positions,
+ Inquery_T *inquery, Count_T *counts, int oligospace) {
+ Chrpos_T *table;
+ UINT4 *pointers_end, p;
int totalcounts = 0;
- int i, j;
+ int i, j, k;
__m128i *inquery_ptr, *counts_ptr, *end_ptr, qcounts;
__m128i terms_ptr[1];
Count_T *terms;
@@ -26745,15 +49065,14 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
zero = _mm_set1_epi8(0);
#endif
- debug(i = 0);
+ i = 0;
while (counts_ptr < end_ptr) {
debug(printf("%d\n",i));
- debug(i += 16);
debug(print_counts(*counts_ptr,"counts"));
- qcounts = _mm_and_si128(*counts_ptr,*inquery_ptr++); /* counts in query */
+ qcounts = _mm_and_si128(*counts_ptr,*inquery_ptr++); /* counts in query (zeroed if INQUERY_FALSE, which can happen if count > MAXCOUNT) */
_mm_store_si128(counts_ptr++,qcounts); /* and store back, so we don't need inquery or overabundant any more */
if (
-#ifdef HAVE_SSE4_1
+#if defined(HAVE_SSE4_1)
_mm_testz_si128(qcounts,qcounts)
#else
/*cmp*/_mm_movemask_epi8(_mm_cmpeq_epi8(qcounts,zero)) == 0xFFFF
@@ -26765,10 +49084,36 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
} else {
/* A valid count found */
_mm_store_si128(terms_ptr,qcounts);
- totalcounts += terms[0] + terms[1] + terms[2] + terms[3] + terms[4] + terms[5] + terms[6] + terms[7] +
- terms[8] + terms[9] + terms[10] + terms[11] + terms[12] + terms[13] + terms[14] + terms[15];
+#ifdef HAVE_AVX2
+ if (_mm_extract_epi32(qcounts,0)) {
+ totalcounts += terms[0];
+ } else {
+ counts[i] = 0;
+ }
+ if (_mm_extract_epi32(qcounts,1)) {
+ totalcounts += terms[1];
+ } else {
+ counts[i+1] = 0;
+ }
+ if (_mm_extract_epi32(qcounts,2)) {
+ totalcounts += terms[2];
+ } else {
+ counts[i+2] = 0;
+ }
+ if (_mm_extract_epi32(qcounts,3)) {
+ totalcounts += terms[3];
+ } else {
+ counts[i+3] = 0;
+ }
+#else
+ for (k = 0; k < SIMD_NELTS; k++) {
+ totalcounts += terms[k];
+ }
+#endif
*(++nskip_ptr) = 0; /* Advance ptr and initialize */
}
+
+ i += SIMD_NELTS;
}
#if 0
@@ -26788,11 +49133,12 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
debug(printf("totalcounts is %d\n",totalcounts));
if (totalcounts == 0) {
- positions_space = (Chrpos_T *) NULL;
+ table = (Chrpos_T *) NULL;
} else {
/* Need to assign positions[0] so we can free the space */
- pointers_end = &(pointers[-1]); /* or pointers_allocated[0] */
- p = positions_space = (Chrpos_T *) MALLOC(totalcounts * sizeof(Chrpos_T));
+ pointers_end = &(pointers[-1]); /* or pointers_allocated[0] */
+ table = (Chrpos_T *) MALLOC(totalcounts * sizeof(Chrpos_T));
+ p = 0;
i = 0;
nskip_ptr = nskip;
@@ -26808,9 +49154,23 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
#else
/* Not necessary to assign since we check for counts[i] == 0 */
pointers_end[i] = /* positions[i] = */ p;
- i += j*16;
+ i += j*SIMD_NELTS;
#endif
+#ifdef HAVE_AVX2
+ pointers_end[i] = positions[i] = p; /* 0 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 1 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 2 */
+ p += counts[i++];
+
+ pointers_end[i] = positions[i] = p; /* 3 */
+ p += counts[i++];
+
+#else
pointers_end[i] = positions[i] = p; /* 0 */
p += counts[i++];
@@ -26858,6 +49218,7 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
pointers_end[i] = positions[i] = p; /* 15 */
p += counts[i++];
+#endif
j = *nskip_ptr++;
}
@@ -26873,7 +49234,7 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
#else
if (j > 0) {
pointers_end[i] = /* positions[i] = */ p;
- /* i += j*16; */
+ /* i += j*SIMD_NELTS; */
}
#endif
}
@@ -26888,16 +49249,15 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
FREEA(nskip);
- return positions_space;
+ return table;
}
#else
-
static Chrpos_T *
-allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
- bool *inquery, Count_T *counts, int oligospace,
- Shortoligomer_T mask, int indexsize) {
- Chrpos_T *positions_space, *p;
+allocate_positions (UINT4 *pointers, UINT4 *positions,
+ Inquery_T *inquery, Count_T *counts, int oligospace) {
+ Chrpos_T *table;
+ UINT4 p;
int totalcounts;
int i;
@@ -26924,19 +49284,20 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions,
if (totalcounts == 0) {
- positions_space = (Chrpos_T *) NULL;
+ table = (Chrpos_T *) NULL;
} else {
- p = positions_space = (Chrpos_T *) CALLOC(totalcounts,sizeof(Chrpos_T));
+ table = (Chrpos_T *) CALLOC(totalcounts,sizeof(Chrpos_T));
+ p = 0;
for (i = 0; i < oligospace; i++) {
positions[i] = p;
p += counts[i];
}
- memcpy((void *) pointers,&(positions[1]),(oligospace-1)*sizeof(Chrpos_T *));
+ memcpy((void *) pointers,&(positions[1]),(oligospace-1)*sizeof(UINT4));
pointers[oligospace-1] = p;
}
- return positions_space;
+ return table;
}
#endif
@@ -26957,7 +49318,7 @@ counts_compare (Count_T *counts1, Count0_T *counts2, Oligospace_T oligospace) {
}
static void
-positions_compare (Chrpos_T **positions1, Count_T *counts1, Count_T *inquery1,
+positions_compare (Chrpos_T **positions1, Count_T *counts1, Inquery_T *inquery1,
Chrpos_T **positions2, Count0_T *counts2, Oligospace_T oligospace,
int indexsize, Shortoligomer_T mask) {
Oligospace_T i;
@@ -26970,7 +49331,7 @@ positions_compare (Chrpos_T **positions1, Count_T *counts1, Count_T *inquery1,
if (inquery1[i] == INQUERY_FALSE) {
/* Skip */
} else if (counts1[i] != (Count_T) counts2[i]) {
- /* Can happen if count > 127 */
+ /* Can happen if count > MAXCOUNT */
if (i == (POLY_A & mask) || i == (POLY_C & mask) || i == (POLY_G & mask) || i == (POLY_T & mask)) {
/* Ignore */
} else {
@@ -27284,11 +49645,7 @@ Oligoindex_set_inquery (int *badoligos, int *repoligos, int *trimoligos, int *tr
return 1.0;
} else {
-#ifdef HAVE_SSE2
- memset(this->inquery,/*INQUERY_FALSE*/0,this->oligospace * sizeof(Count_T));
-#else
- memset(this->inquery,/*false*/0,this->oligospace * sizeof(bool));
-#endif
+ memset(this->inquery,INQUERY_FALSE,this->oligospace * sizeof(Inquery_T));
}
for (i = querystart, p = &(queryuc_ptr[querystart]); i < queryend; i++, p++) {
@@ -27309,18 +49666,11 @@ Oligoindex_set_inquery (int *badoligos, int *repoligos, int *trimoligos, int *tr
printf("At querypos %d, oligo %s seen\n",i,nt);
FREE(nt));
- this->counts[masked] += 1; /* For determination of trimming */
-#ifdef HAVE_SSE2
+ this->counts[masked] += 1;
if (this->inquery[masked] == INQUERY_FALSE) {
nunique += 1;
this->inquery[masked] = INQUERY_TRUE;
}
-#else
- if (this->inquery[masked] == false) {
- nunique += 1;
- this->inquery[masked] = true;
- }
-#endif
in_counter--;
}
}
@@ -27353,8 +49703,8 @@ Oligoindex_set_inquery (int *badoligos, int *repoligos, int *trimoligos, int *tr
#endif
in_counter = 0;
- querypos = -indexsize;
- for (i = 0, p = queryuc_ptr; i < querylength; i++, p++) {
+ querypos = querystart - indexsize;
+ for (i = querystart, p = &(queryuc_ptr[querystart]); i < queryend; i++, p++) {
in_counter++;
querypos++;
@@ -27458,13 +49808,8 @@ Oligoindex_set_inquery (int *badoligos, int *repoligos, int *trimoligos, int *tr
/* Old code, no longer used for GMAP/GSNAP, but kept for PMAP in oligoindex_pmap.c */
/* Second, run genomicuc through this procedure, to determine the genomic positions for each oligo. */
static int
-allocate_positions (Chrpos_T **pointers, Chrpos_T **positions, bool *overabundant,
-#ifdef HAVE_SSE2
- Count_T *inquery,
-#else
- bool *inquery,
-#endif
- Count_T *counts, int *relevant_counts, int oligospace, int indexsize,
+allocate_positions (Chrpos_T *table, UINT4 *pointers, UINT4 *positions, bool *overabundant,
+ Inquery_T *inquery, Count_T *counts, int *relevant_counts, int oligospace, int indexsize,
Shortoligomer_T mask, char *sequence, int seqlength, int sequencepos) {
int i = 0, n;
int in_counter = 0;
@@ -27575,7 +49920,7 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions, bool *overabundan
}
positions[i] = ptr; /* For positions[oligospace], used for indicating if pointer hits next position */
/* Does not copy positions[oligospace] */
- memcpy((void *) pointers,positions,oligospace*sizeof(Chrpos_T *));
+ memcpy((void *) pointers,positions,oligospace*sizeof(UINT4));
}
return totalcounts;
@@ -27590,12 +49935,7 @@ allocate_positions (Chrpos_T **pointers, Chrpos_T **positions, bool *overabundan
/* Logic of this procedure should match that of allocate_positions */
static int
store_positions (Chrpos_T **pointers, bool *overabundant,
-#ifdef HAVE_SSE2
- Count_T *inquery,
-#else
- bool *inquery,
-#endif
- Oligospace_T oligospace, int indexsize, Shortoligomer_T mask,
+ Inquery_T *inquery, Oligospace_T oligospace, int indexsize, Shortoligomer_T mask,
char *sequence, int seqlength, int sequencepos) {
int nstored = 0;
int i = 0;
@@ -27674,7 +50014,7 @@ Oligoindex_hr_tally (T this, Univcoord_T mappingstart, Univcoord_T mappingend, b
Count0_T *counts_old;
Chrpos_T **positions_old;
#endif
- Oligospace_T oligo;
+ /* Oligospace_T oligo; */
/* Sets counts for trimming when trimp is true */
@@ -27688,24 +50028,24 @@ Oligoindex_hr_tally (T this, Univcoord_T mappingstart, Univcoord_T mappingend, b
debug0(printf("plus, origin is %u\n",chrpos));
#ifdef USE_SIMD_FOR_COUNTS
- count_positions_fwd_simd(this->counts,this->indexsize,mappingstart,mappingend,genestrand);
+ count_positions_fwd_simd(this->counts,this->inquery,this->indexsize,mappingstart,mappingend,genestrand);
#else
- count_positions_fwd_std(this->counts,this->indexsize,mappingstart,mappingend,genestrand);
+ count_positions_fwd_std(this->counts,this->inquery,this->indexsize,mappingstart,mappingend,genestrand);
#endif
- if ((this->positions_space = allocate_positions(this->pointers,this->positions,this->inquery,this->counts,
- this->oligospace,this->mask,this->indexsize)) != NULL) {
+ if ((this->table = allocate_positions(this->pointers,this->positions,this->inquery,this->counts,
+ this->oligospace)) != NULL) {
#ifdef USE_SIMD_FOR_COUNTS
- store_positions_fwd_simd(this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
+ store_positions_fwd_simd(this->table,this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
chrpos,genestrand);
#else
- store_positions_fwd_std(this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
+ store_positions_fwd_std(this->table,this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
chrpos,genestrand);
#endif
debug9(printf("plus, origin is %u\n",chrpos));
- debug9(dump_positions(this->positions,this->counts,this->inquery,this->oligospace,this->indexsize));
+ debug9(dump_positions(this->table,this->positions,this->counts,this->inquery,this->oligospace,this->indexsize));
#ifdef DEBUG14
positions_old = Oligoindex_old_tally(&counts_old,mappingstart,mappingend,plusp,
@@ -27723,23 +50063,23 @@ Oligoindex_hr_tally (T this, Univcoord_T mappingstart, Univcoord_T mappingend, b
debug0(printf("minus, origin is %u\n",chrpos));
#ifdef USE_SIMD_FOR_COUNTS
- count_positions_rev_simd(this->counts,this->indexsize,mappingstart,mappingend,genestrand);
+ count_positions_rev_simd(this->counts,this->inquery,this->indexsize,mappingstart,mappingend,genestrand);
#else
- count_positions_rev_std(this->counts,this->indexsize,mappingstart,mappingend,genestrand);
+ count_positions_rev_std(this->counts,this->inquery,this->indexsize,mappingstart,mappingend,genestrand);
#endif
- if ((this->positions_space = allocate_positions(this->pointers,this->positions,this->inquery,this->counts,
- this->oligospace,this->mask,this->indexsize)) != NULL) {
+ if ((this->table = allocate_positions(this->pointers,this->positions,this->inquery,this->counts,
+ this->oligospace)) != NULL) {
#ifdef USE_SIMD_FOR_COUNTS
- store_positions_rev_simd(this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
+ store_positions_rev_simd(this->table,this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
chrpos,genestrand);
#else
- store_positions_rev_std(this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
+ store_positions_rev_std(this->table,this->pointers,this->positions,this->counts,this->indexsize,mappingstart,mappingend,
chrpos,genestrand);
#endif
debug9(printf("minus, origin is %u\n",chrpos));
- debug9(dump_positions(this->positions,this->counts,this->inquery,this->oligospace,this->indexsize));
+ debug9(dump_positions(this->table,this->positions,this->counts,this->inquery,this->oligospace,this->indexsize));
#ifdef DEBUG14
positions_old = Oligoindex_old_tally(&counts_old,mappingstart,mappingend,plusp,
@@ -27802,11 +50142,7 @@ Oligoindex_clear_inquery (T this, char *queryuc_ptr, int querystart, int queryen
#endif
this->counts[masked] = 0;
-#ifdef HAVE_SSE2
this->inquery[masked] = INQUERY_FALSE;
-#else
- this->inquery[masked] = false;
-#endif
in_counter--;
}
}
@@ -27827,11 +50163,7 @@ Oligoindex_untally (T this, char *queryuc_ptr, int querylength) {
#else
if ((Oligospace_T) querylength > this->oligospace) {
/* For very long sequences, it may be better to just clear all oligos directly */
-#ifdef HAVE_SSE2
- memset((void *) this->inquery,INQUERY_FALSE,this->oligospace*sizeof(Count_T));
-#else
- memset((void *) this->inquery,false,this->oligospace*sizeof(bool));
-#endif
+ memset((void *) this->inquery,INQUERY_FALSE,this->oligospace*sizeof(Inquery_T));
memset((void *) this->counts,0,this->oligospace*sizeof(Count_T));
} else {
@@ -27844,8 +50176,8 @@ Oligoindex_untally (T this, char *queryuc_ptr, int querylength) {
}
#endif
- if (this->positions_space != NULL) {
- FREE(this->positions_space);
+ if (this->table != NULL) {
+ FREE(this->table);
}
return;
@@ -27858,6 +50190,7 @@ Oligoindex_free (T *old) {
if (*old) {
FREE((*old)->pointers_allocated);
FREE((*old)->positions);
+ FREE((*old)->table);
#ifdef HAVE_SSE2
_mm_free((*old)->counts_allocated);
_mm_free((*old)->inquery_allocated);
@@ -27894,11 +50227,17 @@ lookup (int *nhits, T this, Shortoligomer_T masked) {
#endif
if ((*nhits = this->counts[masked]) >= 1) {
- debug(nt = shortoligo_nt(masked,this->indexsize);
- printf("masked is %s (%u) => %d entries: %u...%u\n",
- nt,masked,*nhits,this->positions[masked][0],this->positions[masked][*nhits-1]);
- FREE(nt));
- return this->positions[masked];
+#ifdef DEBUG
+ nt = shortoligo_nt(masked,this->indexsize);
+ printf("masked is %s (%u) => %d entries: %u...%u\n",
+ nt,masked,*nhits,
+#if 0
+ this->positions[masked],this->positions[masked]+(*nhits)-1,
+#endif
+ this->table[this->positions[masked]],this->table[this->positions[masked]+(*nhits)-1]);
+ FREE(nt);
+#endif
+ return &(this->table[this->positions[masked]]);
} else {
debug(nt = shortoligo_nt(masked,this->indexsize);
printf("masked %s not found\n",nt);
@@ -27981,7 +50320,7 @@ Oligoindex_get_mappings (List_T diagonals, bool *coveredp, Chrpos_T **mappings,
chrinit = (chrhigh - chroffset) - chrend;
}
- if (querylength + genomiclength > array->max_querylength + array->max_genomiclength) {
+ if (querylength + genomiclength > (Chrpos_T) (array->max_querylength + array->max_genomiclength)) {
/* Cannot use pre-allocated storage */
/* Needs to be CALLOC, since we depend on the value being false as a signal that genomicdiag[diagi] should be initialized */
genomicdiag_init_p = (bool *) CALLOC(querylength+genomiclength+1,sizeof(bool));
@@ -28035,6 +50374,7 @@ Oligoindex_get_mappings (List_T diagonals, bool *coveredp, Chrpos_T **mappings,
cum_nohits[querypos] = cum_nohits[querypos-1];
if (in_counter == indexsize) {
masked = oligo & this->mask;
+
if (coveredp[querypos] == false) {
mappings[querypos] = lookup(&nhits,this,masked);
npositions[querypos] = nhits;
@@ -28145,7 +50485,7 @@ Oligoindex_get_mappings (List_T diagonals, bool *coveredp, Chrpos_T **mappings,
}
}
- if (querylength + genomiclength > array->max_querylength + array->max_genomiclength) {
+ if (querylength + genomiclength > (Chrpos_T) (array->max_querylength + array->max_genomiclength)) {
FREE(genomicdiag);
FREE(genomicdiag_init_p);
}
diff --git a/src/oligoindex_hr.h b/src/oligoindex_hr.h
index 31e1429..c52da8b 100644
--- a/src/oligoindex_hr.h
+++ b/src/oligoindex_hr.h
@@ -1,4 +1,4 @@
-/* $Id: oligoindex_hr.h 166641 2015-05-29 21:13:04Z twu $ */
+/* $Id: oligoindex_hr.h 180701 2015-12-10 19:54:31Z twu $ */
#ifndef OLIGOINDEX_HR_INCLUDED
#define OLIGOINDEX_HR_INCLUDED
@@ -14,21 +14,53 @@
#define OVERABUNDANCE_PCT 0.97
#define OVERABUNDANCE_MIN 200
-typedef UINT4 Shortoligomer_T;
+#ifdef HAVE_AVX2
+/* Attempted to use int, so we don't need to check for count > 255. However, SIMD is much faster on bytes than on ints */
+typedef int Count_T;
+typedef unsigned int Inquery_T;
+#define INQUERY_FALSE 0x00000000
+#define INQUERY_TRUE 0xFFFFFFFF
+#define SIMD_NELTS 8 /* 8 ints in 256 bits */
-#if 1
-typedef unsigned char Count_T;
+/* #define CHECK_FOR_OVERFLOW 1 -- Optional if we use int for Count_T */
+#define CHECK_FOR_OVERFLOW 1
+
+#ifdef CHECK_FOR_OVERFLOW
+#define MAXCOUNT 255
+#define INCR_COUNT(counts,inquery) if (++counts > MAXCOUNT) inquery = INQUERY_FALSE;
+#else
+#define INCR_COUNT(counts,inquery) counts += 1;
+#endif
+
+
+#elif defined(HAVE_SSE2)
+typedef char Count_T;
+typedef unsigned char Inquery_T;
#define INQUERY_FALSE 0x00
#define INQUERY_TRUE 0xFF
#define SIMD_NELTS 16 /* 16 bytes in 128 bits */
+#define CHECK_FOR_OVERFLOW 1 /* Required, since a char can hold only 127 positive counts */
+#ifdef CHECK_FOR_OVERFLOW
+#define INCR_COUNT(counts,inquery) if (++counts < 0) inquery = INQUERY_FALSE;
#else
-/* Attempted to use int, so we don't need to check for count > 255. However, SIMD is much faster on bytes than on ints */
-typedef unsigned int Count_T;
-#define INQUERY_FALSE 0x00000000
-#define INQUERY_TRUE 0xFFFFFFFF
-#define SIMD_NELTS 4 /* 4 ints in 128 bits */
+#define INCR_COUNT(counts,inquery) counts += 1;
+#endif
+
+#else
+typedef char Count_T;
+typedef bool Inquery_T;
+#define INQUERY_FALSE false
+#define INQUERY_TRUE true
+
+#define CHECK_FOR_OVERFLOW 1 /* Required, since a char can hold only 127 positive counts */
+#ifdef CHECK_FOR_OVERFLOW
+#define INCR_COUNT(counts,inquery) if (++counts < 0) inquery = false;
+#else
+#define INCR_COUNT(counts,inquery) counts += 1;
+#endif
+
#endif
diff --git a/src/outbuffer.c b/src/outbuffer.c
index a02fc2e..d01d375 100644
--- a/src/outbuffer.c
+++ b/src/outbuffer.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: outbuffer.c 173039 2015-08-31 19:12:10Z twu $";
+static char rcsid[] = "$Id: outbuffer.c 184468 2016-02-18 00:10:24Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -95,7 +95,7 @@ static FILE *output_failedinput;
#endif
-
+#ifndef GSNAP
/* Taken from Univ_IIT_dump_sam */
static void
dump_sam_usersegment (FILE *fp, Sequence_T usersegment,
@@ -120,6 +120,8 @@ dump_sam_usersegment (FILE *fp, Sequence_T usersegment,
return;
}
+#endif
+
#ifndef GSNAP
static void
diff --git a/src/output.c b/src/output.c
index 4afafef..c662a34 100644
--- a/src/output.c
+++ b/src/output.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: output.c 183725 2016-02-04 00:40:15Z twu $";
+static char rcsid[] = "$Id: output.c 184470 2016-02-18 00:11:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -165,7 +165,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
Shortread_T queryseq1;
Stage3end_T *stage3array, stage3;
Chrpos_T chrpos;
- int npaths, pathnum, first_absmq, second_absmq;
+ int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq;
char *abbrev;
fp = Filestring_new(Request_id(request));
@@ -186,7 +186,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
SAM_print_nomapping(fp,ABBREV_NOMAPPING_1,
queryseq1,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/0,/*npaths*/0,
+ /*first_read_p*/true,/*pathnum*/0,/*npaths_primary*/0,/*npaths_altloc*/0,
/*artificial_mate_p*/false,/*npaths_mate*/0,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
if (failedinput_root != NULL) {
@@ -201,7 +201,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
} else {
queryseq1 = Request_queryseq1(request);
- stage3array = (Stage3end_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
stage3 = stage3array[0];
if (Stage3end_hittype(stage3) == SAMECHR_SPLICE || Stage3end_hittype(stage3) == TRANSLOC_SPLICE) {
chrpos = 0;
@@ -217,11 +217,11 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
abbrev = ABBREV_UNPAIRED_UNIQ;
}
SAM_print(fp,*fp_failedinput_1,abbrev,stage3,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),/*acc2*/NULL,
- /*pathnum*/1,npaths,Stage3end_absmq_score(stage3array[0]),first_absmq,second_absmq,
+ /*pathnum*/1,npaths_primary,npaths_altloc,Stage3end_absmq_score(stage3array[0]),first_absmq,second_absmq,
Stage3end_mapq_score(stage3array[0]),
chromosome_iit,queryseq1,/*queryseq2*/NULL,
/*pairedlength*/0,chrpos,/*mate_chrpos*/0U,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/0,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
@@ -230,15 +230,15 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
*fp_failedinput_2 = (Filestring_T) NULL;
Filestring_set_split_output(fp,OUTPUT_UT);
- stage3array = (Stage3end_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
if (failsonlyp == true) {
/* Skip */
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
queryseq1 = Request_queryseq1(request);
SAM_print_nomapping(fp,ABBREV_UNPAIRED_TRANSLOC,
queryseq1,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*first_read_p*/true,/*pathnum*/1,npaths_primary,npaths_altloc,
/*artificial_mate_p*/false,/*npaths_mate*/0,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
if (failedinput_root != NULL) {
@@ -248,7 +248,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
} else {
queryseq1 = Request_queryseq1(request);
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
if (Stage3end_hittype(stage3) == SAMECHR_SPLICE || Stage3end_hittype(stage3) == TRANSLOC_SPLICE) {
chrpos = 0;
@@ -258,12 +258,12 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
}
SAM_print(fp,*fp_failedinput_1,ABBREV_UNPAIRED_TRANSLOC,
stage3,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
- /*acc2*/NULL,pathnum,npaths,
+ /*acc2*/NULL,pathnum,npaths_primary,npaths_altloc,
Stage3end_absmq_score(stage3array[pathnum-1]),first_absmq,second_absmq,
Stage3end_mapq_score(stage3array[pathnum-1]),
chromosome_iit,queryseq1,/*queryseq2*/NULL,
/*pairedlength*/0,chrpos,/*mate_chrpos*/0U,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/0,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
@@ -271,17 +271,17 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
} else if (resulttype == SINGLEEND_MULT) {
*fp_failedinput_2 = (Filestring_T) NULL;
- stage3array = (Stage3end_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
if (failsonlyp == true) {
/* Skip */
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
Filestring_set_split_output(fp,OUTPUT_UX);
queryseq1 = Request_queryseq1(request);
SAM_print_nomapping(fp,ABBREV_UNPAIRED_MULT_XS,
queryseq1,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
/*acc2*/NULL,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,
+ /*first_read_p*/true,/*pathnum*/1,npaths_primary,npaths_altloc,
/*artificial_mate_p*/false,/*npaths_mate*/0,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
if (failedinput_root != NULL) {
@@ -291,7 +291,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
} else {
Filestring_set_split_output(fp,OUTPUT_UM);
queryseq1 = Request_queryseq1(request);
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
if (Stage3end_hittype(stage3) == SAMECHR_SPLICE || Stage3end_hittype(stage3) == TRANSLOC_SPLICE) {
chrpos = 0;
@@ -301,12 +301,12 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
}
SAM_print(fp,*fp_failedinput_1,ABBREV_UNPAIRED_MULT,
stage3,/*mate*/NULL,/*acc1*/Shortread_accession(queryseq1),
- /*acc2*/NULL,pathnum,npaths,
+ /*acc2*/NULL,pathnum,npaths_primary,npaths_altloc,
Stage3end_absmq_score(stage3array[pathnum-1]),first_absmq,second_absmq,
Stage3end_mapq_score(stage3array[pathnum-1]),
chromosome_iit,queryseq1,/*queryseq2*/NULL,
/*pairedlength*/0,chrpos,/*mate_chrpos*/0U,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/0,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
@@ -329,7 +329,7 @@ filestring_fromresult_sam (Filestring_T *fp_failedinput_1, Filestring_T *fp_fail
static void
-print_header_singleend (Filestring_T fp, Request_T request, bool translocationp, int npaths) {
+print_header_singleend (Filestring_T fp, Request_T request, bool translocationp, int npaths_primary, int npaths_altloc) {
Shortread_T queryseq1;
if (print_m8_p == false) {
@@ -337,7 +337,7 @@ print_header_singleend (Filestring_T fp, Request_T request, bool translocationp,
FPRINTF(fp,">");
Shortread_print_oneline(fp,queryseq1);
- FPRINTF(fp,"\t%d",npaths);
+ FPRINTF(fp,"\t%d",npaths_primary + npaths_altloc);
if (translocationp == true) {
FPRINTF(fp," (transloc)");
}
@@ -366,7 +366,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput_1, Filestring_T *fp_fa
Resulttype_T resulttype;
Shortread_T queryseq1, queryseq2;
Stage3end_T *stage3array, stage3;
- int npaths, pathnum, first_absmq, second_absmq;
+ int npaths_primary, npaths_altloc, pathnum, first_absmq, second_absmq;
fp = Filestring_new(Request_id(request));
if (failedinput_root == NULL) {
@@ -385,7 +385,7 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput_1, Filestring_T *fp_fa
/* Skip */
} else {
Filestring_set_split_output(fp,OUTPUT_NM);
- print_header_singleend(fp,request,/*translocationp*/false,/*npaths*/0);
+ print_header_singleend(fp,request,/*translocationp*/false,/*npaths_primary*/0,/*npaths_altloc*/0);
FPRINTF(fp,"\n");
if (failedinput_root != NULL) {
@@ -402,10 +402,10 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput_1, Filestring_T *fp_fa
Filestring_set_split_output(fp,OUTPUT_UU);
queryseq1 = Request_queryseq1(request);
- stage3array = (Stage3end_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
stage3 = stage3array[0];
- print_header_singleend(fp,request,/*translocationp*/false,/*npaths*/1);
+ print_header_singleend(fp,request,/*translocationp*/false,npaths_primary,npaths_altloc);
Stage3end_print(fp,stage3,Stage3end_score(stage3),
chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
invert_first_p,/*hit5*/(Stage3end_T) NULL,/*hit3*/(Stage3end_T) NULL,
@@ -420,20 +420,20 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput_1, Filestring_T *fp_fa
*fp_failedinput_2 = (Filestring_T) NULL;
Filestring_set_split_output(fp,OUTPUT_UT);
- stage3array = (Stage3end_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
if (failsonlyp == true) {
/* Skip */
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
- print_header_singleend(fp,request,/*translocationp*/true,npaths);
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
+ print_header_singleend(fp,request,/*translocationp*/true,npaths_primary,npaths_altloc);
FPRINTF(fp,"\n");
} else {
queryseq1 = Request_queryseq1(request);
- print_header_singleend(fp,request,/*translocationp*/true,npaths);
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ print_header_singleend(fp,request,/*translocationp*/true,npaths_primary,npaths_altloc);
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
Stage3end_print(fp,stage3,Stage3end_score(stage3),
chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
@@ -448,14 +448,14 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput_1, Filestring_T *fp_fa
} else if (resulttype == SINGLEEND_MULT) {
*fp_failedinput_2 = (Filestring_T) NULL;
- stage3array = (Stage3end_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = (Stage3end_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
if (failsonlyp == true) {
/* Skip */
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
Filestring_set_split_output(fp,OUTPUT_UX);
- print_header_singleend(fp,request,/*translocationp*/false,npaths);
+ print_header_singleend(fp,request,/*translocationp*/false,npaths_primary,npaths_altloc);
if (print_m8_p == false) {
FPRINTF(fp,"\n");
}
@@ -464,8 +464,8 @@ filestring_fromresult_gsnap (Filestring_T *fp_failedinput_1, Filestring_T *fp_fa
queryseq1 = Request_queryseq1(request);
Filestring_set_split_output(fp,OUTPUT_UM);
- print_header_singleend(fp,request,/*translocationp*/false,npaths);
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ print_header_singleend(fp,request,/*translocationp*/false,npaths_primary,npaths_altloc);
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array[pathnum-1];
Stage3end_print(fp,stage3,Stage3end_score(stage3),
chromosome_iit,queryseq1,/*headerseq*/queryseq1,/*acc_suffix*/"",
@@ -596,7 +596,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
char *abbrev;
Sequence_T queryseq;
Stage3_T *stage3array;
- int npaths, pathnum, effective_maxpaths, first_absmq, second_absmq;
+ int npaths_primary, npaths_altloc, pathnum, effective_maxpaths, first_absmq, second_absmq;
Chimera_T chimera = NULL;
int chimerapos, chimeraequivpos, chimera_cdna_direction;
int querylength;
@@ -614,14 +614,14 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
queryseq = Request_queryseq(request);
querylength = Sequence_fulllength_given(queryseq);
- stage3array = Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array = Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
chimerapos = chimeraequivpos = -1;
chimera_cdna_direction = 0;
donor_prob = acceptor_prob = 0.0;
/* Translation */
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
Filestring_set_split_output(fp,OUTPUT_NM);
abbrev = ABBREV_NOMAPPING_1;
effective_maxpaths = 0;
@@ -683,7 +683,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else if (maxpaths_report == 0) {
effective_maxpaths = 1;
- if (npaths > 1) {
+ if (npaths_primary + npaths_altloc > 1) {
Filestring_set_split_output(fp,OUTPUT_UM);
abbrev = ABBREV_UNPAIRED_MULT;
} else if (Stage3_circularpos(stage3array[0]) > 0) {
@@ -696,7 +696,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
if (failsonlyp == true) {
printp = false;
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
printp = false;
} else {
Stage3_translate(stage3array[0],
@@ -707,7 +707,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
}
} else {
- if (npaths > 1) {
+ if (npaths_primary + npaths_altloc > 1) {
Filestring_set_split_output(fp,OUTPUT_UM);
abbrev = ABBREV_UNPAIRED_MULT;
} else if (Stage3_circularpos(stage3array[0]) > 0) {
@@ -718,15 +718,15 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
abbrev = ABBREV_UNPAIRED_UNIQ;
}
- if (npaths < maxpaths_report) {
- effective_maxpaths = npaths;
+ if (npaths_primary + npaths_altloc < maxpaths_report) {
+ effective_maxpaths = npaths_primary + npaths_altloc;
} else {
effective_maxpaths = maxpaths_report;
}
if (failsonlyp == true) {
printp = false;
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
printp = false;
} else {
for (pathnum = 1; pathnum <= effective_maxpaths; pathnum++) {
@@ -745,7 +745,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else {
if (*fp_failedinput != NULL &&
- (npaths == 0 && quiet_if_excessive_p && npaths > maxpaths_report)) {
+ (npaths_primary + npaths_altloc == 0 && quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report)) {
PUTC('>',*fp_failedinput);
Sequence_print_header(*fp_failedinput,headerseq,checksump);
Sequence_print(*fp_failedinput,queryseq,/*uppercasep*/false,wraplength,/*trimmedp*/false);
@@ -756,13 +756,13 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
PUTC('>',fp);
Sequence_print_header(fp,headerseq,checksump);
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
print_npaths(fp,/*npaths*/0,chrsubset_name,
/*mergedp*/false,/*chimera*/NULL,Result_failuretype(result));
} else {
- print_npaths(fp,npaths,chrsubset_name,mergedp,chimera,NO_FAILURE);
+ print_npaths(fp,npaths_primary + npaths_altloc,chrsubset_name,mergedp,chimera,NO_FAILURE);
for (pathnum = 1; pathnum <= effective_maxpaths; pathnum++) {
Stage3_print_pathsummary(fp,stage3array[pathnum-1],pathnum,
chromosome_iit,contig_iit,
@@ -793,7 +793,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else if (printtype == COMPRESSED) {
for (pathnum = 1; pathnum <= effective_maxpaths; pathnum++) {
Stage3_print_compressed(fp,stage3array[pathnum-1],queryseq,chromosome_iit,
- dbversion,usersegment,pathnum,npaths,
+ dbversion,usersegment,pathnum,/*npaths*/npaths_primary + npaths_altloc,
checksump,chimerapos,chimeraequivpos,
donor_prob,acceptor_prob,chimera_cdna_direction);
}
@@ -801,7 +801,7 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else if (printtype == CONTINUOUS) {
PUTC('>',fp);
Sequence_print_header(fp,headerseq,checksump);
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
FPRINTF(fp,"\n\n\n");
} else {
Stage3_print_alignment(fp,stage3array[0],genome,chromosome_iit,printtype,
@@ -812,8 +812,8 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else if (printtype == CONTINUOUS_BY_EXON) {
PUTC('>',fp);
Sequence_print_header(fp,headerseq,checksump);
- print_npaths(fp,npaths,chrsubset_name,mergedp,chimera,NO_FAILURE);
- if (npaths == 0) {
+ print_npaths(fp,npaths_primary + npaths_altloc,chrsubset_name,mergedp,chimera,NO_FAILURE);
+ if (npaths_primary + npaths_altloc == 0) {
FPRINTF(fp,"\n\n\n");
} else {
Stage3_print_pathsummary(fp,stage3array[0],/*pathnum*/1,
@@ -885,35 +885,35 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
#ifndef PMAP
} else if (printtype == SAM) {
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
Pair_print_sam_nomapping(fp,abbrev,/*acc1*/Sequence_accession(headerseq),/*acc2*/NULL,
Sequence_fullpointer(queryseq),Sequence_quality_string(queryseq),
Sequence_fulllength(queryseq),quality_shift,
Sequence_firstp(queryseq),sam_paired_p,sam_read_group_id);
- } else if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
Pair_print_sam_nomapping(fp,abbrev,/*acc1*/Sequence_accession(headerseq),/*acc2*/NULL,
Sequence_fullpointer(queryseq),Sequence_quality_string(queryseq),
Sequence_fulllength(queryseq),quality_shift,
Sequence_firstp(queryseq),sam_paired_p,sam_read_group_id);
} else if (mergedp == true) {
- Stage3_print_sam(fp,abbrev,stage3array[0],/*pathnum*/1,/*npaths*/1,
- Stage3_absmq_score(stage3array[0]),first_absmq,second_absmq,
+ Stage3_print_sam(fp,abbrev,stage3array[0],/*pathnum*/1,/*npaths_primary*/1,/*npaths_altloc*/0,
+ Stage3_absmq_score(stage3array[0]),second_absmq,
Stage3_mapq_score(stage3array[0]),
chromosome_iit,usersegment,queryseq,
/*chimera_part*/0,/*chimera*/NULL,quality_shift,sam_paired_p,
sam_read_group_id);
} else if (chimera != NULL) {
- Stage3_print_sam(fp,abbrev,stage3array[0],/*pathnum*/1,npaths,
- Stage3_absmq_score(stage3array[0]),first_absmq,second_absmq,
+ Stage3_print_sam(fp,abbrev,stage3array[0],/*pathnum*/1,npaths_primary,npaths_altloc,
+ Stage3_absmq_score(stage3array[0]),second_absmq,
Stage3_mapq_score(stage3array[0]),
chromosome_iit,usersegment,queryseq,
/*chimera_part*/-1,chimera,quality_shift,sam_paired_p,
sam_read_group_id);
- Stage3_print_sam(fp,abbrev,stage3array[1],/*pathnum*/1,npaths,
- Stage3_absmq_score(stage3array[0]),first_absmq,second_absmq,
+ Stage3_print_sam(fp,abbrev,stage3array[1],/*pathnum*/1,npaths_primary,npaths_altloc,
+ Stage3_absmq_score(stage3array[0]),second_absmq,
Stage3_mapq_score(stage3array[0]),
chromosome_iit,usersegment,queryseq,
/*chimera_part*/+1,chimera,quality_shift,sam_paired_p,
@@ -921,8 +921,8 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else {
for (pathnum = 1; pathnum <= effective_maxpaths; pathnum++) {
- Stage3_print_sam(fp,abbrev,stage3array[pathnum-1],pathnum,npaths,
- Stage3_absmq_score(stage3array[pathnum-1]),first_absmq,second_absmq,
+ Stage3_print_sam(fp,abbrev,stage3array[pathnum-1],pathnum,npaths_primary,npaths_altloc,
+ Stage3_absmq_score(stage3array[pathnum-1]),second_absmq,
Stage3_mapq_score(stage3array[pathnum-1]),
chromosome_iit,usersegment,queryseq,
/*chimera_part*/0,/*chimera*/NULL,quality_shift,sam_paired_p,
@@ -940,13 +940,13 @@ Output_filestring_fromresult (Filestring_T *fp_failedinput, Result_T result, Req
} else if (printtype == SPLICESITES) {
/* Print only best path */
- if (npaths > 0) {
+ if (npaths_primary + npaths_altloc > 0) {
Stage3_print_splicesites(fp,stage3array[0],chromosome_iit,queryseq);
}
} else if (printtype == INTRONS) {
/* Print only best path */
- if (npaths > 0) {
+ if (npaths_primary + npaths_altloc > 0) {
Stage3_print_introns(fp,stage3array[0],chromosome_iit,queryseq);
}
diff --git a/src/pair.c b/src/pair.c
index 56e3894..4b44204 100644
--- a/src/pair.c
+++ b/src/pair.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: pair.c 186092 2016-03-17 22:28:37Z twu $";
+static char rcsid[] = "$Id: pair.c 186094 2016-03-17 22:30:40Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -49,6 +49,7 @@ static char rcsid[] = "$Id: pair.c 186092 2016-03-17 22:28:37Z twu $";
#define MIN_INTRONLEN 20 /* For deciding between N and D in cigar string */
+
/* Check for ANSI mode, which does not include rint */
#ifdef __STRICT_ANSI__
#define rint(x) floor(0.5+(x))
@@ -127,6 +128,13 @@ static char rcsid[] = "$Id: pair.c 186092 2016-03-17 22:28:37Z twu $";
#define debug11(x)
#endif
+/* circularpos */
+#ifdef DEBUG12
+#define debug12(x) x
+#else
+#define debug12(x)
+#endif
+
@@ -225,7 +233,7 @@ Pair_print_ends (List_T pairs) {
void
-Pair_set_genomepos (struct Pair_T *pairarray, int npairs,
+Pair_set_genomepos (struct T *pairarray, int npairs,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp) {
int i;
Chrpos_T chraliaslength;
@@ -376,7 +384,7 @@ Pair_clip_bounded_array (struct T *source, int npairs, int minpos, int maxpos) {
/* Head of list is the medial part of the read */
List_T
-Pair_protect_end5 (List_T pairs, Pairpool_T pairpool) {
+Pair_protect_end5 (List_T pairs) {
List_T p;
T pair;
@@ -416,8 +424,8 @@ Pair_protect_end5 (List_T pairs, Pairpool_T pairpool) {
/* Head of list is the 3' distal end of the read */
List_T
-Pair_protect_end3 (List_T pairs, Pairpool_T pairpool) {
- List_T result = NULL, p;
+Pair_protect_end3 (List_T pairs) {
+ List_T p;
T pair;
p = pairs = List_reverse(pairs); /* Now head is medial end */
@@ -426,7 +434,7 @@ Pair_protect_end3 (List_T pairs, Pairpool_T pairpool) {
while (p != NULL && ((T) p->first)->gapp == false) {
pair = (T) p->first;
pair->protectedp = true;
- result = Pairpool_push_existing(result,pairpool,pair);
+ /* result = Pairpool_push_existing(result,pairpool,pair); */
p = p->rest;
}
@@ -434,7 +442,7 @@ Pair_protect_end3 (List_T pairs, Pairpool_T pairpool) {
if (p != NULL) {
pair = (T) p->first;
pair->protectedp = true;
- result = Pairpool_push_existing(result,pairpool,pair);
+ /* result = Pairpool_push_existing(result,pairpool,pair); */
p = p->rest;
}
@@ -442,7 +450,7 @@ Pair_protect_end3 (List_T pairs, Pairpool_T pairpool) {
while (p != NULL && ((T) p->first)->cdna != ' ' && ((T) p->first)->genome != ' ') {
pair = (T) p->first;
pair->protectedp = true;
- result = Pairpool_push_existing(result,pairpool,pair);
+ /* result = Pairpool_push_existing(result,pairpool,pair); */
p = p->rest;
}
@@ -450,11 +458,11 @@ Pair_protect_end3 (List_T pairs, Pairpool_T pairpool) {
while (p != NULL) {
pair = (T) p->first;
pair->protectedp = false;
- result = Pairpool_push_existing(result,pairpool,pair);
+ /* result = Pairpool_push_existing(result,pairpool,pair); */
p = p->rest;
}
- return result;
+ return List_reverse(pairs);
}
@@ -686,9 +694,9 @@ print_genomic_sequence (Filestring_T fp, struct T *ptr, int n, int npairs,
this = ptr;
if (chrstring == NULL) {
- sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%llu",(unsigned long long) (chroffset+this->genomepos + ONEBASEDP));
} else {
- sprintf(Buffer,"%s:%u",chrstring,this->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%s:%llu",chrstring,(unsigned long long) (this->genomepos + ONEBASEDP));
}
FPRINTF(fp,"%*s ",margin,Buffer);
for (i = 0; n < npairs && i < wraplength; n++, i++) {
@@ -713,9 +721,9 @@ print_genomicalt_sequence (Filestring_T fp, struct T *ptr, int n, int npairs,
this = ptr;
if (chrstring == NULL) {
- sprintf(Buffer,"%u",chroffset+this->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%llu",(unsigned long long) (chroffset+this->genomepos + ONEBASEDP));
} else {
- sprintf(Buffer,"%s:%u",chrstring,this->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%s:%llu",chrstring, (unsigned long long) (this->genomepos + ONEBASEDP));
}
FPRINTF(fp,"%*s ",margin,Buffer);
for (i = 0; n < npairs && i < wraplength; n++, i++) {
@@ -740,16 +748,16 @@ compute_margin (struct T *start, struct T *end, char *chrstring,
char Buffer[100];
if (chrstring == NULL) {
- sprintf(Buffer,"%u",chroffset + start->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%llu",(unsigned long long) (chroffset + start->genomepos + ONEBASEDP));
} else {
- sprintf(Buffer,"%s:%u",chrstring,start->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%s:%llu",chrstring,(unsigned long long) (start->genomepos + ONEBASEDP));
}
margin = (int) strlen(Buffer) + 1;
if (chrstring == NULL) {
- sprintf(Buffer,"%u",chroffset + end->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%llu",(unsigned long long) (chroffset + end->genomepos + ONEBASEDP));
} else {
- sprintf(Buffer,"%s:%u",chrstring,end->genomepos + ONEBASEDP);
+ sprintf(Buffer,"%s:%llu",chrstring,(unsigned long long) (end->genomepos + ONEBASEDP));
}
if ((int) strlen(Buffer) + 1 > margin) {
margin = (int) strlen(Buffer) + 1;
@@ -1204,10 +1212,10 @@ Pair_print_pathsummary (Filestring_T fp, int pathnum, T start, T end, Chrnum_T c
IIT_T altstrain_iit, char *strain, Univ_IIT_T contig_iit, char *dbversion,
int querylength_given, int skiplength, int trim_start, int trim_end,
int nexons, int matches, int unknowns, int mismatches,
- int qopens, int qindels, int topens, int tindels, int goodness,
+ int qopens, int qindels, int topens, int tindels,
bool watsonp, int cdna_direction,
int translation_start, int translation_end, int translation_length,
- int relaastart, int relaaend, int stage2_source, int stage2_indexsize) {
+ int relaastart, int relaaend) {
int querypos1, querypos2, den;
double fracidentity, coverage, trimmed_coverage;
Univcoord_T position1, position2;
@@ -2645,6 +2653,7 @@ print_gff3_exons_forward (Filestring_T fp, struct T *pairs, int npairs, int path
sprintf(token,"N%u",(intron_start - intron_end) + 1);
}
+ sprintf(token,"N%u",intron_end - intron_start + 1);
tokens = push_token(tokens,token);
} else if (gff_introns_p == true) {
if (i > 0) {
@@ -3160,35 +3169,49 @@ Pair_print_gff3 (Filestring_T fp, struct T *pairs, int npairs, int pathnum, char
}
+/* Don't want to use SOFT_CLIPS_AVOID_CIRCULARIZATION, because the
+ pairs array already contains the trim information */
int
Pair_circularpos (int *alias, struct T *pairs, int npairs, Chrpos_T chrlength, bool plusp, int querylength) {
Chrpos_T low, high;
struct T *ptr;
int i, ninsertions, querypos;
+ /* Chrpos_T chrhigh; */
+ debug12(Pair_dump_array(pairs,npairs,true));
+
+ /* chrhigh = chrlength + chrlength; */
if (plusp == true) {
- low = pairs[0].genomepos /*- pairs[0].querypos*/;
- high = pairs[npairs-1].genomepos /*+ (querylength - pairs[npairs-1].querypos)*/;
+ low = pairs[0].genomepos; /* includes "trim_left" */
+ high = pairs[npairs-1].genomepos; /* includes "trim_right" */
+ debug12(printf("plus: low %u, high %u\n",low,high));
if (low >= chrlength) {
- /* ptr->genomepos + ptr->querypos >= chrlength (SOFT_CLIPS_AVOID_CIRCULARIZATION */
- /* ptr->genomepos >= chrlength */
-
/* All of read after trimming is in circular alias */
- if (high > chrlength + chrlength) {
- *alias = +2;
+#if 0
+ if (high > chrhigh) { /* Differs from code in stage3hr.c */
+ *alias = +2; /* Extends beyond end of second copy */
} else {
- *alias = +1;
+ *alias = +1; /* All of read is in second copy */
}
+#else
+ *alias = +1;
+#endif
+ debug12(printf("Returning -1 with alias %d\n",*alias));
return -1;
} else if (high < chrlength) {
/* All of read after trimming is in circular proper */
- if (pairs[0].genomepos < (Chrpos_T) pairs[0].querypos) {
- *alias = -2;
+#if 0
+ if (low < (Chrpos_T) trim_left) {
+ *alias = -2; /* Extends beyond beginning of first copy */
} else {
- *alias = -1;
+ *alias = -1; /* All of read is in first copy */
}
+#else
+ *alias = -1;
+#endif
+ debug12(printf("Returning -1 with alias %d\n",*alias));
return -1;
} else {
@@ -3206,32 +3229,41 @@ Pair_circularpos (int *alias, struct T *pairs, int npairs, Chrpos_T chrlength, b
}
*alias = 0;
+ debug12(printf("Returning %d with no alias\n",(querypos - ninsertions)));
return querypos - ninsertions;
}
} else {
- low = pairs[npairs-1].genomepos /*- (querylength - pairs[npairs-1].querypos)*/;
- high = pairs[0].genomepos /*+ pairs[0].querypos*/;
+ low = pairs[npairs-1].genomepos; /* includes "trim_right" */
+ high = pairs[0].genomepos; /* includes "trim_left" */
+ debug12(printf("minus: low %u, high %u\n",low,high));
if (low >= chrlength) {
- /* ptr->genomepos + (querylength - ptr->querypos) >= chrlength (SOFT_CLIPS_AVOID_CIRCULARIZATION) */
- /* ptr->genomepos >= chrlength */
-
/* All of read after trimming is in circular alias */
- if (high > chrlength + chrlength) {
- *alias = +2;
+#if 0
+ if (high > chrhigh) { /* Differs from code in stage3hr.c */
+ *alias = +2; /* Extends beyond end of second copy */
} else {
- *alias = +1;
+ *alias = +1; /* All of read is in second copy */
}
+#else
+ *alias = +1;
+#endif
+ debug12(printf("Returning -1 with alias %d\n",*alias));
return -1;
} else if (high < chrlength) {
/* All of read after trimming is in circular proper */
- if (pairs[npairs-1].genomepos < (Chrpos_T) (querylength - pairs[npairs-1].querypos)) {
- *alias = -2;
+#if 0
+ if (low < (Chrpos_T) trim_right) {
+ *alias = -2; /* Extends beyond beginning of first copy */
} else {
- *alias = -1;
+ *alias = -1; /* All of read is in first copy */
}
+#else
+ *alias = -1;
+#endif
+ debug12(printf("Returning -1 with alias %d\n",*alias));
return -1;
} else {
@@ -3247,11 +3279,9 @@ Pair_circularpos (int *alias, struct T *pairs, int npairs, Chrpos_T chrlength, b
}
--ptr;
}
- /* printf("Ended up at querypos %d, genomepos %u < chrlength %u\n",ptr->querypos,ptr->genomepos,chrlength); */
- /* printf("Returning querylength %d - querypos %d - ninsertions %d = %d\n",
- querylength,ptr->querypos,ninsertions,querylength - ptr->querypos - ninsertions); */
*alias = 0;
+ debug12(printf("Returning %d with no alias\n",(querylength - querypos - ninsertions)));
return (querylength - querypos - ninsertions);
}
}
@@ -3527,8 +3557,9 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
struct T *pairs, *ptr, *ptr0, *this = NULL;
int exon_querystart = -1, exon_queryend;
Chrpos_T exon_genomestart = -1U, exon_genomeend;
+ Chrpos_T ntrim_start, ntrim_end;
int querypos, nmismatches_refdiff, nmismatches_bothdiff, nmatches,
- ntrim_start, ntrim_end, nindels, prev_nindels, i;
+ nindels, prev_nindels, i;
int last_querypos = -1;
Chrpos_T last_genomepos = -1U;
Univcoord_T pos;
@@ -3562,23 +3593,24 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
endtype = start_endtype;
nmismatches_refdiff = nmismatches_bothdiff = nmatches = 0;
- ntrim_start = ptr->querypos;
+ ntrim_start = (Chrpos_T) ptr->querypos;
+ ntrim_end = 0;
/* Print leading trimmed characters */
if (watsonp == true) {
if (ntrim_start >= (exon_genomestart - 1)) {
- for (querypos = 0; querypos < ntrim_start - exon_genomestart + 1; querypos++) {
+ for (querypos = 0; (Chrpos_T) querypos < ntrim_start - exon_genomestart + 1; querypos++) {
FPRINTF(fp,"*");
}
pos = chroffset;
- for ( ; querypos < ntrim_start; querypos++) {
+ for ( ; (Chrpos_T) querypos < ntrim_start; querypos++) {
c = Genome_get_char_blocks(&c_alt,pos++);
FPRINTF(fp,"%c",tolower(c));
}
} else {
pos = chroffset + (exon_genomestart - 1) - ntrim_start;
- for (querypos = 0; querypos < ntrim_start; querypos++) {
+ for (querypos = 0; (Chrpos_T) querypos < ntrim_start; querypos++) {
c = Genome_get_char_blocks(&c_alt,pos++);
FPRINTF(fp,"%c",tolower(c));
}
@@ -3586,18 +3618,18 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
} else {
if ((pos = chroffset + (exon_genomestart - 1) + ntrim_start) >= chrhigh) {
- assert(ntrim_start - (int) (chrhigh - chroffset - exon_genomestart + 1) < querylength);
- for (querypos = 0; querypos <= ntrim_start - (int) (chrhigh - chroffset - exon_genomestart + 1); querypos++) {
+ assert(ntrim_start - (chrhigh - chroffset - exon_genomestart + 1) < (Chrpos_T) querylength);
+ for (querypos = 0; (Chrpos_T) querypos <= ntrim_start - (int) (chrhigh - chroffset - exon_genomestart + 1); querypos++) {
FPRINTF(fp,"*");
}
pos = chrhigh - 1;
- for ( ; querypos < ntrim_start; querypos++) {
+ for ( ; (Chrpos_T) querypos < ntrim_start; querypos++) {
c = Genome_get_char_blocks(&c_alt,pos--);
FPRINTF(fp,"%c",tolower(complCode[(int) c]));
}
} else {
- for (querypos = 0; querypos < ntrim_start; querypos++) {
+ for (querypos = 0; (Chrpos_T) querypos < ntrim_start; querypos++) {
c = Genome_get_char_blocks(&c_alt,pos--);
FPRINTF(fp,"%c",tolower(complCode[(int) c]));
}
@@ -3673,6 +3705,7 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
case GMAP_VIA_SUBSTRINGS: FPRINTF(fp,",method:gmap_via_substrings"); break;
case GMAP_VIA_SEGMENTS: FPRINTF(fp,",method:gmap_via_segments"); break;
case GMAP_VIA_REGION: FPRINTF(fp,",method:gmap_via_region"); break;
+ case GMAP_NOT_APPLICABLE: abort();
}
if (pairedp == true) {
FPRINTF(fp,"\t");
@@ -3757,6 +3790,7 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
case GMAP_VIA_SUBSTRINGS: FPRINTF(fp,",method:gmap_via_substrings"); break;
case GMAP_VIA_SEGMENTS: FPRINTF(fp,",method:gmap_via_segments"); break;
case GMAP_VIA_REGION: FPRINTF(fp,",method:gmap_via_region"); break;
+ case GMAP_NOT_APPLICABLE: abort();
}
if (pairedp == true) {
FPRINTF(fp,"\t");
@@ -3828,6 +3862,7 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
case GMAP_VIA_SUBSTRINGS: FPRINTF(fp,",method:gmap_via_substrings"); break;
case GMAP_VIA_SEGMENTS: FPRINTF(fp,",method:gmap_via_segments"); break;
case GMAP_VIA_REGION: FPRINTF(fp,",method:gmap_via_region"); break;
+ case GMAP_NOT_APPLICABLE: abort();
}
if (pairedp == true) {
FPRINTF(fp,"\t");
@@ -3903,16 +3938,16 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
pos = chroffset + (exon_genomeend - 1);
if (pos + ntrim_end >= chrhigh) {
assert((int) (chrhigh - chroffset - exon_genomeend) < querylength);
- for (i = 0; i < (int) (chrhigh - chroffset - exon_genomeend); i++) {
+ for (i = 0; (Chrpos_T) i < (chrhigh - chroffset - exon_genomeend); i++) {
c = Genome_get_char_blocks(&c_alt,++pos);
FPRINTF(fp,"%c",tolower(c));
}
- for ( ; i < ntrim_end; i++) {
+ for ( ; (Chrpos_T) i < ntrim_end; i++) {
FPRINTF(fp,"*");
}
} else {
- for (i = 0; i < ntrim_end; i++) {
+ for (i = 0; (Chrpos_T) i < ntrim_end; i++) {
c = Genome_get_char_blocks(&c_alt,++pos);
FPRINTF(fp,"%c",tolower(c));
}
@@ -3921,16 +3956,16 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
} else {
pos = chroffset + (exon_genomeend - 1);
if (ntrim_end >= (exon_genomeend - 1)) {
- for (i = 0; i < exon_genomeend - 1; i++) {
+ for (i = 0; (Chrpos_T) i < exon_genomeend - 1; i++) {
c = Genome_get_char_blocks(&c_alt,--pos);
FPRINTF(fp,"%c",tolower(complCode[(int) c]));
}
- for ( ; i < ntrim_end; i++) {
+ for ( ; (Chrpos_T) i < ntrim_end; i++) {
FPRINTF(fp,"*");
}
} else {
- for (i = 0; i < ntrim_end; i++) {
+ for (i = 0; (Chrpos_T) i < ntrim_end; i++) {
c = Genome_get_char_blocks(&c_alt,--pos);
FPRINTF(fp,"%c",tolower(complCode[(int) c]));
}
@@ -3953,6 +3988,7 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
case GMAP_VIA_SUBSTRINGS: FPRINTF(fp,",method:gmap_via_substrings"); break;
case GMAP_VIA_SEGMENTS: FPRINTF(fp,",method:gmap_via_segments"); break;
case GMAP_VIA_REGION: FPRINTF(fp,",method:gmap_via_region"); break;
+ case GMAP_NOT_APPLICABLE: abort();
}
if (pairedp == true) {
FPRINTF(fp,"\t");
@@ -3973,6 +4009,7 @@ Pair_print_gsnap (Filestring_T fp, struct T *pairs_querydir, int npairs, int nse
return;
}
+#endif /* PMAP */
#ifdef GSNAP
@@ -4434,6 +4471,7 @@ Pair_fix_cdna_direction_array (struct T *pairs_querydir, int npairs, int cdna_di
case ATAC_FWD: this->comp = FWD_ATAC_INTRON_COMP; break;
default: this->comp = NONINTRON_COMP;
}
+#ifndef PMAP
} else if (cdna_direction < 0) {
switch (this->introntype) {
case ATAC_REV: this->comp = REV_ATAC_INTRON_COMP; break;
@@ -4441,6 +4479,7 @@ Pair_fix_cdna_direction_array (struct T *pairs_querydir, int npairs, int cdna_di
case GTAG_REV: this->comp = REV_CANONICAL_INTRON_COMP; break;
default: this->comp = NONINTRON_COMP; break;
}
+#endif
}
}
}
@@ -4559,6 +4598,7 @@ print_tokens_sam (Filestring_T fp, List_T tokens) {
return;
}
+#if 0
static void
print_tokens_stdout (List_T tokens) {
List_T p;
@@ -4571,6 +4611,7 @@ print_tokens_stdout (List_T tokens) {
return;
}
+#endif
/* Derived from print_tokens_gff3 */
@@ -4598,7 +4639,7 @@ Pair_tokens_cigarlength (List_T tokens) {
/* Only for GMAP program */
static unsigned int
-compute_sam_flag_nomate (int pathnum, int npaths, bool first_read_p, bool watsonp, bool sam_paired_p) {
+compute_sam_flag_nomate (int npaths, bool first_read_p, bool watsonp, bool sam_paired_p) {
unsigned int flag = 0U;
if (sam_paired_p == true) {
@@ -4781,7 +4822,7 @@ print_quality_revcomp (Filestring_T fp, char *quality, int querylength,
}
-
+#if 0
static int
sensedir_from_cdna_direction (int cdna_direction) {
if (cdna_direction > 0) {
@@ -4792,6 +4833,7 @@ sensedir_from_cdna_direction (int cdna_direction) {
return SENSE_NULL;
}
}
+#endif
/* Derived from print_gff3_cdna_match */
@@ -4802,16 +4844,16 @@ print_sam_line (Filestring_T fp, char *abbrev, bool first_read_p, char *acc1, ch
int nmismatches_refdiff, int nmismatches_bothdiff, int nindels,
bool intronp, char *queryseq_ptr, char *quality_string,
int hardclip_start, int hardclip_end, int querylength, Chimera_T chimera, int quality_shift,
- int pathnum, int npaths, int absmq_score, int first_absmq, int second_absmq, unsigned int flag,
- Chrnum_T chrnum, Univ_IIT_T chromosome_iit, Chrpos_T chrpos, Chrpos_T chrlength,
+ int pathnum, int npaths_primary, int npaths_altloc, int absmq_score, int second_absmq, unsigned int flag,
+ Univ_IIT_T chromosome_iit, Chrpos_T chrpos, Chrpos_T chrlength,
#ifdef GSNAP
Shortread_T queryseq, Resulttype_T resulttype, int pair_mapq_score, int end_mapq_score,
- char *mate_chrstring, Chrnum_T mate_chrnum, Chrnum_T mate_effective_chrnum,
- Chrpos_T mate_chrpos, Chrpos_T mate_chrlength, int mate_sensedir, int pairedlength,
+ char *mate_chrstring, Chrpos_T mate_chrpos, Chrpos_T mate_chrlength, int mate_sensedir, int pairedlength,
+ bool invertp,
#else
- int mapq_score, struct T *pairarray, int npairs,
+ int mapq_score,
#endif
- char *sam_read_group_id, bool invertp, bool merged_overlap_p, bool sarrayp) {
+ char *sam_read_group_id, bool merged_overlap_p, bool sarrayp) {
#if 0
/* Should already be checked when Stage3_T or Stage3end_T object was created */
@@ -4953,7 +4995,7 @@ print_sam_line (Filestring_T fp, char *abbrev, bool first_read_p, char *acc1, ch
print_tokens_sam(fp,md_tokens);
/* 12. TAGS: NH */
- FPRINTF(fp,"\tNH:i:%d",npaths);
+ FPRINTF(fp,"\tNH:i:%d",npaths_primary + npaths_altloc);
/* 12. TAGS: HI */
FPRINTF(fp,"\tHI:i:%d",pathnum);
@@ -5239,7 +5281,7 @@ Pair_compute_cigar (bool *intronp, int *hardclip_start, int *hardclip_end, struc
int Mlength = 0, Ilength = 0, Dlength = 0;
bool in_exon = false, deletionp;
struct T *ptr, *prev, *this = NULL;
- int exon_querystart = -1;
+ /* int exon_querystart = -1; */
int exon_queryend = -1;
Chrpos_T exon_genomestart = -1;
Chrpos_T exon_genomeend, genome_gap;
@@ -5325,7 +5367,7 @@ Pair_compute_cigar (bool *intronp, int *hardclip_start, int *hardclip_end, struc
/* Remaining possibilities are MATCH_COMP, DYNPROG_MATCH_COMP, AMBIGUOUS_COMP, INDEL_COMP,
SHORTGAP_COMP, or MISMATCH_COMP */
if (in_exon == false) {
- exon_querystart = this->querypos + 1;
+ /* exon_querystart = this->querypos + 1; */
exon_genomestart = this->genomepos + 1;
if (watsonp) {
intron_end = exon_genomestart - 1;
@@ -5509,11 +5551,13 @@ Pair_compute_cigar (bool *intronp, int *hardclip_start, int *hardclip_end, struc
}
+#if 0
/* Copied from samprint.c */
static bool
check_cigar_types (Intlist_T cigar_types) {
Intlist_T p;
- int type, last_type = 'M';
+ int type;
+ /* int last_type = 'M'; */
bool M_present_p = false;
for (p = cigar_types; p != NULL; p = Intlist_next(p)) {
@@ -5533,12 +5577,14 @@ check_cigar_types (Intlist_T cigar_types) {
return M_present_p;
}
+#endif
+#if 0
bool
Pair_check_cigar (struct T *pairs, int npairs, int querylength_given,
int clipdir, int hardclip5, int hardclip3,
- bool watsonp, int cdna_direction, bool first_read_p, bool circularp) {
+ bool watsonp, bool first_read_p, bool circularp) {
bool result;
Intlist_T cigar_types = NULL;
int hardclip_low, hardclip_high;
@@ -5668,7 +5714,7 @@ Pair_check_cigar (struct T *pairs, int npairs, int querylength_given,
if (in_exon == false) {
#if 0
/* Needed only for full token */
- exon_querystart = this->querypos + 1;
+ /* exon_querystart = this->querypos + 1; */
exon_genomestart = this->genomepos + 1;
if (watsonp) {
intron_end = exon_genomestart - 1;
@@ -5679,7 +5725,7 @@ Pair_check_cigar (struct T *pairs, int npairs, int querylength_given,
if (prev != NULL) {
/* Gap */
- /* genome_gap = abs(intron_end - intron_start) + 1; */
+ /* genome_gap = intron_end - intron_start + 1; */
deletionp = false;
#ifdef CONVERT_INTRONS_TO_DELETIONS
@@ -5839,6 +5885,7 @@ Pair_check_cigar (struct T *pairs, int npairs, int querylength_given,
Intlist_free(&cigar_types);
return result;
}
+#endif
@@ -6269,10 +6316,10 @@ void
Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairarray, int npairs, List_T cigar_tokens, bool intronp,
char *acc1, char *acc2, Chrnum_T chrnum, Univ_IIT_T chromosome_iit, Sequence_T usersegment,
char *queryseq_ptr, char *quality_string,
- int clipdir, int hardclip_low, int hardclip_high, int querylength_given,
+ int hardclip_low, int hardclip_high, int querylength_given,
bool watsonp, int sensedir, int chimera_part, Chimera_T chimera,
- int quality_shift, bool first_read_p, int pathnum, int npaths,
- int absmq_score, int first_absmq, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength,
+ int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc,
+ int absmq_score, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength,
#ifdef GSNAP
Shortread_T queryseq, Resulttype_T resulttype, unsigned int flag,
int pair_mapq_score, int end_mapq_score,
@@ -6282,7 +6329,7 @@ Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairarray, int npairs,
#else
int mapq_score, bool sam_paired_p,
#endif
- char *sam_read_group_id, bool invertp, bool circularp, bool merged_overlap_p, bool sarrayp) {
+ char *sam_read_group_id, bool invertp, bool merged_overlap_p, bool sarrayp) {
char *chrstring = NULL;
#ifdef GSNAP
char *mate_chrstring, *mate_chrstring_alloc = NULL;
@@ -6294,7 +6341,7 @@ Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairarray, int npairs,
int nmismatches_refdiff, nmismatches_bothdiff, nindels;
bool ignore_intronp;
int hardclip_start, hardclip_end;
- int hardclip_start_zero = 0, hardclip_end_zero = 0;
+ /* int hardclip_start_zero = 0, hardclip_end_zero = 0; */
struct T *clipped_pairarray;
int clipped_npairs;
bool cigar_tokens_alloc;
@@ -6323,11 +6370,11 @@ Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairarray, int npairs,
}
}
#else
- flag = compute_sam_flag_nomate(pathnum,npaths,first_read_p,watsonp,sam_paired_p);
+ flag = compute_sam_flag_nomate(npaths_primary + npaths_altloc,first_read_p,watsonp,sam_paired_p);
#endif
- debug4(printf("Entered Pair_print_sam with clipdir %d, watsonp %d, first_read_p %d, hardclip_low %d, and hardclip_high %d\n",
- clipdir,watsonp,first_read_p,hardclip_low,hardclip_high));
+ debug4(printf("Entered Pair_print_sam with watsonp %d, first_read_p %d, hardclip_low %d, and hardclip_high %d\n",
+ watsonp,first_read_p,hardclip_low,hardclip_high));
if (watsonp == true) {
hardclip_start = hardclip_low;
@@ -6371,17 +6418,15 @@ Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairarray, int npairs,
watsonp,sensedir,cigar_tokens,md_tokens,
nmismatches_refdiff,nmismatches_bothdiff,nindels,
intronp,queryseq_ptr,quality_string,hardclip_start,hardclip_end,
- querylength_given,chimera,quality_shift,pathnum,npaths,
- absmq_score,first_absmq,second_absmq,flag,
- chrnum,chromosome_iit,chrpos,chrlength,
+ querylength_given,chimera,quality_shift,pathnum,npaths_primary,npaths_altloc,
+ absmq_score,second_absmq,flag,chromosome_iit,chrpos,chrlength,
#ifdef GSNAP
queryseq,resulttype,pair_mapq_score,end_mapq_score,mate_chrstring,
- mate_chrnum,mate_effective_chrnum,mate_chrpos,mate_chrlength,
- mate_sensedir,pairedlength,
+ mate_chrpos,mate_chrlength,mate_sensedir,pairedlength,invertp,
#else
- mapq_score,clipped_pairarray,clipped_npairs,
+ mapq_score,
#endif
- sam_read_group_id,invertp,merged_overlap_p,sarrayp);
+ sam_read_group_id,merged_overlap_p,sarrayp);
/* Print procedures free the character strings */
Pair_tokens_free(&md_tokens);
@@ -6421,7 +6466,7 @@ Pair_print_sam_nomapping (Filestring_T fp, char *abbrev, char *acc1, char *acc2,
}
/* 2. FLAG */
- flag = compute_sam_flag_nomate(/*pathnum*/0,/*npaths*/0,first_read_p,/*watsonp*/true,sam_paired_p);
+ flag = compute_sam_flag_nomate(/*npaths*/0,first_read_p,/*watsonp*/true,sam_paired_p);
FPRINTF(fp,"\t%u",flag);
/* 3. RNAME: chr */
@@ -6462,10 +6507,6 @@ Pair_print_sam_nomapping (Filestring_T fp, char *abbrev, char *acc1, char *acc2,
}
-#endif
-
-
-
Uintlist_T
Pair_exonbounds (struct T *pairs, int npairs, Univcoord_T chroffset) {
Uintlist_T exonbounds = NULL;
@@ -7046,7 +7087,8 @@ Pair_print_exons (Filestring_T fp, struct T *pairs, int npairs, int wraplength,
int
Pair_nmatches_posttrim (int *max_match_length, List_T pairs, int pos5, int pos3) {
int nmatches = 0, match_length;
- bool in_intron = false, indelp = false;
+ bool in_intron = false;
+ /* bool indelp = false; */
List_T p;
T this;
@@ -7062,7 +7104,7 @@ Pair_nmatches_posttrim (int *max_match_length, List_T pairs, int pos5, int pos3)
in_intron = false;
}
if (this->comp == INDEL_COMP || this->comp == SHORTGAP_COMP) {
- indelp = true;
+ /* indelp = true; */
#ifndef PMAP
} else if (unknown_base(this->cdna) || unknown_base(this->genome) || this->comp == AMBIGUOUS_COMP) {
/* (*unknowns)++; */
@@ -7098,7 +7140,8 @@ Pair_nmatches_posttrim (int *max_match_length, List_T pairs, int pos5, int pos3)
int
Pair_array_nmatches_posttrim (struct T *pairarray, int npairs, int pos5, int pos3) {
int nmatches = 0;
- bool in_intron = false, indelp = false;
+ bool in_intron = false;
+ /* bool indelp = false; */
int i;
T this;
@@ -7113,7 +7156,7 @@ Pair_array_nmatches_posttrim (struct T *pairarray, int npairs, int pos5, int pos
in_intron = false;
}
if (this->comp == INDEL_COMP || this->comp == SHORTGAP_COMP) {
- indelp = true;
+ /* indelp = true; */
#ifndef PMAP
} else if (unknown_base(this->cdna) || unknown_base(this->genome) || this->comp == AMBIGUOUS_COMP) {
/* (*unknowns)++; */
@@ -7142,7 +7185,8 @@ Pair_nmismatches_region (int *nindelbreaks, struct T *pairs, int npairs,
int trim_left, int trim_right, int start_amb_nmatches, int end_amb_nmatches,
int querylength) {
int nmismatches = 0;
- bool in_intron = false, indelp = false;
+ /* bool in_intron = false; */
+ /* bool indelp = false; */
int i = 0;
T this;
@@ -7525,7 +7569,7 @@ Pair_fracidentity_changepoint (List_T pairs, int cdna_direction) {
int
-Pair_fracidentity_score (List_T pairs, int cdna_direction) {
+Pair_fracidentity_score (List_T pairs) {
int score = 0;
int i = 0;
@@ -7681,7 +7725,7 @@ static const Except_T Array_bounds_error = { "Exceeded array bounds" };
void
-Pair_matchscores (int *matchscores, struct T *ptr, int npairs, int querylength) {
+Pair_matchscores (int *matchscores, struct T *ptr, int npairs) {
T this;
int querypos;
int i;
@@ -9107,6 +9151,149 @@ Pair_end_bound (int *cdna_direction, List_T pairs, int breakpoint) {
}
+void
+Pair_trim_distances (int *trim5, int *trim3, List_T pairs) {
+ int trim_right = 0, trim_left = -1; /* Needs to be -1 to avoid trimming when pairs is NULL */
+ int bestscore, score;
+ int pairi;
+ List_T p;
+ T this;
+ bool in_indelp;
+
+ debug8(printf("Entered Pair_trim_distances\n"));
+ if (pairs == NULL) {
+ *trim5 = *trim3 = 0;
+ return;
+ }
+
+
+ /* Find trim_right */
+ bestscore = 0;
+ score = 0;
+ in_indelp = false;
+ this = (T) NULL;
+ for (p = pairs, pairi = 0; p != NULL; p = p->rest, pairi++) {
+ this = p->first;
+
+ if (this->comp == INDEL_COMP || this->comp == SHORTGAP_COMP) {
+ if (in_indelp == false) {
+ score += trim_indel_score;
+ if (score < 0) {
+ score = 0;
+ }
+ in_indelp = true;
+ }
+
+ } else {
+ in_indelp = false;
+ if (this->gapp) {
+ /* Don't count */
+
+ } else if (this->comp == INTRONGAP_COMP) {
+ /* Do nothing */
+
+ } else if (
+ /* cdna of N is used commonly in PMAP */
+#ifndef PMAP
+ this->cdna == 'N' ||
+#endif
+ this->comp == MISMATCH_COMP) {
+ score += trim_mismatch_score;
+ if (score < 0) {
+ score = 0;
+ } else if (score >= bestscore) { /* Want >= and not >, so extend to ends */
+ bestscore = score;
+ trim_right = pairi;
+ }
+
+ } else if (this->comp == MATCH_COMP || this->comp == DYNPROG_MATCH_COMP || this->comp == AMBIGUOUS_COMP) {
+ score += TRIM_MATCH_SCORE;
+ if (score >= bestscore) { /* Want >= and not >, so extend to ends */
+ bestscore = score;
+ trim_right = pairi;
+ }
+
+ } else {
+ fprintf(stderr,"Can't parse comp %c, gapp %d\n",this->comp,this->gapp);
+ abort();
+ }
+ }
+
+ debug8(printf("pairi %d, querypos %d, genomepos %u, comp %c: Trim right score %d, trim_right %d, protectedp %d\n",
+ pairi,this->querypos,this->genomepos,this->comp,score,trim_right,this->protectedp));
+ }
+
+ *trim3 = pairi - 1 - trim_right;
+ debug8(printf("Final: Trim right pairi %d, score %d, trim3 %d\n",pairi,score,*trim3));
+
+
+ /* Find trim_left */
+ pairs = List_reverse(pairs);
+ bestscore = 0;
+ score = 0;
+ in_indelp = false;
+ this = (T) NULL;
+ for (p = pairs, pairi = 0; p != NULL; p = p->rest, pairi++) {
+ this = p->first;
+
+ if (this->comp == INDEL_COMP || this->comp == SHORTGAP_COMP) {
+ if (in_indelp == false) {
+ score += trim_indel_score;
+ if (score < 0) {
+ score = 0;
+ }
+ in_indelp = true;
+ }
+
+ } else {
+ in_indelp = false;
+
+ if (this->gapp) {
+ /* Don't count */
+
+ } else if (this->comp == INTRONGAP_COMP) {
+ /* Do nothing */
+
+ } else if (
+ /* cdna of N is used commonly in PMAP */
+#ifndef PMAP
+ this->cdna == 'N' ||
+#endif
+ this->comp == MISMATCH_COMP) {
+ score += trim_mismatch_score;
+ if (score < 0) {
+ score = 0;
+ } else if (score >= bestscore) { /* Want >= and not >, so extend to ends */
+ bestscore = score;
+ trim_left = pairi;
+ }
+
+ } else if (this->comp == MATCH_COMP || this->comp == DYNPROG_MATCH_COMP || this->comp == AMBIGUOUS_COMP) {
+ score += TRIM_MATCH_SCORE;
+ if (score >= bestscore) { /* Want >= and not >, so extend to ends */
+ bestscore = score;
+ trim_left = pairi;
+ }
+
+ } else {
+ fprintf(stderr,"Can't parse comp %c, gapp %d\n",this->comp,this->gapp);
+ abort();
+ }
+ }
+
+ debug8(printf("pairi %d, querypos %d, genomepos %u, comp %c: Trim left score %d, trim_left %d, protectedp %d\n",
+ pairi,this->querypos,this->genomepos,this->comp,score,trim_left,this->protectedp));
+ }
+
+ *trim5 = pairi - 1 - trim_left;
+ debug8(printf("Final: Trim left pairi %d, score %d, trim5 %d\n",pairi,score,*trim5));
+
+ /* Restore original order */
+ pairs = List_reverse(pairs);
+ return;
+}
+
+
List_T
Pair_trim_ends (bool *trim5p, bool *trim3p, List_T pairs, int ambig_end_length_5, int ambig_end_length_3) {
@@ -9151,7 +9338,12 @@ Pair_trim_ends (bool *trim5p, bool *trim3p, List_T pairs, int ambig_end_length_5
} else if (this->comp == INTRONGAP_COMP) {
/* Do nothing */
- } else if (this->cdna == 'N' || this->comp == MISMATCH_COMP) {
+ } else if (
+ /* cdna of N is used commonly in PMAP */
+#ifndef PMAP
+ this->cdna == 'N' ||
+#endif
+ this->comp == MISMATCH_COMP) {
score += trim_mismatch_score;
if (score < 0) {
score = 0;
@@ -9220,7 +9412,12 @@ Pair_trim_ends (bool *trim5p, bool *trim3p, List_T pairs, int ambig_end_length_5
} else if (this->comp == INTRONGAP_COMP) {
/* Do nothing */
- } else if (this->cdna == 'N' || this->comp == MISMATCH_COMP) {
+ } else if (
+ /* cdna of N is used commonly in PMAP */
+#ifndef PMAP
+ this->cdna == 'N' ||
+#endif
+ this->comp == MISMATCH_COMP) {
score += trim_mismatch_score;
if (score < 0) {
score = 0;
diff --git a/src/pair.h b/src/pair.h
index 2bd8bf7..f38a793 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -1,4 +1,4 @@
-/* $Id: pair.h 174482 2015-09-22 00:58:39Z twu $ */
+/* $Id: pair.h 184432 2016-02-17 20:00:02Z twu $ */
#ifndef PAIR_INCLUDED
#define PAIR_INCLUDED
@@ -66,9 +66,9 @@ extern int
Pair_clip_bounded_array (struct T *source, int npairs, int minpos, int maxpos);
extern List_T
-Pair_protect_end5 (List_T pairs, Pairpool_T pairpool);
+Pair_protect_end5 (List_T pairs);
extern List_T
-Pair_protect_end3 (List_T pairs, Pairpool_T pairpool);
+Pair_protect_end3 (List_T pairs);
extern void
Pair_protect_list (List_T pairs);
@@ -96,10 +96,10 @@ Pair_print_pathsummary (Filestring_T fp, int pathnum, T start, T end, Chrnum_T c
IIT_T altstrain_iit, char *strain, Univ_IIT_T contig_iit, char *dbversion,
int querylength_given, int skiplength, int trim_start, int trim_end,
int nexons, int matches, int unknowns, int mismatches,
- int qopens, int qindels, int topens, int tindels, int goodness,
+ int qopens, int qindels, int topens, int tindels,
bool watsonp, int cdna_direction,
int translation_start, int translation_end, int translation_length,
- int relaastart, int relaaend, int stage2_source, int stage2_indexsize);
+ int relaastart, int relaaend);
extern void
Pair_print_coordinates (Filestring_T fp, struct T *pairs, int npairs, Chrnum_T chrnum,
@@ -187,11 +187,6 @@ Pair_alias_circular (struct T *pairs, int npairs, Chrpos_T chrlength);
extern void
Pair_unalias_circular (struct T *pairs, int npairs, Chrpos_T chrlength);
-extern bool
-Pair_check_cigar (struct T *pairs, int npairs, int querylength_given,
- int clipdir, int hardclip5, int hardclip3,
- bool watsonp, int cdna_direction, bool first_read_p, bool circularp);
-
extern List_T
Pair_clean_cigar (List_T tokens, bool watsonp);
extern List_T
@@ -202,10 +197,10 @@ extern void
Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairs, int npairs, List_T cigar_tokens, bool intronp,
char *acc1, char *acc2, Chrnum_T chrnum, Univ_IIT_T chromosome_iit, Sequence_T usersegment,
char *queryseq_ptr, char *quality_string,
- int clipdir, int hardclip_low, int hardclip_high, int querylength_given,
+ int hardclip_low, int hardclip_high, int querylength_given,
bool watsonp, int sensedir, int chimera_part, Chimera_T chimera,
- int quality_shift, bool first_read_p, int pathnum, int npaths,
- int absmq_score, int first_absmq, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength,
+ int quality_shift, bool first_read_p, int pathnum, int npaths_primary, int npaths_altloc,
+ int absmq_score, int second_absmq, Chrpos_T chrpos, Chrpos_T chrlength,
#ifdef GSNAP
Shortread_T queryseq, Resulttype_T resulttype, unsigned int flag,
int pair_mapq_score, int end_mapq_score,
@@ -215,7 +210,7 @@ Pair_print_sam (Filestring_T fp, char *abbrev, struct T *pairs, int npairs, List
#else
int mapq_score, bool sam_paired_p,
#endif
- char *sam_read_group_id, bool invertp, bool circularp, bool merged_overlap_p, bool sarrayp);
+ char *sam_read_group_id, bool invertp, bool merged_overlap_p, bool sarrayp);
extern void
Pair_print_sam_nomapping (Filestring_T fp, char *abbrev, char *acc1, char *acc2, char *queryseq_ptr,
@@ -294,7 +289,7 @@ Pair_fracidentity_array (int *matches, int *unknowns, int *mismatches, int *qope
int *topens, int *tindels, int *ncanonical, int *nsemicanonical, int *nnoncanonical,
double *min_splice_prob, struct T *ptr, int npairs, int cdna_direction);
extern int
-Pair_fracidentity_score (List_T pairs, int cdna_direction);
+Pair_fracidentity_score (List_T pairs);
extern double
Pair_frac_error (List_T pairs, int cdna_direction);
@@ -306,7 +301,7 @@ Pair_fracidentity_bounded (int *matches, int *unknowns, int *mismatches,
struct T *pairs, int npairs,
int cdna_direction, int minpos, int maxpos);
extern void
-Pair_matchscores (int *matchscores, struct T *ptr, int npairs, int querylength);
+Pair_matchscores (int *matchscores, struct T *ptr, int npairs);
extern int
Pair_maxnegscore (List_T pairs);
@@ -351,6 +346,9 @@ extern T
Pair_end_bound (int *cdna_direction, List_T pairs, int breakpoint);
+extern void
+Pair_trim_distances (int *trim5, int *trim3, List_T pairs);
+
extern List_T
Pair_trim_ends (bool *trim5p, bool *trim3p, List_T pairs, int ambig_end_length_5, int ambig_end_length_3);
diff --git a/src/pairpool.c b/src/pairpool.c
index 987f912..adc6af8 100644
--- a/src/pairpool.c
+++ b/src/pairpool.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: pairpool.c 147823 2014-09-15 23:13:11Z twu $";
+static char rcsid[] = "$Id: pairpool.c 184430 2016-02-17 19:56:26Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -200,6 +200,7 @@ Pairpool_push (List_T list, T this, int querypos, int genomepos, char cdna, char
int n;
assert(querypos >= 0);
+ assert(genomepos >= 0);
if (this->pairctr >= this->npairs) {
this->pairptr = add_new_pairchunk(this);
@@ -1058,13 +1059,15 @@ get_genomic_nt (char *g_alt, int genomicpos, Univcoord_T chroffset, Univcoord_T
List_T
Pairpool_add_genomeskip (bool *add_dashes_p, List_T pairs, int r, int c, int dist,
- char *genomesequence, char *genomesequenceuc,
- int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex, bool use_genomicseg_p) {
+ char *genomesequence, int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex) {
int j;
- char left1, left2, right2, right1, left1_alt, left2_alt, right2_alt, right1_alt, c2, c2_alt;
- int introntype;
+#ifdef DEBUG
+ char left1, left2, right2, right1;
+ char left1_alt, left2_alt, right2_alt, right1_alt;
+#endif
+ char c2, c2_alt;
+ /* int introntype; */
int querycoord, leftgenomecoord, rightgenomecoord, genomecoord, temp, step;
querycoord = r-1;
@@ -1087,25 +1090,22 @@ Pairpool_add_genomeskip (bool *add_dashes_p, List_T pairs, int r, int c, int dis
if (dist < MICROINTRON_LENGTH) {
*add_dashes_p = true;
} else {
+#ifdef DEBUG
/* Check for intron */
- if (use_genomicseg_p) {
- left1 = left1_alt = genomesequenceuc[leftgenomecoord];
- left2 = left2_alt = genomesequenceuc[leftgenomecoord+1];
- right2 = right2_alt = genomesequenceuc[rightgenomecoord-1];
- right1 = right1_alt = genomesequenceuc[rightgenomecoord];
+ if (genomesequence != NULL) {
+ left1 = left1_alt = genomesequence[leftgenomecoord];
+ left2 = left2_alt = genomesequence[leftgenomecoord+1];
+ right2 = right2_alt = genomesequence[rightgenomecoord-1];
+ right1 = right1_alt = genomesequence[rightgenomecoord];
} else {
left1 = get_genomic_nt(&left1_alt,genomeoffset+leftgenomecoord,chroffset,chrhigh,watsonp);
left2 = get_genomic_nt(&left2_alt,genomeoffset+leftgenomecoord+1,chroffset,chrhigh,watsonp);
right2 = get_genomic_nt(&right2_alt,genomeoffset+rightgenomecoord-1,chroffset,chrhigh,watsonp);
right1 = get_genomic_nt(&right1_alt,genomeoffset+rightgenomecoord,chroffset,chrhigh,watsonp);
}
-#ifdef EXTRACT_GENOMICSEG
- assert(left1 == genomesequenceuc[leftgenomecoord]);
- assert(left2 == genomesequenceuc[leftgenomecoord+1]);
- assert(right2 == genomesequenceuc[rightgenomecoord-1]);
- assert(right1 == genomesequenceuc[rightgenomecoord]);
#endif
+#if 0
#ifdef PMAP
introntype = Intron_type(left1,left2,right2,right1,
left1_alt,left2_alt,right2_alt,right1_alt,
@@ -1115,6 +1115,7 @@ Pairpool_add_genomeskip (bool *add_dashes_p, List_T pairs, int r, int c, int dis
left1_alt,left2_alt,right2_alt,right1_alt,
cdna_direction);
#endif
+#endif
#if 0
if (introntype == NONINTRON) {
@@ -1132,22 +1133,33 @@ Pairpool_add_genomeskip (bool *add_dashes_p, List_T pairs, int r, int c, int dis
} else {
genomecoord = rightgenomecoord;
}
- for (j = 0; j < dist; j++) {
- if (use_genomicseg_p) {
+
+ if (genomesequence != NULL) {
+ for (j = 0; j < dist; j++) {
c2 = c2_alt = genomesequence[genomecoord];
- } else {
- c2 = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
+
+ debug(printf("Pushing %d,%d [%d,%d] (-,%c),",r,c,queryoffset+querycoord,genomeoffset+genomecoord,c2));
+ pairs = Pairpool_push(pairs,pairpool,queryoffset+querycoord,genomeoffset+genomecoord,
+ ' ',INDEL_COMP,c2,c2_alt,dynprogindex);
+ debug(c--);
+ genomecoord += step;
}
+
+ } else {
+ for (j = 0; j < dist; j++) {
+ c2 = get_genomic_nt(&c2_alt,genomeoffset+genomecoord,chroffset,chrhigh,watsonp);
#ifdef EXTRACT_GENOMICSEG
- assert(c2 == genomesequence[genomecoord]);
+ assert(c2 == genomesequence[genomecoord]);
#endif
- debug(printf("Pushing %d,%d [%d,%d] (-,%c),",r,c,queryoffset+querycoord,genomeoffset+genomecoord,c2));
- pairs = Pairpool_push(pairs,pairpool,queryoffset+querycoord,genomeoffset+genomecoord,
- ' ',INDEL_COMP,c2,c2_alt,dynprogindex);
- debug(c--);
- genomecoord += step;
+ debug(printf("Pushing %d,%d [%d,%d] (-,%c),",r,c,queryoffset+querycoord,genomeoffset+genomecoord,c2));
+ pairs = Pairpool_push(pairs,pairpool,queryoffset+querycoord,genomeoffset+genomecoord,
+ ' ',INDEL_COMP,c2,c2_alt,dynprogindex);
+ debug(c--);
+ genomecoord += step;
+ }
}
+
} else {
debug(printf("Large gap %c%c..%c%c. Adding gap of type %d.\n",
left1,left2,right2,right1,introntype));
diff --git a/src/pairpool.h b/src/pairpool.h
index 4d2733e..ec4fe41 100644
--- a/src/pairpool.h
+++ b/src/pairpool.h
@@ -1,4 +1,4 @@
-/* $Id: pairpool.h 147823 2014-09-15 23:13:11Z twu $ */
+/* $Id: pairpool.h 184430 2016-02-17 19:56:26Z twu $ */
#ifndef PAIRPOOL_INCLUDED
#define PAIRPOOL_INCLUDED
@@ -61,10 +61,8 @@ Pairpool_add_queryskip (List_T pairs, int r, int c, int dist, char *querysequenc
int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, int dynprogindex);
extern List_T
Pairpool_add_genomeskip (bool *add_dashes_p, List_T pairs, int r, int c, int dist,
- char *genomesequence, char *genomesequenceuc,
- int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- int cdna_direction, bool watsonp, int dynprogindex, bool use_genomicseg_p);
+ char *genomesequence, int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp, int dynprogindex);
extern List_T
Pairpool_compact_copy (List_T list, T dest);
diff --git a/src/parserange.c b/src/parserange.c
index c2b226c..c66fcf2 100644
--- a/src/parserange.c
+++ b/src/parserange.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: parserange.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: parserange.c 184170 2016-02-12 19:37:19Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -184,8 +184,8 @@ translate_chromosomepos_universal (Univcoord_T *genomicstart, Chrpos_T *genomicl
Univ_IIT_label(chromosome_iit,index,&allocp),Interval_low(interval)));
*genomicstart = Univinterval_low(interval)+left;
if (*genomicstart < Univinterval_low(interval)) {
- fprintf(stderr,"%lu + %lu = %lu (exceeds a 32-bit unsigned int)\n",
- Univinterval_low(interval),left,*genomicstart);
+ fprintf(stderr,"%llu + %llu = %llu (exceeds a 32-bit unsigned int)\n",
+ (unsigned long long) Univinterval_low(interval),(unsigned long long) left,(unsigned long long) *genomicstart);
exit(9);
}
if (length == 0) {
@@ -200,6 +200,7 @@ translate_chromosomepos_universal (Univcoord_T *genomicstart, Chrpos_T *genomicl
}
+#if 0
static int
translate_chromosomepos_segment (Univcoord_T *segmentstart, Chrpos_T *segmentlength,
char *chromosome, Univcoord_T left, Chrpos_T length,
@@ -220,6 +221,7 @@ translate_chromosomepos_segment (Univcoord_T *segmentstart, Chrpos_T *segmentlen
return rc;
}
+#endif
static int
@@ -325,7 +327,7 @@ Parserange_query (char **divstring, Univcoord_T *coordstart, Univcoord_T *coorde
} else if (coords == NULL || *coords == '\0') {
debug(printf(" entire div\n"));
if ((iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ONE,*divstring,
- /*add_iit_p*/true,/*labels_read_p*/false)) == NULL) {
+ /*add_iit_p*/true)) == NULL) {
if (Access_file_exists_p(filename) == false) {
fprintf(stderr,"Cannot read file %s\n",filename);
} else {
@@ -388,7 +390,7 @@ Parserange_universal (char **div, bool *revcomp,
char *coords, *filename;
Univcoord_T result, left;
Chrpos_T length;
- Univ_IIT_T chromosome_iit, contig_iit;
+ Univ_IIT_T chromosome_iit;
Univinterval_T interval;
int theindex;
int rc;
@@ -457,7 +459,7 @@ Parserange_universal (char **div, bool *revcomp,
strlen(".contig.iit")+1) * sizeof(char));
sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot);
contig_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true);
+ /*divstring*/NULL,/*add_iit_p*/false);
FREEA(filename);
debug(printf("Interpreting segment %s as a contig\n",*div));
@@ -511,7 +513,7 @@ Parserange_universal (char **div, bool *revcomp,
strlen(".contig.iit")+1) * sizeof(char));
sprintf(filename,"%s/%s.contig.iit",genomesubdir,fileroot);
contig_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/false,/*labels_read_p*/true);
+ /*divstring*/NULL,/*add_iit_p*/false);
FREEA(filename);
rc = translate_contig(&(*genomicstart),&(*genomiclength),query,left=0,length=0,contig_iit);
@@ -608,7 +610,10 @@ Parserange_universal_iit (char **div, bool *revcomp,
if (rc != 0) {
/* Try contig */
debug(printf("Interpreting segment %s as a contig\n",*div));
- if (coords == NULL) {
+ if (contig_iit == NULL) {
+ debug(printf(" but contig_iit is not given\n"));
+ rc = -1;
+ } else if (coords == NULL) {
debug(printf(" entire contig\n"));
rc = translate_contig(&(*genomicstart),&(*genomiclength),*div,left=0,length=0,contig_iit);
} else if (Parserange_iscoordp(&result,coords)) {
diff --git a/src/pbinom.c b/src/pbinom.c
index eedcbf4..3b59eab 100644
--- a/src/pbinom.c
+++ b/src/pbinom.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: pbinom.c 40271 2011-05-28 02:29:18Z twu $";
+static char rcsid[] = "$Id: pbinom.c 184472 2016-02-18 00:12:16Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -1596,6 +1596,7 @@ beta_inc_AXPY (const double A, const double Y,
}
}
+#if 0
static double
gsl_cdf_beta_P (const double x, const double a, const double b) {
double P;
@@ -1612,6 +1613,7 @@ gsl_cdf_beta_P (const double x, const double a, const double b) {
return P;
}
+#endif
static double
gsl_cdf_beta_Q (const double x, const double a, const double b) {
@@ -1652,6 +1654,7 @@ gsl_cdf_binomial_P (const unsigned int k, const double p, const unsigned int n)
return P;
}
+#if 0
static double
gsl_cdf_binomial_Q (const unsigned int k, const double p, const unsigned int n) {
double Q;
@@ -1673,6 +1676,7 @@ gsl_cdf_binomial_Q (const unsigned int k, const double p, const unsigned int n)
return Q;
}
+#endif
/* Same as R function */
diff --git a/src/popcount.c b/src/popcount.c
index 09227a0..7ce7cc5 100644
--- a/src/popcount.c
+++ b/src/popcount.c
@@ -1,10 +1,10 @@
-static char rcsid[] = "$Id: popcount.c 157233 2015-01-22 18:58:26Z twu $";
+static char rcsid[] = "$Id: popcount.c 171614 2015-08-10 23:27:29Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
-#ifndef HAVE_BUILTIN_CTZ
+#if !defined(HAVE_SSE4_2) || !defined(HAVE_BUILTIN_CTZ)
const int mod_37_bit_position[] =
{
32, 0, 1, 26, 2, 23, 27, 0, 3, 16, 24, 30, 28, 11, 0, 13, 4,
@@ -13,7 +13,7 @@ const int mod_37_bit_position[] =
};
#endif
-#ifndef HAVE_BUILTIN_POPCOUNT
+#if !defined(HAVE_SSE4_2) || !defined(HAVE_BUILTIN_POPCOUNT)
const int count_bits[] =
{ 0, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4, 1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5,
1, 2, 2, 3, 2, 3, 3, 4, 2, 3, 3, 4, 3, 4, 4, 5, 2, 3, 3, 4, 3, 4, 4, 5, 3, 4, 4, 5, 4, 5, 5, 6,
@@ -2066,7 +2066,7 @@ const int count_bits[] =
};
#endif
-#ifndef HAVE_BUILTIN_CLZ
+#if !defined(HAVE_SSE4_2) || !defined(HAVE_BUILTIN_CLZ)
const int clz_table[] =
{16,15,14,14,13,13,13,13,12,12,12,12,12,12,12,12,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,11,
10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,
diff --git a/src/popcount.h b/src/popcount.h
index 17802ae..b8ceb05 100644
--- a/src/popcount.h
+++ b/src/popcount.h
@@ -1,19 +1,19 @@
-/* $Id: popcount.h 157225 2015-01-22 18:47:23Z twu $ */
+/* $Id: popcount.h 171614 2015-08-10 23:27:29Z twu $ */
#ifndef POPCOUNT_INCLUDED
#define POPCOUNT_INCLUDED
#ifdef HAVE_CONFIG_H
#include <config.h> /* For HAVE_BUILTIN_CTZ, HAVE_BUILTIN_POPCOUNT, HAVE_BUILTIN_CLZ */
#endif
-#ifndef HAVE_BUILTIN_CTZ
+#if !defined(HAVE_SSE4_2) || !defined(HAVE_BUILTIN_CTZ)
extern const int mod_37_bit_position[];
#endif
-#ifndef HAVE_BUILTIN_POPCOUNT
+#if !defined(HAVE_SSE4_2) || !defined(HAVE_BUILTIN_POPCOUNT)
extern const int count_bits[];
#endif
-#ifndef HAVE_BUILTIN_CLZ
+#if !defined(HAVE_SSE4_2) || !defined(HAVE_BUILTIN_CLZ)
extern const int clz_table[];
#endif
diff --git a/src/result.c b/src/result.c
index 85bbddf..84d79ba 100644
--- a/src/result.c
+++ b/src/result.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: result.c 81292 2012-12-11 20:32:28Z twu $";
+static char rcsid[] = "$Id: result.c 182440 2016-01-15 22:42:45Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -25,7 +25,8 @@ struct T {
List_T gregionlist; /* For debugging of stage 1 */
List_T diagonals; /* For debugging of diag */
Stage3_T *array;
- int npaths;
+ int npaths_primary;
+ int npaths_altloc;
int first_absmq;
int second_absmq;
Diagnostic_T diagnostic;
@@ -50,8 +51,9 @@ Result_chimera (T this) {
Stage3_T *
-Result_array (int *npaths, int *first_absmq, int *second_absmq, T this) {
- *npaths = this->npaths;
+Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this) {
+ *npaths_primary = this->npaths_primary;
+ *npaths_altloc = this->npaths_altloc;
*first_absmq = this->first_absmq;
*second_absmq = this->second_absmq;
return this->array;
@@ -83,7 +85,7 @@ Result_failuretype (T this) {
T
Result_new (int id, bool mergedp, Chimera_T chimera, Stage3_T *array,
- int npaths, int first_absmq, int second_absmq,
+ int npaths_primary, int npaths_altloc, int first_absmq, int second_absmq,
Diagnostic_T diagnostic, Failure_T failuretype) {
T new = (T) MALLOC_OUT(sizeof(*new));
@@ -93,7 +95,8 @@ Result_new (int id, bool mergedp, Chimera_T chimera, Stage3_T *array,
new->gregionlist = (List_T) NULL;
new->diagonals = (List_T) NULL;
new->array = array;
- new->npaths = npaths;
+ new->npaths_primary = npaths_primary;
+ new->npaths_altloc = npaths_altloc;
new->first_absmq = first_absmq;
new->second_absmq = second_absmq;
new->diagnostic = diagnostic;
@@ -102,41 +105,6 @@ Result_new (int id, bool mergedp, Chimera_T chimera, Stage3_T *array,
return new;
}
-T
-Result_new_stage1debug (int id, List_T gregionlist,
- Diagnostic_T diagnostic, Failure_T failuretype) {
- T new = (T) MALLOC_OUT(sizeof(*new));
-
- new->id = id;
- new->mergedp = false;
- new->chimera = (Chimera_T) NULL;
- new->gregionlist = gregionlist;
- new->diagonals = (List_T) NULL;
- new->array = (Stage3_T *) NULL;
- new->npaths = List_length(gregionlist);
- new->diagnostic = diagnostic;
- new->failuretype = failuretype;
-
- return new;
-}
-
-T
-Result_new_diag_debug (int id, List_T diagonals,
- Diagnostic_T diagnostic, Failure_T failuretype) {
- T new = (T) MALLOC_OUT(sizeof(*new));
-
- new->id = id;
- new->mergedp = false;
- new->chimera = (Chimera_T) NULL;
- new->gregionlist = (List_T) NULL;
- new->diagonals = diagonals;
- new->array = (Stage3_T *) NULL;
- new->npaths = List_length(diagonals);
- new->diagnostic = diagnostic;
- new->failuretype = failuretype;
-
- return new;
-}
void
Result_free (T *old) {
@@ -163,7 +131,7 @@ Result_free (T *old) {
stage3,Stage3_pairarray(stage3)));
Stage3_free(&stage3);
- for (i = 2; i < (*old)->npaths; i++) {
+ for (i = 2; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
stage3 = (*old)->array[i];
debug(printf("Freeing %d stage3 %p and pairarray %p\n",
i,stage3,Stage3_pairarray(stage3)));
@@ -174,7 +142,7 @@ Result_free (T *old) {
} else {
if ((*old)->array) {
- for (i = 0; i < (*old)->npaths; i++) {
+ for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
stage3 = (*old)->array[i];
Stage3_free(&stage3);
}
diff --git a/src/result.h b/src/result.h
index 4eda294..70de19c 100644
--- a/src/result.h
+++ b/src/result.h
@@ -1,4 +1,4 @@
-/* $Id: result.h 63195 2012-05-03 17:39:12Z twu $ */
+/* $Id: result.h 182440 2016-01-15 22:42:45Z twu $ */
#ifndef RESULT_INCLUDED
#define RESULT_INCLUDED
@@ -18,7 +18,7 @@ Result_mergedp (T this);
extern Chimera_T
Result_chimera (T this);
extern Stage3_T *
-Result_array (int *npaths, int *first_absmq, int *second_absmq, T this);
+Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this);
extern List_T
Result_gregionlist (T this);
extern List_T
@@ -30,13 +30,8 @@ Result_failuretype (T this);
extern T
Result_new (int id, bool mergedp, Chimera_T chimera, Stage3_T *array,
- int npaths, int first_absmq, int second_absmq, Diagnostic_T diagnostic, Failure_T failuretype);
-extern T
-Result_new_stage1debug (int id, List_T gregionlist,
- Diagnostic_T diagnostic, Failure_T failuretype);
-extern T
-Result_new_diag_debug (int id, List_T diagonals,
- Diagnostic_T diagnostic, Failure_T failuretype);
+ int npaths_primary, int npaths_altloc, int first_absmq, int second_absmq,
+ Diagnostic_T diagnostic, Failure_T failuretype);
extern void
Result_free (T *old);
diff --git a/src/resulthr.c b/src/resulthr.c
index 3f10925..b54806c 100644
--- a/src/resulthr.c
+++ b/src/resulthr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: resulthr.c 155282 2014-12-12 19:42:54Z twu $";
+static char rcsid[] = "$Id: resulthr.c 186728 2016-03-30 23:04:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -24,11 +24,13 @@ struct T {
Resulttype_T resulttype;
int id;
void **array;
- int npaths;
+ int npaths_primary;
+ int npaths_altloc;
int first_absmq;
int second_absmq;
void **array2;
- int npaths2;
+ int npaths2_primary;
+ int npaths2_altloc;
int first_absmq2;
int second_absmq2;
double worker_runtime;
@@ -100,8 +102,9 @@ Result_id (T this) {
void **
-Result_array (int *npaths, int *first_absmq, int *second_absmq, T this) {
- *npaths = this->npaths;
+Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this) {
+ *npaths_primary = this->npaths_primary;
+ *npaths_altloc = this->npaths_altloc;
*first_absmq = this->first_absmq;
*second_absmq = this->second_absmq;
return this->array;
@@ -110,8 +113,9 @@ Result_array (int *npaths, int *first_absmq, int *second_absmq, T this) {
/* For second end, when not paired with first end */
void **
-Result_array2 (int *npaths, int *first_absmq, int *second_absmq, T this) {
- *npaths = this->npaths2;
+Result_array2 (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this) {
+ *npaths_primary = this->npaths2_primary;
+ *npaths_altloc = this->npaths2_altloc;
*first_absmq = this->first_absmq2;
*second_absmq = this->second_absmq2;
return this->array2;
@@ -124,11 +128,12 @@ Result_worker_runtime (T this) {
T
-Result_single_read_new (int id, void **resultarray, int npaths, int first_absmq, int second_absmq) {
+Result_single_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc,
+ int first_absmq, int second_absmq) {
T new = (T) MALLOC_OUT(sizeof(*new));
Stage3end_T stage3end;
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
new->resulttype = SINGLEEND_NOMAPPING;
} else if (Stage3end_chrnum((Stage3end_T) resultarray[0]) == 0) {
#if 0
@@ -143,7 +148,7 @@ Result_single_read_new (int id, void **resultarray, int npaths, int first_absmq,
#endif
} else {
- if (npaths > 1) {
+ if (npaths_primary + npaths_altloc > 1) {
new->resulttype = SINGLEEND_MULT;
} else {
stage3end = ((Stage3end_T *) resultarray)[0];
@@ -157,7 +162,8 @@ Result_single_read_new (int id, void **resultarray, int npaths, int first_absmq,
new->id = id;
new->array = resultarray;
- new->npaths = npaths;
+ new->npaths_primary = npaths_primary;
+ new->npaths_altloc = npaths_altloc;
new->first_absmq = first_absmq;
new->second_absmq = second_absmq;
@@ -165,15 +171,12 @@ Result_single_read_new (int id, void **resultarray, int npaths, int first_absmq,
}
T
-Result_paired_read_new (int id, void **resultarray, int npaths, int first_absmq, int second_absmq,
- Pairtype_T final_pairtype) {
+Result_paired_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc,
+ int first_absmq, int second_absmq, Pairtype_T final_pairtype) {
T new = (T) MALLOC_OUT(sizeof(*new));
Stage3pair_T stage3pair;
- if (npaths == 0) {
- abort();
-
- } else if (final_pairtype == CONCORDANT_TRANSLOCATIONS) {
+ if (final_pairtype == CONCORDANT_TRANSLOCATIONS) {
#if 0
if (npaths == 1) {
new->resulttype = CONCORDANT_TRANSLOC;
@@ -186,14 +189,14 @@ Result_paired_read_new (int id, void **resultarray, int npaths, int first_absmq,
#endif
} else if (final_pairtype == PAIRED_UNSPECIFIED) {
- if (npaths == 1) {
+ if (npaths_primary + npaths_altloc <= 1) {
new->resulttype = PAIRED_UNIQ;
} else {
new->resulttype = PAIRED_MULT;
}
} else if (final_pairtype == CONCORDANT) {
- if (npaths > 1) {
+ if (npaths_primary + npaths_altloc > 1) {
new->resulttype = CONCORDANT_MULT;
} else {
stage3pair = ((Stage3pair_T *) resultarray)[0];
@@ -211,7 +214,8 @@ Result_paired_read_new (int id, void **resultarray, int npaths, int first_absmq,
new->id = id;
new->array = resultarray;
- new->npaths = npaths;
+ new->npaths_primary = npaths_primary;
+ new->npaths_altloc = npaths_altloc;
new->first_absmq = first_absmq;
new->second_absmq = second_absmq;
@@ -219,15 +223,20 @@ Result_paired_read_new (int id, void **resultarray, int npaths, int first_absmq,
}
T
-Result_paired_as_singles_new (int id, void **hits5, int npaths5, int first_absmq5, int second_absmq5,
- void **hits3, int npaths3, int first_absmq3, int second_absmq3) {
+Result_paired_as_singles_new (int id, void **hits5, int npaths5_primary, int npaths5_altloc,
+ int first_absmq5, int second_absmq5,
+ void **hits3, int npaths3_primary, int npaths3_altloc,
+ int first_absmq3, int second_absmq3) {
T new = (T) MALLOC_OUT(sizeof(*new));
Stage3end_T stage3end_5, stage3end_3;
+ int npaths5, npaths3;
debug(printf("npaths5 = %d, npaths3 = %d\n",npaths5,npaths3));
+ npaths5 = npaths5_primary + npaths5_altloc;
+ npaths3 = npaths3_primary + npaths3_altloc;
if (npaths5 == 0 && npaths3 == 0) {
new->resulttype = PAIREDEND_NOMAPPING;
- } else if (npaths5 == 0 && npaths3 == 1) {
+ } else if (npaths5 == 0 && npaths3_primary <= 1) {
stage3end_3 = (Stage3end_T) hits3[0];
if (Stage3end_chrnum(stage3end_3) == 0) {
new->resulttype = HALFMAPPING_TRANSLOC;
@@ -236,7 +245,7 @@ Result_paired_as_singles_new (int id, void **hits5, int npaths5, int first_absmq
} else {
new->resulttype = HALFMAPPING_UNIQ;
}
- } else if (npaths5 == 1 && npaths3 == 0) {
+ } else if (npaths5_primary <= 1 && npaths3 == 0) {
stage3end_5 = (Stage3end_T) hits5[0];
if (Stage3end_chrnum(stage3end_5) == 0) {
new->resulttype = HALFMAPPING_TRANSLOC;
@@ -247,7 +256,7 @@ Result_paired_as_singles_new (int id, void **hits5, int npaths5, int first_absmq
}
} else if (npaths5 == 0 || npaths3 == 0) {
new->resulttype = HALFMAPPING_MULT;
- } else if (npaths5 == 1 && npaths3 == 1) {
+ } else if (npaths5_primary <= 1 && npaths3_primary <= 1) {
stage3end_5 = (Stage3end_T) hits5[0];
stage3end_3 = (Stage3end_T) hits3[0];
if (Stage3end_chrnum(stage3end_5) == 0 ||
@@ -265,11 +274,13 @@ Result_paired_as_singles_new (int id, void **hits5, int npaths5, int first_absmq
new->id = id;
new->array = hits5;
- new->npaths = npaths5;
+ new->npaths_primary = npaths5_primary;
+ new->npaths_altloc = npaths5_altloc;
new->first_absmq = first_absmq5;
new->second_absmq = second_absmq5;
new->array2 = hits3;
- new->npaths2 = npaths3;
+ new->npaths2_primary = npaths3_primary;
+ new->npaths2_altloc = npaths3_altloc;
new->first_absmq2 = first_absmq3;
new->second_absmq2 = second_absmq3;
@@ -286,7 +297,7 @@ Result_free (T *old) {
case SINGLEEND_NOMAPPING: case PAIREDEND_NOMAPPING: break;
case SINGLEEND_UNIQ: case SINGLEEND_TRANSLOC: case SINGLEEND_MULT:
- for (i = 0; i < (*old)->npaths; i++) {
+ for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
stage3 = (*old)->array[i];
Stage3end_free(&stage3);
}
@@ -294,7 +305,7 @@ Result_free (T *old) {
break;
case PAIRED_UNIQ: case PAIRED_MULT: case CONCORDANT_UNIQ: case CONCORDANT_TRANSLOC: case CONCORDANT_MULT:
- for (i = 0; i < (*old)->npaths; i++) {
+ for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
stage3pair = (*old)->array[i];
Stage3pair_free(&stage3pair);
}
@@ -302,13 +313,13 @@ Result_free (T *old) {
break;
default:
- for (i = 0; i < (*old)->npaths2; i++) {
+ for (i = 0; i < (*old)->npaths2_primary + (*old)->npaths2_altloc; i++) {
stage3 = (*old)->array2[i];
Stage3end_free(&stage3);
}
FREE_OUT((*old)->array2);
- for (i = 0; i < (*old)->npaths; i++) {
+ for (i = 0; i < (*old)->npaths_primary + (*old)->npaths_altloc; i++) {
stage3 = (*old)->array[i];
Stage3end_free(&stage3);
}
diff --git a/src/resulthr.h b/src/resulthr.h
index c205ce2..ba8e9b4 100644
--- a/src/resulthr.h
+++ b/src/resulthr.h
@@ -1,4 +1,4 @@
-/* $Id: resulthr.h 155282 2014-12-12 19:42:54Z twu $ */
+/* $Id: resulthr.h 182440 2016-01-15 22:42:45Z twu $ */
#ifndef RESULTHR_INCLUDED
#define RESULTHR_INCLUDED
@@ -31,17 +31,21 @@ Result_id (T this);
extern int
Result_worker_id (T this);
extern void **
-Result_array (int *npaths, int *first_absmq, int *second_absmq, T this);
+Result_array (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this);
extern void **
-Result_array2 (int *npaths, int *first_absmq, int *second_absmq, T this);
+Result_array2 (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, T this);
extern T
-Result_single_read_new (int id, void **resultarray, int npaths, int first_absmq, int second_absmq);
+Result_single_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc,
+ int first_absmq, int second_absmq);
extern T
-Result_paired_read_new (int id, void **resultarray, int npaths, int first_absmq, int second_absmq,
+Result_paired_read_new (int id, void **resultarray, int npaths_primary, int npaths_altloc,
+ int first_absmq, int second_absmq,
Pairtype_T final_pairtype);
extern T
-Result_paired_as_singles_new (int id, void **hits5, int npaths5, int first_absmq5, int second_absmq5,
- void **hits3, int npaths3, int first_absmq3, int second_absmq3);
+Result_paired_as_singles_new (int id, void **hits5, int npaths5_primary, int npaths5_altloc,
+ int first_absmq5, int second_absmq5,
+ void **hits3, int npaths3_primary, int npaths3_altloc,
+ int first_absmq3, int second_absmq3);
extern void
Result_free (T *old);
diff --git a/src/sam_sort.c b/src/sam_sort.c
index a49097b..e7ce482 100644
--- a/src/sam_sort.c
+++ b/src/sam_sort.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: sam_sort.c 186087 2016-03-17 22:12:51Z twu $";
+static char rcsid[] = "$Id: sam_sort.c 186672 2016-03-29 23:46:34Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -27,9 +27,6 @@ static char rcsid[] = "$Id: sam_sort.c 186087 2016-03-17 22:12:51Z twu $";
#include "getopt.h"
-/* To do: Check of reverse complements of paired-reads work properly.
- May want to use low/high instead of first/second read */
-
/************************************************************************
*
* Check for correctness:
@@ -123,10 +120,13 @@ static char *dbversion = NULL;
static char *user_genomedir = NULL;
static bool sam_headers_p = true;
+
static bool mark_duplicates_p = false;
static bool mark_first_p = false;
static bool print_unique_p = true;
static bool print_duplicates_p = true;
+static bool restore_original_order_p = false;
+
static bool secondary_sort_method = NO_SECONDARY_SORT;
static bool multiple_primaries_p = false;
@@ -150,6 +150,7 @@ static struct option long_options[] = {
{"mark-first", no_argument, 0, 0}, /* mark_first_p */
{"dups-only", no_argument, 0, 0}, /* mark_duplicates_p, print_unique_p, print_duplicates_p */
{"uniq-only", no_argument, 0, 0}, /* mark_duplicates_p, print_unique_p, print_duplicates_p */
+ {"restore-orig-order", no_argument, 0, 0}, /* restore_original_order_p */
{"multiple-primaries", no_argument, 0, 0}, /* multiple_primaries_p */
{"no-sam-headers", no_argument, 0, 0}, /* sam_headers_p */
@@ -200,6 +201,8 @@ Other options\n\
\n\
--dups-only Print only duplicate reads\n\
--uniq-only Print only unique reads\n\
+ --restore-orig-order Restore original order of SAM file. Useful when --mark-dups is specified\n\
+ and sorting is not desired\n\
--multiple-primaries Specify if GSNAP or GMAP was run with the --multiple-primaries flag\n\
--no-sam-headers Do not print SAM header lines\n\
");
@@ -239,12 +242,13 @@ struct T {
Univcoord_T genomicpos_extend_softclip;
Univcoord_T mate_genomicpos;
int filei;
- off_t linestart;
+ size_t linestart;
int linelen;
char *acc; /* Needed for ACC_SECONDARY_SORT */
- int readindex; /* inputi or outputi. Needed for marking duplicates to find the other queryseq */
+ int lineindex; /* Original line order */
+ int readindex; /* inputi or outputi. Grouped by accession. Needed for marking duplicates to find the other queryseq */
char *queryseq5;
char *queryseq3;
@@ -279,10 +283,11 @@ Cell_standardize_queryseqs (T this) {
/* initial_softclip needs to be determined only if we are marking duplicates */
static void
-Cell_fill (struct T *this, int readindex, unsigned int flag, SAM_split_output_type split_output,
+Cell_fill (struct T *this, int lineindex, int readindex, unsigned int flag, SAM_split_output_type split_output,
bool query_lowp, int initial_softclip, Univcoord_T genomicpos,
- int filei, off_t fileposition, int linelen) {
+ int filei, size_t fileposition, int linelen) {
+ this->lineindex = lineindex;
this->readindex = readindex;
this->flag = flag;
@@ -305,8 +310,9 @@ Cell_fill (struct T *this, int readindex, unsigned int flag, SAM_split_output_ty
/* initial_softclip needs to be determined only if we are marking duplicates */
static void
Cell_fill_nodups (struct T *this, unsigned int flag, SAM_split_output_type split_output,
- Univcoord_T genomicpos, int filei, off_t fileposition, int linelen) {
+ Univcoord_T genomicpos, int filei, size_t fileposition, int linelen) {
+ this->lineindex = 0;
this->readindex = 0;
this->flag = flag;
@@ -328,7 +334,7 @@ Cell_fill_nodups (struct T *this, unsigned int flag, SAM_split_output_type split
#if 0
static void
-print_fromfile (FILE *fp, off_t fileposition, int linelength) {
+print_fromfile (FILE *fp, size_t fileposition, int linelength) {
char buffer[CHUNK];
moveto(fp,fileposition);
@@ -406,6 +412,20 @@ Cell_print_fromfile (FILE *fp_input, T this, Filestring_T headers) {
static int
+Cell_lineindex_cmp (const void *a, const void *b) {
+ T x = * (T *) a;
+ T y = * (T *) b;
+
+ if (x->lineindex < y->lineindex) {
+ return -1;
+ } else if (y->lineindex < x->lineindex) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+static int
Cell_genomicpos_cmp (const void *a, const void *b) {
T x = * (T *) a;
T y = * (T *) b;
@@ -595,7 +615,7 @@ process_without_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ni
struct T *cells_allocated, *ptr;
int i, j, k;
- off_t fileposition;
+ size_t fileposition;
int linelen;
unsigned int flag;
SAM_split_output_type split_output;
@@ -801,7 +821,7 @@ process_with_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ninpu
int i, k;
int j, j_low, j_high, mate_allocated;
- off_t fileposition;
+ size_t fileposition;
int linelen;
Univcoord_T genomicpos;
char *hiti;
@@ -811,7 +831,7 @@ process_with_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ninpu
SAM_split_output_type split_output;
int initial_softclip;
char *acc, *last_acc, *read;
- int readindex, nreads;
+ int lineindex, readindex, nreads;
int acclength, last_acclength, readlength;
bool query_lowp;
bool *duplicatep = NULL;
@@ -833,6 +853,7 @@ process_with_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ninpu
last_acc = MALLOC(sizeof(char));
last_acc[0] = '\0';
last_acclength = 0;
+ lineindex = -1;
readindex = -1; /* readindex is 0-based */
fprintf(stderr,"Reading SAM files...\n");
@@ -849,6 +870,7 @@ process_with_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ninpu
acc = Samread_parse_acc_and_softclip_fromfile(&acclength,&flag,&split_output,&hiti,
&genomicpos,&initial_softclip,&query_lowp,
fp_sam,chromosome_iit,chroffsets,linelen);
+ lineindex++;
if (acclength != last_acclength) {
readindex++;
} else if (strcmp(acc,last_acc)) {
@@ -890,7 +912,7 @@ process_with_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ninpu
}
FREE(hiti);
- Cell_fill(cells[k++],readindex,flag,split_output,query_lowp,initial_softclip,genomicpos,filei,fileposition,linelen);
+ Cell_fill(cells[k++],lineindex,readindex,flag,split_output,query_lowp,initial_softclip,genomicpos,filei,fileposition,linelen);
fileposition += linelen;
l = Intlist_next(l);
@@ -1189,7 +1211,10 @@ process_with_dups (FILE **sam_inputs, int *headerlengths, int *ncells, int ninpu
/* Re-sort entries, based on genomicpos (not extended by initial_softclip), and secondary criterion */
Stopwatch_start(stopwatch);
fprintf(stderr,"Re-sorting entries...");
- if (secondary_sort_method == NO_SECONDARY_SORT) {
+ if (restore_original_order_p == true) {
+ qsort(cells,ncells_total,sizeof(T),Cell_lineindex_cmp);
+
+ } else if (secondary_sort_method == NO_SECONDARY_SORT) {
qsort(cells,ncells_total,sizeof(T),Cell_genomicpos_cmp);
} else if (secondary_sort_method == ORIG_SECONDARY_SORT) {
@@ -1290,7 +1315,7 @@ main (int argc, char *argv[]) {
int nchromosomes, i;
Univcoord_T *chroffsets;
Chrpos_T *chrlengths;
- off_t fileposition;
+ size_t fileposition;
int lastchar;
char buffer[BUFFERLEN], *lastp, *p;
@@ -1363,6 +1388,9 @@ main (int argc, char *argv[]) {
print_unique_p = true;
print_duplicates_p = false;
+ } else if (!strcmp(long_name,"restore-orig-order")) {
+ restore_original_order_p = true;
+
} else if (!strcmp(long_name,"multiple-primaries")) {
multiple_primaries_p = true;
diff --git a/src/samprint.c b/src/samprint.c
index 221dd1d..bf47f05 100644
--- a/src/samprint.c
+++ b/src/samprint.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: samprint.c 183725 2016-02-04 00:40:15Z twu $";
+static char rcsid[] = "$Id: samprint.c 186666 2016-03-29 21:52:28Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -231,8 +231,7 @@ SAM_compute_chrpos (int hardclip_low, int hardclip_high, Stage3end_T this, int q
/* Want concordant substring */
if (Stage3end_plusp(this) == true) {
if (first_read_p == true) {
- /* Eventually want substringN */
- substring = Stage3end_substring2(this);
+ substring = Stage3end_substringN(this);
} else {
substring = Stage3end_substring1(this);
}
@@ -240,8 +239,7 @@ SAM_compute_chrpos (int hardclip_low, int hardclip_high, Stage3end_T this, int q
if (first_read_p == true) {
substring = Stage3end_substring1(this);
} else {
- /* Eventually want substringN */
- substring = Stage3end_substring2(this);
+ substring = Stage3end_substringN(this);
}
}
return Substring_compute_chrpos(substring,hardclip_low,hide_soft_clips_p);
@@ -359,7 +357,7 @@ make_complement_buffered (char *complement, char *sequence, unsigned int length)
void
SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3end_T mate, char *acc1, char *acc2,
Univ_IIT_T chromosome_iit, Resulttype_T resulttype, bool first_read_p,
- int pathnum, int npaths, bool artificial_mate_p, int npaths_mate,
+ int pathnum, int npaths_primary, int npaths_altloc, bool artificial_mate_p, int npaths_mate,
Chrpos_T mate_chrpos, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p) {
unsigned int flag;
@@ -411,8 +409,8 @@ SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3
}
/* 12. TAGS: NH */
- if (npaths > 0) {
- FPRINTF(fp,"\tNH:i:%d",npaths);
+ if (npaths_primary + npaths_altloc > 0) {
+ FPRINTF(fp,"\tNH:i:%d",npaths_primary + npaths_altloc);
if (add_paired_nomappers_p == true) {
FPRINTF(fp,"\tHI:i:%d",pathnum);
}
@@ -433,6 +431,7 @@ SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3
}
+#if 0
/* Derived from print_tokens_gff3 */
static void
print_tokens_sam (Filestring_T fp, List_T tokens) {
@@ -447,7 +446,9 @@ print_tokens_sam (Filestring_T fp, List_T tokens) {
return;
}
+#endif
+#if 0
static List_T
push_token (List_T tokens, char *token) {
char *copy;
@@ -456,6 +457,7 @@ push_token (List_T tokens, char *token) {
strcpy(copy,token);
return List_push(tokens,(void *) copy);
}
+#endif
#if 0
@@ -605,6 +607,7 @@ compute_cigar_old (List_T tokens, char type, int stringlength, int querypos, int
#endif
+#if 0
/* Currently used for insertions and deletions */
static List_T
compute_cigar (List_T tokens, char type, int stringlength, int querypos, int querylength,
@@ -713,8 +716,10 @@ compute_cigar (List_T tokens, char type, int stringlength, int querypos, int que
return tokens;
}
+#endif
+#if 0
/* Modified from compute_cigar */
static Intlist_T
compute_cigar_types_only (Intlist_T types, char type, int stringlength, int querypos, int querylength,
@@ -810,6 +815,7 @@ compute_cigar_types_only (Intlist_T types, char type, int stringlength, int quer
return types;
}
+#endif
static void
@@ -1137,6 +1143,7 @@ print_md_string (bool *printp, int *nmismatches_refdiff, int *nmismatches_bothdi
}
+#if 0
/* Copy also in pair.c for GMAP */
static bool
check_cigar_types (Intlist_T cigar_types) {
@@ -1161,12 +1168,13 @@ check_cigar_types (Intlist_T cigar_types) {
return M_present_p;
}
+#endif
static void
print_substrings (Filestring_T fp, char *abbrev, Stage3end_T stage3end, Stage3end_T mate,
- char *acc1, char *acc2, int pathnum, int npaths,
+ char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Shortread_T queryseq, int pairedlength,
Chrpos_T chrpos, Chrpos_T mate_chrpos, int hardclip_low, int hardclip_high,
@@ -1213,7 +1221,7 @@ print_substrings (Filestring_T fp, char *abbrev, Stage3end_T stage3end, Stage3en
/* 2. FLAG */
flag = SAM_compute_flag(plusp,mate,resulttype,first_read_p,
- pathnum,npaths,artificial_mate_p,npaths_mate,
+ pathnum,npaths_primary + npaths_altloc,artificial_mate_p,npaths_mate,
absmq_score,first_absmq,invertp,invert_mate_p);
FPRINTF(fp,"\t%u",flag);
@@ -2011,7 +2019,7 @@ print_substrings (Filestring_T fp, char *abbrev, Stage3end_T stage3end, Stage3en
/* 12. TAGS: NH */
/* 12. TAGS: HI */
/* 12. TAGS: NM */
- FPRINTF(fp,"\tNH:i:%d\tHI:i:%d\tNM:i:%d",npaths,pathnum,nmismatches_refdiff + nindels);
+ FPRINTF(fp,"\tNH:i:%d\tHI:i:%d\tNM:i:%d",npaths_primary + npaths_altloc,pathnum,nmismatches_refdiff + nindels);
if (snps_iit) {
/* 12. TAGS: XW and XV */
@@ -2171,9 +2179,10 @@ halfacceptor_dinucleotide (char *acceptor2, char *acceptor1, Substring_T accepto
static void
print_halfdonor (Filestring_T fp, char *abbrev, Substring_T donor, Stage3end_T this, Stage3end_T mate,
- char *acc1, char *acc2, int pathnum, int npaths, int absmq_score, int first_absmq, int second_absmq, int mapq_score,
+ char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
+ int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Shortread_T queryseq, int pairedlength,
- Chrpos_T concordant_chrpos, Chrpos_T donor_chrpos, Chrpos_T acceptor_chrpos, Chrpos_T mate_chrpos,
+ Chrpos_T donor_chrpos, Chrpos_T acceptor_chrpos, Chrpos_T mate_chrpos,
int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p,
bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
@@ -2207,8 +2216,8 @@ print_halfdonor (Filestring_T fp, char *abbrev, Substring_T donor, Stage3end_T t
/* 2. FLAG */
flag = SAM_compute_flag(plusp,mate,resulttype,first_read_p,
- pathnum,npaths,artificial_mate_p,npaths_mate,absmq_score,first_absmq,
- invertp,invert_mate_p);
+ pathnum,npaths_primary + npaths_altloc,artificial_mate_p,npaths_mate,
+ absmq_score,first_absmq,invertp,invert_mate_p);
FPRINTF(fp,"\t%u",flag);
/* 3. RNAME: chr */
@@ -2561,7 +2570,7 @@ print_halfdonor (Filestring_T fp, char *abbrev, Substring_T donor, Stage3end_T t
/* 12. TAGS: NH */
/* 12. TAGS: HI */
/* 12. TAGS: NM */
- FPRINTF(fp,"\tNH:i:%d\tHI:i:%d\tNM:i:%d",npaths,pathnum,nmismatches_refdiff);
+ FPRINTF(fp,"\tNH:i:%d\tHI:i:%d\tNM:i:%d",npaths_primary + npaths_altloc,pathnum,nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
@@ -2687,9 +2696,10 @@ print_halfdonor (Filestring_T fp, char *abbrev, Substring_T donor, Stage3end_T t
static void
print_halfacceptor (Filestring_T fp, char *abbrev, Substring_T acceptor, Stage3end_T this, Stage3end_T mate,
- char *acc1, char *acc2, int pathnum, int npaths, int absmq_score, int first_absmq, int second_absmq, int mapq_score,
+ char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
+ int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Shortread_T queryseq, int pairedlength,
- Chrpos_T concordant_chrpos, Chrpos_T donor_chrpos, Chrpos_T acceptor_chrpos, Chrpos_T mate_chrpos,
+ Chrpos_T donor_chrpos, Chrpos_T acceptor_chrpos, Chrpos_T mate_chrpos,
int hardclip_low, int hardclip_high, Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
bool use_hardclip_p, bool print_xt_p, int acceptor_sensedir, char donor_strand, char acceptor_strand,
@@ -2722,8 +2732,8 @@ print_halfacceptor (Filestring_T fp, char *abbrev, Substring_T acceptor, Stage3e
/* 2. FLAG */
flag = SAM_compute_flag(plusp,mate,resulttype,first_read_p,
- pathnum,npaths,artificial_mate_p,npaths_mate,absmq_score,first_absmq,
- invertp,invert_mate_p);
+ pathnum,npaths_primary + npaths_altloc,artificial_mate_p,npaths_mate,
+ absmq_score,first_absmq,invertp,invert_mate_p);
FPRINTF(fp,"\t%u",flag);
/* 3. RNAME: chr */
@@ -3068,7 +3078,7 @@ print_halfacceptor (Filestring_T fp, char *abbrev, Substring_T acceptor, Stage3e
/* 12. TAGS: NH */
/* 12. TAGS: HI */
/* 12. TAGS: NM */
- FPRINTF(fp,"\tNH:i:%d\tHI:i:%d\tNM:i:%d",npaths,pathnum,nmismatches_refdiff);
+ FPRINTF(fp,"\tNH:i:%d\tHI:i:%d\tNM:i:%d",npaths_primary + npaths_altloc,pathnum,nmismatches_refdiff);
if (snps_iit) {
/* 12. TAGS: XW and XV */
@@ -3194,13 +3204,13 @@ print_halfacceptor (Filestring_T fp, char *abbrev, Substring_T acceptor, Stage3e
/* Distant splicing, including scramble, inversion, translocation */
static void
print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T mate,
- char *acc1, char *acc2, int pathnum, int npaths,
+ char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
int absmq_score, int first_absmq, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Shortread_T queryseq, int pairedlength,
Chrpos_T mate_chrpos, int hardclip_low, int hardclip_high,
Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p) {
- Chrpos_T donor_chrpos, acceptor_chrpos, concordant_chrpos;
+ Chrpos_T donor_chrpos, acceptor_chrpos;
Substring_T donor, acceptor;
char *donor_chr, *acceptor_chr;
char donor1, donor2, acceptor2, acceptor1;
@@ -3271,20 +3281,20 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
/* NEEDS WORK: Need to decide whether to split halfdonor or halfacceptor */
/* Not sure if circular chromosomes should participate in distant splicing anyway */
if (0 && (circularpos = Stage3end_circularpos(this)) > 0) {
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- /*concordant_chrpos*/1,/*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
+ /*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3292,10 +3302,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
} else {
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3305,20 +3315,20 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
}
if (0 && (circularpos = Stage3end_circularpos(this)) > 0) {
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- /*concordant_chrpos*/1,donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
+ donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3326,10 +3336,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
} else {
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3340,20 +3350,20 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
} else if (Stage3end_sensedir(this) == SENSE_ANTI) {
if (0 && (circularpos = Stage3end_circularpos(this)) > 0) {
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- /*concordant_chrpos*/1,donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
+ donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3361,10 +3371,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
} else {
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3374,20 +3384,20 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
}
if (0 && (circularpos = Stage3end_circularpos(this)) > 0) {
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- /*concordant_chrpos*/1,/*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
+ /*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3395,10 +3405,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
} else {
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3410,20 +3420,20 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
} else {
/* SENSE_NULL (DNA distant chimera) */
if (0 && (circularpos = Stage3end_circularpos(this)) > 0) {
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
acceptor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- /*concordant_chrpos*/1,donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
+ donor_chrpos,/*acceptor_chrpos*/1,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3431,10 +3441,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
} else {
- print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfacceptor(fp,abbrev,acceptor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3444,20 +3454,20 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
}
if (0 && (circularpos = Stage3end_circularpos(this)) > 0) {
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
donor_sensedir,donor_strand,acceptor_strand,donor_chr,acceptor_chr,
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- /*concordant_chrpos*/1,/*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
+ /*donor_chrpos*/1,acceptor_chrpos,mate_chrpos,
/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3465,10 +3475,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
donor1,donor2,acceptor2,acceptor1,donor_prob,acceptor_prob,
/*circularp*/true);
} else {
- print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths,
+ print_halfdonor(fp,abbrev,donor,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,
chromosome_iit,queryseq,pairedlength,
- concordant_chrpos,donor_chrpos,acceptor_chrpos,mate_chrpos,
+ donor_chrpos,acceptor_chrpos,mate_chrpos,
hardclip_low,hardclip_high,resulttype,first_read_p,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*use_hardclip_p*/true,/*print_xt_p*/true,
@@ -3490,10 +3500,10 @@ print_exon_exon (Filestring_T fp, char *abbrev, Stage3end_T this, Stage3end_T ma
void
SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
- Stage3end_T this, Stage3end_T mate, char *acc1, char *acc2, int pathnum, int npaths,
+ Stage3end_T this, Stage3end_T mate, char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
int absmq_score, int first_absmq, int second_absmq, int mapq_score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
Shortread_T queryseq_mate, int pairedlength, Chrpos_T chrpos, Chrpos_T mate_chrpos,
- int clipdir, int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high,
+ int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high,
Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate,
int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p,
bool merge_samechr_p) {
@@ -3503,14 +3513,13 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
hittype = Stage3end_hittype(this);
- /* printf("hittype %s, chrpos %u\n",Stage3end_hittype_string(this),chrpos); */
/* Test for nomapping was chrpos == 0, but we can actually align to chrpos 0 */
/* Also, can use this test here because --quiet-if-excessive cases go directly to SAM_print_nomapping */
- if (npaths == 0) {
+ if (npaths_primary + npaths_altloc == 0) {
SAM_print_nomapping(fp,abbrev,queryseq,mate,acc1,acc2,chromosome_iit,resulttype,first_read_p,
- /*pathnum*/0,/*npaths*/0,artificial_mate_p,npaths_mate,mate_chrpos,
- quality_shift,sam_read_group_id,invertp,invert_mate_p);
+ /*pathnum*/0,/*npaths_primary*/0,/*npaths_altloc*/0,artificial_mate_p,npaths_mate,
+ mate_chrpos,quality_shift,sam_read_group_id,invertp,invert_mate_p);
if (fp_failedinput != NULL) {
if (first_read_p == true) {
@@ -3542,7 +3551,7 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
}
flag = SAM_compute_flag(Stage3end_plusp(this),mate,resulttype,first_read_p,
- pathnum,npaths,artificial_mate_p,npaths_mate,
+ pathnum,npaths_primary + npaths_altloc,artificial_mate_p,npaths_mate,
absmq_score,first_absmq,invertp,invert_mate_p);
querylength = Shortread_fulllength(queryseq);
@@ -3550,79 +3559,77 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
#if 0
&& Pair_check_cigar(Stage3end_pairarray(this),Stage3end_npairs(this),querylength,
/*clipdir*/+1,/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
- /*watsonp*/Stage3end_plusp(this),Stage3end_sensedir(this),
- first_read_p,/*circularp*/true) == true &&
+ /*watsonp*/Stage3end_plusp(this),first_read_p,/*circularp*/true) == true &&
Pair_check_cigar(Stage3end_pairarray(this),Stage3end_npairs(this),querylength,
/*clipdir*/+1,/*hardclip_low*/circularpos,/*hardclip_high*/0,
- /*watsonp*/Stage3end_plusp(this),Stage3end_sensedir(this),
- first_read_p,/*circularp*/true) == true
+ /*watsonp*/Stage3end_plusp(this),first_read_p,/*circularp*/true) == true
#endif
) {
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
Stage3end_cigar_tokens(this),Stage3end_gmap_intronp(this),
acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
- /*clipdir*/+1,/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,Shortread_fulllength(queryseq),
+ /*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,Shortread_fulllength(queryseq),
/*watsonp*/Stage3end_plusp(this),Stage3end_sensedir(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,first_read_p,
- pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,Stage3end_chrlength(this),
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,Stage3end_chrlength(this),
queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),
mate_chrpos,Stage3end_chrlength(mate),/*mate_sensedir*/Stage3end_sensedir(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/true,/*merged_overlap_p*/false,
+ pairedlength,sam_read_group_id,invertp,/*merged_overlap_p*/false,
Stage3end_sarrayp(this));
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
Stage3end_cigar_tokens(this),Stage3end_gmap_intronp(this),
acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
- /*clipdir*/+1,/*hardclip_low*/circularpos,/*hardclip_high*/0,Shortread_fulllength(queryseq),
+ /*hardclip_low*/circularpos,/*hardclip_high*/0,Shortread_fulllength(queryseq),
/*watsonp*/Stage3end_plusp(this),Stage3end_sensedir(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,first_read_p,
- pathnum,npaths,absmq_score,first_absmq,second_absmq,/*chrpos*/1,Stage3end_chrlength(this),
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,/*chrpos*/1,Stage3end_chrlength(this),
queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),
mate_chrpos,Stage3end_chrlength(mate),/*mate_sensedir*/Stage3end_sensedir(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/true,/*merged_overlap_p*/false,
+ pairedlength,sam_read_group_id,invertp,/*merged_overlap_p*/false,
Stage3end_sarrayp(this));
} else if (first_read_p == true) {
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
Stage3end_cigar_tokens(this),Stage3end_gmap_intronp(this),
acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
- clipdir,hardclip5_low,hardclip5_high,Shortread_fulllength(queryseq),
+ hardclip5_low,hardclip5_high,Shortread_fulllength(queryseq),
Stage3end_plusp(this),Stage3end_sensedir(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/true,
- pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,Stage3end_chrlength(this),
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,Stage3end_chrlength(this),
queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),
mate_chrpos,Stage3end_chrlength(mate),/*mate_sensedir*/Stage3end_sensedir(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/false,/*merged_overlap_p*/false,
+ pairedlength,sam_read_group_id,invertp,/*merged_overlap_p*/false,
Stage3end_sarrayp(this));
} else {
Pair_print_sam(fp,abbrev,Stage3end_pairarray(this),Stage3end_npairs(this),
Stage3end_cigar_tokens(this),Stage3end_gmap_intronp(this),
acc1,acc2,Stage3end_chrnum(this),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
Shortread_fullpointer(queryseq),Shortread_quality_string(queryseq),
- clipdir,hardclip3_low,hardclip3_high,Shortread_fulllength(queryseq),
+ hardclip3_low,hardclip3_high,Shortread_fulllength(queryseq),
Stage3end_plusp(this),Stage3end_sensedir(this),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/false,
- pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,Stage3end_chrlength(this),
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,Stage3end_chrlength(this),
queryseq,resulttype,flag,/*pair_mapq_score*/mapq_score,/*end_mapq_score*/mapq_score,
Stage3end_chrnum(mate),Stage3end_effective_chrnum(mate),
mate_chrpos,Stage3end_chrlength(mate),/*mate_sensedir*/Stage3end_sensedir(mate),
- pairedlength,sam_read_group_id,invertp,/*circularp*/false,/*merged_overlap_p*/false,
+ pairedlength,sam_read_group_id,invertp,/*merged_overlap_p*/false,
Stage3end_sarrayp(this));
}
} else if (hittype == TRANSLOC_SPLICE || (hittype == SAMECHR_SPLICE && merge_samechr_p == false)) {
if (first_read_p == true) {
- print_exon_exon(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
+ print_exon_exon(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,chromosome_iit,queryseq,pairedlength,
mate_chrpos,hardclip5_low,hardclip5_high,resulttype,/*first_read_p*/true,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p);
} else {
- print_exon_exon(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
+ print_exon_exon(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,chromosome_iit,queryseq,pairedlength,
mate_chrpos,hardclip3_low,hardclip3_high,resulttype,/*first_read_p*/false,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
@@ -3637,24 +3644,24 @@ SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
check_cigar_single(hittype,this,querylength,/*hardclip_low*/circularpos,/*hardclip_high*/0) == true
#endif
) {
- print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
+ print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
chrpos,mate_chrpos,/*hardclip_low*/0,/*hardclip_high*/querylength-circularpos,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/true);
- print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
+ print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
/*chrpos*/1,mate_chrpos,/*hardclip_low*/circularpos,/*hardclip_high*/0,
resulttype,first_read_p,artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/true);
} else if (first_read_p == true) {
- print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
+ print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
chrpos,mate_chrpos,hardclip5_low,hardclip5_high,resulttype,/*first_read_p*/true,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
invertp,invert_mate_p,/*circularp*/false);
} else {
- print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths,
+ print_substrings(fp,abbrev,this,mate,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
absmq_score,first_absmq,second_absmq,mapq_score,queryseq,pairedlength,
chrpos,mate_chrpos,hardclip3_low,hardclip3_high,resulttype,/*first_read_p*/false,
artificial_mate_p,npaths_mate,quality_shift,sam_read_group_id,
@@ -3676,7 +3683,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
Stage3pair_T *stage3pairarray, stage3pair;
Stage3end_T *stage3array1, *stage3array2, stage3, mate, hit5, hit3;
Chrpos_T chrpos, chrpos5, chrpos3;
- int npaths, npaths_max, npaths1, npaths2, pathnum;
+ int npaths_primary, npaths_altloc, npaths_max, npaths_primary_max, npaths_altloc_max,
+ npaths1_primary, npaths1_altloc, npaths2_primary, npaths2_altloc, pathnum;
int first_absmq, second_absmq, first_absmq1, second_absmq1, first_absmq2, second_absmq2;
int hardclip5_low = 0, hardclip5_high = 0, hardclip3_low = 0, hardclip3_high = 0, clipdir;
char *acc1, *acc2;
@@ -3701,13 +3709,13 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
Filestring_set_split_output(fp,OUTPUT_NM);
SAM_print_nomapping(fp,ABBREV_NOMAPPING_1,queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/0,/*npaths*/0,
+ /*first_read_p*/true,/*pathnum*/0,/*npaths_primary*/0,/*npaths_altloc*/0,
/*artificial_mate_p*/false,/*npaths_mate*/0,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_NOMAPPING_2,queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/0,/*npaths*/0,
+ /*first_read_p*/false,/*pathnum*/0,/*npaths_primary*/0,/*npaths_altloc*/0,
/*artificial_mate_p*/false,/*npaths_mate*/0,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_second_p,invert_first_p);
@@ -3721,7 +3729,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* Unwanted success: skip */
} else if (resulttype == CONCORDANT_UNIQ) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
stage3pair = stage3pairarray[0];
@@ -3755,25 +3763,25 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (merge_overlap_p == false || clipdir == 0) {
/* print first end */
SAM_print(fp,fp_failedinput_1,abbrev,hit5,/*mate*/hit3,
- acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ acc1,acc2,/*pathnum*/1,/*npaths_primary*/1,/*npaths_altloc*/0,
Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
/* print second end */
SAM_print(fp,fp_failedinput_2,abbrev,hit3,/*mate*/hit5,
- acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ acc1,acc2,/*pathnum*/1,/*npaths_primary*/1,/*npaths_altloc*/0,
Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
@@ -3799,20 +3807,20 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
Pair_print_sam(fp,/*abbrev*/ABBREV_UNPAIRED_UNIQ,pairarray,npairs,/*cigar_tokens*/NULL,/*gmap_intronp*/false,
acc1,/*acc2*/NULL,Stage3end_chrnum(hit5),chromosome_iit,/*usersegment*/(Sequence_T) NULL,
/*queryseq_ptr*/queryseq_merged,/*quality_string*/quality_merged,
- /*clipdir*/0,/*hardclip_low*/0,/*hardclip_high*/0,/*querylength*/querylength_merged,
+ /*hardclip_low*/0,/*hardclip_high*/0,/*querylength*/querylength_merged,
Stage3end_plusp(hit5),Stage3end_sensedir(hit5),
/*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/true,
- /*pathnum*/1,/*npaths*/1,
+ /*pathnum*/1,/*npaths_primary*/1,/*npaths_altloc*/0,
#if 0
- Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
+ Stage3pair_absmq_score(stage3pair),/*second_absmq*/0,
#else
- /*absmq_score*/MAX_QUALITY_SCORE,/*first_absmq*/MAX_QUALITY_SCORE,/*second_absmq*/0,
+ /*absmq_score*/MAX_QUALITY_SCORE,/*second_absmq*/0,
#endif
chrpos,Stage3end_chrlength(hit5),/*queryseq*/NULL,resulttype,flag,
/*pair_mapq_score*/MAX_QUALITY_SCORE,/*end_mapq_score*/MAX_QUALITY_SCORE,
/*mate_chrnum*/0,/*mate_effective_chrnum*/0,/*mate_chrpos*/0,/*mate_chrlength*/0,
/*mate_sensedir*/SENSE_NULL,/*pairedlength*/0,
- sam_read_group_id,/*invertp*/false,/*circularp*/false,/*merged_overlap_p*/true,
+ sam_read_group_id,/*invertp*/false,/*merged_overlap_p*/true,
Stage3end_sarrayp(hit5));
if (quality_merged != NULL) {
FREE_OUT(quality_merged);
@@ -3823,27 +3831,27 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
} else if (resulttype == CONCORDANT_TRANSLOC) {
Filestring_set_split_output(fp,OUTPUT_CT);
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
- if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
/* Print as nomapping, but send to fp_concordant_transloc */
SAM_print_nomapping(fp,ABBREV_CONCORDANT_TRANSLOC,
queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths,/*mate_chrpos*/0U,
+ /*first_read_p*/true,/*pathnum*/1,npaths_primary,npaths_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_CONCORDANT_TRANSLOC,
queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths,/*mate_chrpos*/0U,
+ /*first_read_p*/false,/*pathnum*/1,npaths_primary,npaths_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,/*mate_chrpos*/0U,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
} else {
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
/* Note: We are ignoring merge_overlap for concordant_transloc */
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = Stage3pair_hit5(stage3pair);
@@ -3869,48 +3877,48 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* print first end */
SAM_print(fp,fp_failedinput_1,ABBREV_CONCORDANT_TRANSLOC,
- hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths,
+ hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
/* print second end */
SAM_print(fp,fp_failedinput_2,ABBREV_CONCORDANT_TRANSLOC,
- hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths,
+ hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
}
}
} else if (resulttype == CONCORDANT_MULT) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
- if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
/* Print as nomapping, but send to fp_concordant_mult_xs */
Filestring_set_split_output(fp,OUTPUT_CX);
SAM_print_nomapping(fp,ABBREV_CONCORDANT_MULT_XS,
queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ /*first_read_p*/true,/*pathnum*/1,npaths_primary,npaths_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_CONCORDANT_MULT_XS,
queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ /*first_read_p*/false,/*pathnum*/1,npaths_primary,npaths_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_second_p,invert_first_p);
@@ -3922,7 +3930,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
} else {
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
Filestring_set_split_output(fp,OUTPUT_CM);
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = Stage3pair_hit5(stage3pair);
@@ -3949,25 +3957,25 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (merge_overlap_p == false || clipdir == 0) {
/* print first end */
SAM_print(fp,fp_failedinput_1,ABBREV_CONCORDANT_MULT,
- hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths,
+ hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
/* print second end */
SAM_print(fp,fp_failedinput_2,ABBREV_CONCORDANT_MULT,
- hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths,
+ hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- clipdir,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
@@ -3993,19 +4001,20 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
acc1,/*acc2*/NULL,Stage3end_chrnum(hit5),chromosome_iit,
/*usersegment*/(Sequence_T) NULL,
/*queryseq_ptr*/queryseq_merged,/*quality_string*/quality_merged,
- /*clipdir*/0,/*hardclip_low*/0,/*hardclip_high*/0,/*querylength*/querylength_merged,
+ /*hardclip_low*/0,/*hardclip_high*/0,/*querylength*/querylength_merged,
Stage3end_plusp(hit5),Stage3end_sensedir(hit5),
- /*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/true,pathnum,npaths,
+ /*chimera_part*/0,/*chimera*/NULL,quality_shift,/*first_read_p*/true,pathnum,
+ npaths_primary,npaths_altloc,
#if 0
- Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
+ Stage3pair_absmq_score(stage3pair),/*second_absmq*/0,
#else
- /*absmq_score*/MAX_QUALITY_SCORE,/*first_absmq*/MAX_QUALITY_SCORE,/*second_absmq*/0,
+ /*absmq_score*/MAX_QUALITY_SCORE,/*second_absmq*/0,
#endif
chrpos,Stage3end_chrlength(hit5),/*queryseq*/NULL,resulttype,flag,
/*pair_mapq_score*/MAX_QUALITY_SCORE,/*end_mapq_score*/MAX_QUALITY_SCORE,
/*mate_chrnum*/0,/*mate_effective_chrnum*/0,/*mate_chrpos*/0,/*mate_chrlength*/0,
/*mate_sensedir*/SENSE_NULL,/*pairedlength*/0,
- sam_read_group_id,/*invertp*/false,/*circularp*/false,/*merged_overlap_p*/true,
+ sam_read_group_id,/*invertp*/false,/*merged_overlap_p*/true,
Stage3end_sarrayp(hit5));
if (quality_merged != NULL) {
FREE_OUT(quality_merged);
@@ -4017,7 +4026,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
}
} else if (resulttype == PAIRED_UNIQ) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
stage3pair = stage3pairarray[0];
@@ -4047,46 +4056,46 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* print first end */
SAM_print(fp,fp_failedinput_1,abbrev,hit5,/*mate*/hit3,
- acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ acc1,acc2,/*pathnum*/1,/*npaths_primary*/1,/*npaths_altloc*/0,
Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
/* print second end */
SAM_print(fp,fp_failedinput_2,abbrev,hit3,/*mate*/hit5,
- acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ acc1,acc2,/*pathnum*/1,/*npaths_primary*/1,/*npaths_altloc*/0,
Stage3pair_absmq_score(stage3pair),first_absmq,/*second_absmq*/0,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
} else if (resulttype == PAIRED_MULT) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
- if (quiet_if_excessive_p && npaths > maxpaths_report) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths_report) {
/* Print as nomapping, but send to fp_paired_mult */
Filestring_set_split_output(fp,OUTPUT_PX);
SAM_print_nomapping(fp,ABBREV_PAIRED_MULT_XS,
queryseq1,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ /*first_read_p*/true,/*pathnum*/1,npaths_primary,npaths_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_first_p,invert_second_p);
SAM_print_nomapping(fp,ABBREV_PAIRED_MULT_XS,
queryseq2,/*mate*/(Stage3end_T) NULL,
acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ /*first_read_p*/false,/*pathnum*/1,npaths_primary,npaths_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
/*mate_chrpos*/0U,quality_shift,
sam_read_group_id,invert_second_p,invert_first_p);
@@ -4097,7 +4106,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
} else {
/* Stage3pair_eval(stage3pairarray,npaths,maxpaths_report,queryseq1,queryseq2); */
Filestring_set_split_output(fp,OUTPUT_PM);
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hardclip5_low = hardclip5_high = hardclip3_low = hardclip3_high = 0;
@@ -4109,25 +4118,25 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* print first end */
SAM_print(fp,fp_failedinput_1,ABBREV_PAIRED_MULT,
- hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths,
+ hit5,/*mate*/hit3,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,
merge_samechr_p);
/* print second end */
SAM_print(fp,fp_failedinput_2,ABBREV_PAIRED_MULT,
- hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths,
+ hit3,/*mate*/hit5,acc1,acc2,pathnum,npaths_primary,npaths_altloc,
Stage3pair_absmq_score(stage3pair),first_absmq,second_absmq,
Stage3pair_mapq_score(stage3pair),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
Stage3pair_pairlength(stage3pair),/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths,
+ hardclip5_low,hardclip5_high,hardclip3_low,hardclip3_high,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_primary + npaths_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,
merge_samechr_p);
}
@@ -4135,8 +4144,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
} else if (resulttype == UNPAIRED_UNIQ) {
/* Even though they are not related, we should print mate information in this situation */
- stage3array1 = (Stage3end_T *) Result_array(&npaths1,&first_absmq1,&second_absmq1,result);
- stage3array2 = (Stage3end_T *) Result_array2(&npaths2,&first_absmq2,&second_absmq2,result);
+ stage3array1 = (Stage3end_T *) Result_array(&npaths1_primary,&npaths1_altloc,&first_absmq1,&second_absmq1,result);
+ stage3array2 = (Stage3end_T *) Result_array2(&npaths2_primary,&npaths2_altloc,&first_absmq2,&second_absmq2,result);
hardclip5_low = hardclip5_high = hardclip3_low = hardclip3_high = 0;
@@ -4155,12 +4164,13 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* print first end */
/* Stage3end_eval_and_sort(stage3array1,npaths1,maxpaths_report,queryseq1); */
- SAM_print(fp,fp_failedinput_1,abbrev,hit5,/*mate*/hit3,acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ SAM_print(fp,fp_failedinput_1,abbrev,hit5,/*mate*/hit3,acc1,acc2,/*pathnum*/1,
+ /*npaths_primary*/1,/*npaths_altloc*/0,
Stage3end_absmq_score(stage3array1[0]),first_absmq1,/*second_absmq*/0,
Stage3end_mapq_score(stage3array1[0]),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/1,quality_shift,sam_read_group_id,
invert_first_p,invert_second_p,merge_samechr_p);
@@ -4168,18 +4178,20 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* print second end */
/* Stage3end_eval_and_sort(stage3array2,npaths2,maxpaths_report,queryseq2); */
- SAM_print(fp,fp_failedinput_2,abbrev,hit3,/*mate*/hit5,acc1,acc2,/*pathnum*/1,/*npaths*/1,
+ SAM_print(fp,fp_failedinput_2,abbrev,hit3,/*mate*/hit5,acc1,acc2,/*pathnum*/1,
+ /*npaths_primary*/1,/*npaths_altloc*/0,
Stage3end_absmq_score(stage3array2[0]),first_absmq2,/*second_absmq*/0,
Stage3end_mapq_score(stage3array2[0]),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/1,quality_shift,sam_read_group_id,
invert_second_p,invert_first_p,merge_samechr_p);
} else if (resulttype == UNPAIRED_MULT || resulttype == UNPAIRED_TRANSLOC) {
if (resulttype == UNPAIRED_MULT) {
- if (quiet_if_excessive_p && npaths1 > maxpaths_report && npaths2 > maxpaths_report) {
+ if (quiet_if_excessive_p && npaths1_primary + npaths1_altloc > maxpaths_report &&
+ npaths2_primary + npaths2_altloc > maxpaths_report) {
Filestring_set_split_output(fp,OUTPUT_UX);
} else {
Filestring_set_split_output(fp,OUTPUT_UM);
@@ -4190,8 +4202,8 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
abbrev = ABBREV_UNPAIRED_TRANSLOC;
}
- stage3array1 = (Stage3end_T *) Result_array(&npaths1,&first_absmq1,&second_absmq1,result);
- stage3array2 = (Stage3end_T *) Result_array2(&npaths2,&first_absmq2,&second_absmq2,result);
+ stage3array1 = (Stage3end_T *) Result_array(&npaths1_primary,&npaths1_altloc,&first_absmq1,&second_absmq1,result);
+ stage3array2 = (Stage3end_T *) Result_array2(&npaths2_primary,&npaths2_altloc,&first_absmq2,&second_absmq2,result);
#if 0
/* Do eval and sorting first */
@@ -4216,8 +4228,17 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (add_paired_nomappers_p == true) {
/* Artificially pair up results */
- npaths_max = (npaths1 > npaths2) ? npaths1 : npaths2;
- for (pathnum = 1; pathnum <= npaths1 && pathnum <= npaths2 && pathnum <= maxpaths_report; pathnum++) {
+ if (npaths1_primary + npaths1_altloc > npaths2_primary + npaths2_altloc) {
+ npaths_primary_max = npaths1_primary;
+ npaths_altloc_max = npaths1_altloc;
+ npaths_max = npaths1_primary + npaths1_altloc;
+ } else {
+ npaths_primary_max = npaths2_primary;
+ npaths_altloc_max = npaths2_altloc;
+ npaths_max = npaths2_primary + npaths2_altloc;
+ }
+ for (pathnum = 1; pathnum <= npaths1_primary + npaths1_altloc &&
+ pathnum <= npaths2_primary + npaths2_altloc && pathnum <= maxpaths_report; pathnum++) {
/* hardclip5_low = hardclip5_high = 0; */
chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,/*stage3*/stage3array1[pathnum-1],
Shortread_fulllength(queryseq1),/*first_read_p*/true);
@@ -4227,53 +4248,53 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
Shortread_fulllength(queryseq2),/*first_read_p*/false);
stage3 = stage3array1[pathnum-1];
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,/*mate*/stage3array2[pathnum-1],acc1,acc2,pathnum,npaths_max,
- Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,/*mate*/stage3array2[pathnum-1],acc1,acc2,pathnum,
+ npaths_primary_max,npaths_altloc_max,Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
stage3 = stage3array2[pathnum-1];
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,/*mate*/stage3array1[pathnum-1],acc1,acc2,pathnum,npaths_max,
- Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,/*mate*/stage3array1[pathnum-1],acc1,acc2,pathnum,
+ npaths_primary_max,npaths_altloc_max,Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
/* Print remaining results with non-mappers */
- if (npaths1 > npaths2) {
- for ( ; pathnum <= npaths1 && pathnum <= maxpaths_report; pathnum++) {
+ if (npaths1_primary + npaths1_altloc > npaths2_primary + npaths2_altloc) {
+ for ( ; pathnum <= npaths1_primary + npaths1_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array1[pathnum-1];
/* hardclip5_low = hardclip5_high = 0; */
chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,
Shortread_fulllength(queryseq1),/*first_read_p*/true);
chrpos3 = 0;
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,/*mate*/NULL,acc1,acc2,pathnum,npaths_max,
- Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,/*mate*/NULL,acc1,acc2,pathnum,
+ npaths_primary_max,npaths_altloc_max,Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
/* matching nomapper for second end */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/false,pathnum,npaths_max,
+ resulttype,/*first_read_p*/false,pathnum,npaths_primary_max,npaths_altloc_max,
/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
}
- } else if (npaths2 > npaths1) {
- for ( ; pathnum <= npaths2 && pathnum <= maxpaths_report; pathnum++) {
+ } else if (npaths2_primary + npaths2_altloc > npaths1_primary + npaths1_altloc) {
+ for ( ; pathnum <= npaths2_primary + npaths2_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array2[pathnum-1];
/* hardclip3_low = hardclip3_high = 0; */
chrpos5 = 0;
@@ -4282,16 +4303,16 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* matching nomapper for first end */
SAM_print_nomapping(fp,abbrev,queryseq1,/*mate*/stage3,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/true,pathnum,npaths_max,
+ resulttype,/*first_read_p*/true,pathnum,npaths_primary_max,npaths_altloc_max,
/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,/*mate*/NULL,acc1,acc2,pathnum,npaths_max,
- Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,/*mate*/NULL,acc1,acc2,pathnum,
+ npaths_primary_max,npaths_altloc_max,Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/false,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
@@ -4299,10 +4320,10 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
} else {
/* print first end results */
- if (npaths2 == 0) {
+ if (npaths2_primary + npaths2_altloc == 0) {
mate = (Stage3end_T) NULL;
chrpos3 = 0U;
- } else if (quiet_if_excessive_p && npaths2 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths2_primary + npaths2_altloc > maxpaths_report) {
mate = (Stage3end_T) NULL;
chrpos3 = 0U;
} else {
@@ -4311,50 +4332,50 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,mate,Shortread_fulllength(queryseq2),/*first_read_p*/false);
}
- if (npaths1 == 1) {
+ if (npaths1_primary + npaths1_altloc == 1) {
stage3 = stage3array1[0];
hardclip5_low = hardclip5_high = 0;
chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,Shortread_fulllength(queryseq1),/*first_read_p*/true);
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1_primary,npaths1_altloc,
Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
- } else if (quiet_if_excessive_p && npaths1 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths1_primary + npaths1_altloc > maxpaths_report) {
/* Just printing one end as nomapping */
SAM_print_nomapping(fp,abbrev,queryseq1,mate,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/true,/*pathnum*/1,npaths1,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths2,/*mate_chrpos*/chrpos3,
+ resulttype,/*first_read_p*/true,/*pathnum*/1,npaths1_primary,npaths1_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
} else {
- for (pathnum = 1; pathnum <= npaths1 && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths1_primary + npaths1_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array1[pathnum-1];
hardclip5_low = hardclip5_high = 0;
chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/hardclip5_high,stage3,Shortread_fulllength(queryseq1),
/*first_read_p*/true);
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1_primary,npaths1_altloc,
Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
}
/* print second end results */
- if (npaths1 == 0) {
+ if (npaths1_primary + npaths1_altloc == 0) {
mate = (Stage3end_T) NULL;
chrpos5 = 0U;
- } else if (quiet_if_excessive_p && npaths1 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths1_primary + npaths1_altloc > maxpaths_report) {
mate = (Stage3end_T) NULL;
chrpos5 = 0U;
} else {
@@ -4364,56 +4385,56 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*first_read_p*/true);
}
- if (npaths2 == 1) {
+ if (npaths2_primary + npaths2_altloc == 1) {
stage3 = stage3array2[0];
hardclip3_low = hardclip3_high = 0;
chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,Shortread_fulllength(queryseq2),
/*first_read_p*/false);
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2_primary,npaths2_altloc,
Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
- } else if (quiet_if_excessive_p && npaths2 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths2_primary + npaths2_altloc > maxpaths_report) {
/* Just printing one end as nomapping */
SAM_print_nomapping(fp,abbrev,queryseq2,mate,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/false,/*pathnum*/1,npaths2,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths1,/*mate_chrpos*/chrpos5,
+ resulttype,/*first_read_p*/false,/*pathnum*/1,npaths2_primary,npaths2_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
} else {
- for (pathnum = 1; pathnum <= npaths2 && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths2_primary + npaths2_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array2[pathnum-1];
hardclip3_low = hardclip3_high = 0;
chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,Shortread_fulllength(queryseq2),
/*first_read_p*/false);
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2_primary,npaths2_altloc,
Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
}
}
} else {
- stage3array1 = (Stage3end_T *) Result_array(&npaths1,&first_absmq1,&second_absmq1,result);
- stage3array2 = (Stage3end_T *) Result_array2(&npaths2,&first_absmq2,&second_absmq2,result);
+ stage3array1 = (Stage3end_T *) Result_array(&npaths1_primary,&npaths1_altloc,&first_absmq1,&second_absmq1,result);
+ stage3array2 = (Stage3end_T *) Result_array2(&npaths2_primary,&npaths2_altloc,&first_absmq2,&second_absmq2,result);
if (resulttype == HALFMAPPING_UNIQ) {
- if (npaths1 == 1 && Stage3end_circularpos(stage3array1[0]) > 0) {
+ if (npaths1_primary + npaths1_altloc == 1 && Stage3end_circularpos(stage3array1[0]) > 0) {
Filestring_set_split_output(fp,OUTPUT_HC);
abbrev = ABBREV_HALFMAPPING_CIRCULAR;
- } else if (npaths2 == 1 && Stage3end_circularpos(stage3array2[0]) > 0) {
+ } else if (npaths2_primary + npaths2_altloc == 1 && Stage3end_circularpos(stage3array2[0]) > 0) {
Filestring_set_split_output(fp,OUTPUT_HC);
abbrev = ABBREV_HALFMAPPING_CIRCULAR;
} else {
@@ -4424,7 +4445,7 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
Filestring_set_split_output(fp,OUTPUT_HT);
abbrev = ABBREV_HALFMAPPING_TRANSLOC;
} else if (resulttype == HALFMAPPING_MULT) {
- if (quiet_if_excessive_p == true && npaths1 > maxpaths_report && npaths2 > maxpaths_report) {
+ if (quiet_if_excessive_p == true && npaths1_primary + npaths1_altloc > maxpaths_report && npaths2_primary + npaths2_altloc > maxpaths_report) {
Filestring_set_split_output(fp,OUTPUT_HX);
abbrev = ABBREV_HALFMAPPING_MULT_XS;
} else {
@@ -4462,10 +4483,10 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/* print first end results */
- if (npaths2 == 0) {
+ if (npaths2_primary + npaths2_altloc == 0) {
mate = (Stage3end_T) NULL;
chrpos3 = 0U;
- } else if (quiet_if_excessive_p && npaths2 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths2_primary + npaths2_altloc > maxpaths_report) {
mate = (Stage3end_T) NULL;
chrpos3 = 0U;
} else {
@@ -4475,19 +4496,19 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*first_read_p*/false);
}
- if (npaths1 == 0) {
+ if (npaths1_primary + npaths1_altloc == 0) {
/* just printing one end as nomapping */
/* mate should be non-NULL here */
if (add_paired_nomappers_p == true) {
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq1,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/0,npaths1,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths2,/*mate_chrpos*/chrpos3,
+ /*first_read_p*/true,/*pathnum*/0,npaths1_primary,npaths1_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
}
- } else if (npaths1 == 1) {
+ } else if (npaths1_primary + npaths1_altloc == 1) {
/* mate should be NULL here */
stage3 = stage3array1[0];
@@ -4497,45 +4518,45 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (add_paired_nomappers_p == true) {
/* matching nomapper for second end */
- npaths_max = npaths1; /* since npaths2 == 0 */
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths_max,
+ npaths_max = npaths1_primary + npaths1_altloc; /* since npaths2_primary + npaths2_altloc == 0 */
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1_primary,npaths1_altloc,
Stage3end_absmq_score(stage3),first_absmq1,/*second_absmq1*/0,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
- resulttype,/*first_read_p*/false,/*pathnum*/1,npaths1,
+ resulttype,/*first_read_p*/false,/*pathnum*/1,npaths1_primary,npaths1_altloc,
/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
} else {
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths1_primary,npaths1_altloc,
Stage3end_absmq_score(stage3),first_absmq1,/*second_absmq1*/0,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
- } else if (quiet_if_excessive_p && npaths1 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths1_primary + npaths1_altloc > maxpaths_report) {
/* Just printing one end as nomapping */
/* mate should be NULL here */
if (add_paired_nomappers_p == true) {
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq1,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/true,/*pathnum*/1,npaths1,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths2,/*mate_chrpos*/chrpos3,
+ /*first_read_p*/true,/*pathnum*/1,npaths1_primary,npaths1_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
}
} else {
/* mate should be NULL here */
- for (pathnum = 1; pathnum <= npaths1 && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths1_primary + npaths1_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array1[pathnum-1];
hardclip5_low = hardclip5_high = 0;
chrpos5 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,Shortread_fulllength(queryseq1),
@@ -4543,38 +4564,38 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (add_paired_nomappers_p == true) {
/* matching nomapper for second end */
- npaths_max = npaths1; /* since npaths2 == 0 */
+ npaths_max = npaths1_primary + npaths1_altloc; /* since npaths2 == 0 */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
resulttype,/*first_read_p*/false,pathnum,
- npaths1,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
+ npaths1_primary,npaths1_altloc,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths_max,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1_primary,npaths1_altloc,
Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/true,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,quality_shift,sam_read_group_id,
invert_first_p,invert_second_p,merge_samechr_p);
} else {
- SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1,
+ SAM_print(fp,fp_failedinput_1,abbrev,stage3,mate,acc1,acc2,pathnum,npaths1_primary,npaths1_altloc,
Stage3end_absmq_score(stage3),first_absmq1,second_absmq1,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq1,/*queryseq_mate*/queryseq2,
/*pairedlength*/0U,/*chrpos*/chrpos5,/*mate_chrpos*/chrpos3,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/true,/*artificial_mate_p*/false,/*npaths_mate*/npaths2_primary + npaths2_altloc,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p,merge_samechr_p);
}
}
}
/* print second end results */
- if (npaths1 == 0) {
+ if (npaths1_primary + npaths1_altloc == 0) {
mate = (Stage3end_T) NULL;
chrpos5 = 0U;
- } else if (quiet_if_excessive_p && npaths1 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths1_primary + npaths1_altloc > maxpaths_report) {
mate = (Stage3end_T) NULL;
chrpos5 = 0U;
} else {
@@ -4584,19 +4605,19 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
/*first_read_p*/true);
}
- if (npaths2 == 0) {
+ if (npaths2_primary + npaths2_altloc == 0) {
/* Just printing one end as nomapping */
/* mate should be non-NULL here */
if (add_paired_nomappers_p == true) {
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq2,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/0,npaths2,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths1,/*mate_chrpos*/chrpos5,
+ /*first_read_p*/false,/*pathnum*/0,npaths2_primary,npaths2_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
}
- } else if (npaths2 == 1) {
+ } else if (npaths2_primary + npaths2_altloc == 1) {
/* mate should be NULL here */
stage3 = stage3array2[0];
@@ -4606,46 +4627,46 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (add_paired_nomappers_p == true) {
/* matching nomapper for first end */
- npaths_max = npaths2; /* since npaths1 == 0 */
+ npaths_max = npaths2_primary + npaths2_altloc; /* since npaths1_primary + npaths1_altloc == 0 */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
resulttype,/*first_read_p*/true,/*pathnum*/1,
- npaths2,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
+ npaths2_primary,npaths2_altloc,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths_max,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2_primary,npaths2_altloc,
Stage3end_absmq_score(stage3),first_absmq2,/*second_absmq2*/0,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/false,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
} else {
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,/*pathnum*/1,npaths2_primary,npaths2_altloc,
Stage3end_absmq_score(stage3),first_absmq2,/*second_absmq2*/0,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
- } else if (quiet_if_excessive_p && npaths2 > maxpaths_report) {
+ } else if (quiet_if_excessive_p && npaths2_primary + npaths2_altloc > maxpaths_report) {
/* Just printing one end as nomapping */
/* mate should be NULL here */
if (add_paired_nomappers_p == true) {
/* Handle nomappers with each mapped mate */
} else {
SAM_print_nomapping(fp,abbrev,queryseq2,mate,acc1,acc2,chromosome_iit,resulttype,
- /*first_read_p*/false,/*pathnum*/1,npaths2,
- /*artificial_mate_p*/false,/*npaths_mate*/npaths1,/*mate_chrpos*/chrpos5,
+ /*first_read_p*/false,/*pathnum*/1,npaths2_primary,npaths2_altloc,
+ /*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,/*mate_chrpos*/chrpos5,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p);
}
} else {
/* mate should be NULL here */
- for (pathnum = 1; pathnum <= npaths2 && pathnum <= maxpaths_report; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths2_primary + npaths2_altloc && pathnum <= maxpaths_report; pathnum++) {
stage3 = stage3array2[pathnum-1];
hardclip3_low = hardclip3_high = 0;
chrpos3 = SAM_compute_chrpos(/*hardclip_low*/0,/*hardclip_high*/0,stage3,Shortread_fulllength(queryseq2),
@@ -4653,28 +4674,28 @@ SAM_print_paired (Filestring_T fp, Filestring_T fp_failedinput_1, Filestring_T f
if (add_paired_nomappers_p == true) {
/* matching nomapper for first end */
- npaths_max = npaths2; /* since npaths1 == 0 */
+ npaths_max = npaths2_primary + npaths2_altloc; /* since npaths1_primary + npaths1_altloc == 0 */
SAM_print_nomapping(fp,abbrev,queryseq2,/*mate*/stage3,acc1,acc2,chromosome_iit,
resulttype,/*first_read_p*/true,pathnum,
- npaths2,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
+ npaths2_primary,npaths2_altloc,/*artificial_mate_p*/false,/*npaths_mate*/npaths_max,/*mate_chrpos*/chrpos3,
quality_shift,sam_read_group_id,invert_first_p,invert_second_p);
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths_max,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2_primary,npaths2_altloc,
Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
resulttype,/*first_read_p*/false,/*artificial_mate_p*/true,/*npaths_mate*/npaths_max,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
} else {
- SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2,
+ SAM_print(fp,fp_failedinput_2,abbrev,stage3,mate,acc1,acc2,pathnum,npaths2_primary,npaths2_altloc,
Stage3end_absmq_score(stage3),first_absmq2,second_absmq2,
Stage3end_mapq_score(stage3),chromosome_iit,
/*queryseq*/queryseq2,/*queryseq_mate*/queryseq1,
/*pairedlength*/0U,/*chrpos*/chrpos3,/*mate_chrpos*/chrpos5,
- /*clipdir*/0,/*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
- resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1,
+ /*hardclip5_low*/0,/*hardclip5_high*/0,/*hardclip3_low*/0,/*hardclip3_high*/0,
+ resulttype,/*first_read_p*/false,/*artificial_mate_p*/false,/*npaths_mate*/npaths1_primary + npaths1_altloc,
quality_shift,sam_read_group_id,invert_second_p,invert_first_p,merge_samechr_p);
}
}
diff --git a/src/samprint.h b/src/samprint.h
index 4170329..8b6c484 100644
--- a/src/samprint.h
+++ b/src/samprint.h
@@ -1,4 +1,4 @@
-/* $Id: samprint.h 183725 2016-02-04 00:40:15Z twu $ */
+/* $Id: samprint.h 184433 2016-02-17 20:00:43Z twu $ */
#ifndef SAMPRINT_INCLUDED
#define SAMPRINT_INCLUDED
@@ -41,15 +41,15 @@ SAM_compute_flag (bool plusp, Stage3end_T mate, Resulttype_T resulttype,
extern void
SAM_print_nomapping (Filestring_T fp, char *abbrev, Shortread_T queryseq, Stage3end_T mate, char *acc1, char *acc2,
Univ_IIT_T chromosome_iit, Resulttype_T resulttype, bool first_read_p,
- int pathnum, int npaths, bool artificial_mate_p, int npaths_mate,
+ int pathnum, int npaths_primary, int npaths_altloc, bool artificial_mate_p, int npaths_mate,
Chrpos_T mate_chrpos, int quality_shift, char *sam_read_group_id, bool invertp, bool invert_mate_p);
extern void
SAM_print (Filestring_T fp, Filestring_T fp_failedinput, char *abbrev,
- Stage3end_T this, Stage3end_T mate, char *acc1, char *acc2, int pathnum, int npaths,
+ Stage3end_T this, Stage3end_T mate, char *acc1, char *acc2, int pathnum, int npaths_primary, int npaths_altloc,
int absmq_score, int first_absmq, int second_absmq, int mapq_score, Univ_IIT_T chromosome_iit, Shortread_T queryseq,
Shortread_T queryseq2, int pairedlength, Chrpos_T chrpos, Chrpos_T mate_chrpos,
- int clipdir, int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high,
+ int hardclip5_low, int hardclip5_high, int hardclip3_low, int hardclip3_high,
Resulttype_T resulttype, bool first_read_p, bool artificial_mate_p, int npaths_mate, int quality_shift,
char *sam_read_group_id, bool invertp, bool invert_mate_p, bool merge_samechr_p);
diff --git a/src/samread.c b/src/samread.c
index a3253b0..4880ef4 100644
--- a/src/samread.c
+++ b/src/samread.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: samread.c 186088 2016-03-17 22:13:46Z twu $";
+static char rcsid[] = "$Id: samread.c 186089 2016-03-17 22:14:16Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
diff --git a/src/sarray-read.c b/src/sarray-read.c
index 99f1810..2a69e35 100644
--- a/src/sarray-read.c
+++ b/src/sarray-read.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: sarray-read.c 181923 2016-01-08 00:43:56Z twu $";
+static char rcsid[] = "$Id: sarray-read.c 186964 2016-04-04 20:27:35Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -55,7 +55,14 @@ static char rcsid[] = "$Id: sarray-read.c 181923 2016-01-08 00:43:56Z twu $";
#else
#include <tmmintrin.h>
#endif
-#ifdef HAVE_POPCNT
+#if defined(WORDS_BIGENDIAN) || !defined(HAVE_AVX2)
+#else
+#include <immintrin.h>
+#endif
+
+#if !defined(HAVE_SSE4_2)
+/* Skip popcnt */
+#elif defined(HAVE_POPCNT)
#include <immintrin.h>
#elif defined(HAVE_MM_POPCNT)
#include <nmmintrin.h>
@@ -67,14 +74,13 @@ static char rcsid[] = "$Id: sarray-read.c 181923 2016-01-08 00:43:56Z twu $";
#define MAX_HITS_FOR_BEST_ELT 1000
-/* #define USE_CSA 1 */
-
/* A value of 10000 misses various splices, although they are caught by GSNAP algorithm */
#define EXCESS_SARRAY_HITS 100000
#define LOCALSPLICING_NMATCHES_SLOP 1
#define LOCALSPLICING_PROB_SLOP 0.05
#define USE_SHUFFLE_MASK 1 /* Alternative requires AVX, and that part of the code isn't called much */
+/* #define REQUIRE_ALIGNMENT 1 */
#define GUESS_ALLOCATION 10
@@ -221,6 +227,24 @@ print_vector_uint (__m128i x) {
printf("%u %u %u %u\n",s[3],s[2],s[1],s[0]);
return;
}
+
+static void
+print_vector_hex_256 (__m256i x) {
+ UINT4 *s = (UINT4 *) &x;
+
+ /* printf("%d %d %d %d\n",s[0],s[1],s[2],s[3]); */
+ printf("%08X %08X %08X %08X %08X %08X %08X %08X\n",s[7],s[6],s[5],s[4],s[3],s[2],s[1],s[0]);
+ return;
+}
+
+static void
+print_vector_uint_256 (__m256i x) {
+ UINT4 *s = (UINT4 *) &x;
+
+ /* printf("%d %d %d %d\n",s[0],s[1],s[2],s[3]); */
+ printf("%u %u %u %u %u %u %u %u\n",s[7],s[6],s[5],s[4],s[3],s[2],s[1],s[0]);
+ return;
+}
#endif
@@ -232,34 +256,26 @@ struct T {
/* Old format */
int array_shmid;
+ key_t array_key;
Univcoord_T *array;
-#ifdef USE_CSA
-#ifdef DEBUG3B
- Univcoord_T *csa;
-#endif
-
- /* New format */
- int sa_sampling;
- Univcoord_T *array_samples;
- int csaAptrs_shmid, csaAcomp_shmid, csaCptrs_shmid, csaCcomp_shmid,
- csaGptrs_shmid, csaGcomp_shmid, csaTptrs_shmid, csaTcomp_shmid, csaXptrs_shmid, csaXcomp_shmid;
- UINT4 *csaAptrs, *csaAcomp, *csaCptrs, *csaCcomp, *csaGptrs, *csaGcomp, *csaTptrs, *csaTcomp, *csaXptrs, *csaXcomp;
- UINT4 *csa0ptrs[16], *csa0comp[16];
-#endif
-
int lcpchilddc_shmid;
+ key_t lcpchilddc_key;
unsigned char *lcpchilddc;
int lcp_guide_shmid;
+ key_t lcp_guide_key;
int lcp_exceptions_shmid;
+ key_t lcp_exceptions_key;
UINT4 *lcp_guide;
UINT4 *lcp_exceptions;
int n_lcp_exceptions; /* Won't be necessary if we change lcpchilddc to use guide array */
/* int lcp_guide_interval; -- Always use 1024 */
int child_guide_shmid;
+ key_t child_guide_key;
int child_exceptions_shmid;
+ key_t child_exceptions_key;
UINT4 *child_guide;
UINT4 *child_exceptions;
/* int n_child_exceptions; */
@@ -269,17 +285,6 @@ struct T {
Sarrayptr_T initindexi[4]; /* For A, C, G, T */
Sarrayptr_T initindexj[4]; /* For A, C, G, T */
#endif
-#ifdef USE_CSA
- Sarrayptr_T indexA;
- Sarrayptr_T indexC;
- Sarrayptr_T indexG;
- Sarrayptr_T indexT;
- Sarrayptr_T indexX;
-#if defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN)
- __m128i indices0;
- UINT4 index0[16];
-#endif
-#endif
int indexsize;
UINT4 indexspace; /* 4^indexsize. Used by sarray_search to detect when we have a poly-T oligo shorter than indexsize */
@@ -290,23 +295,13 @@ struct T {
UINT4 *indexi_ptrs, *indexi_comp, *indexj_ptrs, *indexj_comp; /* bucket array: oligomer lookup into suffix array */
#else
int indexij_ptrs_shmid;
+ key_t indexij_ptrs_key;
int indexij_comp_shmid;
+ key_t indexij_comp_key;
UINT4 *indexij_ptrs, *indexij_comp;
#endif
- Access_T sarray_access;
- Access_T lcp_access;
- Access_T guideexc_access;
- Access_T indexij_access;
-
- int array_fd; size_t array_len;
-#ifdef USE_CSA
- int csaAptrs_fd; size_t csaAptrs_len; int csaAcomp_fd; size_t csaAcomp_len;
- int csaCptrs_fd; size_t csaCptrs_len; int csaCcomp_fd; size_t csaCcomp_len;
- int csaGptrs_fd; size_t csaGptrs_len; int csaGcomp_fd; size_t csaGcomp_len;
- int csaTptrs_fd; size_t csaTptrs_len; int csaTcomp_fd; size_t csaTcomp_len;
- int csaXptrs_fd; size_t csaXptrs_len; int csaXcomp_fd; size_t csaXcomp_len;
-#endif
+ Access_T array_access; int array_fd; size_t array_len;
#ifdef DEBUG15
int indexi_ptrs_fd; size_t indexi_ptrs_len; int indexi_comp_fd; size_t indexi_comp_len;
@@ -316,16 +311,17 @@ struct T {
int indexi_ptrs_fd; size_t indexi_ptrs_len; int indexi_comp_fd; size_t indexi_comp_len;
int indexj_ptrs_fd; size_t indexj_ptrs_len; int indexj_comp_fd; size_t indexj_comp_len;
#else
- int indexij_ptrs_fd; size_t indexij_ptrs_len; int indexij_comp_fd; size_t indexij_comp_len;
+ Access_T indexij_ptrs_access; int indexij_ptrs_fd; size_t indexij_ptrs_len;
+ Access_T indexij_comp_access; int indexij_comp_fd; size_t indexij_comp_len;
#endif
- int lcpchilddc_fd; size_t lcpchilddc_len;
+ Access_T lcpchilddc_access; int lcpchilddc_fd; size_t lcpchilddc_len;
- int lcp_guide_fd; size_t lcp_guide_len;
- int lcp_exceptions_fd; size_t lcp_exceptions_len;
+ Access_T lcp_guide_access; int lcp_guide_fd; size_t lcp_guide_len;
+ Access_T lcp_exceptions_access; int lcp_exceptions_fd; size_t lcp_exceptions_len;
- int child_guide_fd; size_t child_guide_len;
- int child_exceptions_fd; size_t child_exceptions_len;
+ Access_T child_guide_access; int child_guide_fd; size_t child_guide_len;
+ Access_T child_exceptions_access; int child_exceptions_fd; size_t child_exceptions_len;
};
@@ -352,8 +348,9 @@ static int splicing_penalty;
static Chrpos_T overall_max_distance;
static Chrpos_T shortsplicedist;
static Chrpos_T max_deletionlen;
-static Chrpos_T max_insertionlen;
-static Chrpos_T max_end_deletions;
+static Chrpos_T max_insertionlen_default;
+static int max_end_deletions;
+static int max_middle_insertions_default;
/* Splicing */
static Univcoord_T *splicesites;
@@ -362,6 +359,10 @@ static Chrpos_T *splicedists;
static int nsplicesites;
+#if defined(HAVE_AVX2) && !defined(WORDS_BIGENDIAN)
+static __m256i epi32_convert_256; /* For converting unsigned ints to signed ints */
+#endif
+
#if defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN)
static __m128i epi32_convert; /* For converting unsigned ints to signed ints */
#endif
@@ -445,7 +446,7 @@ Sarray_setup (T sarray_fwd_in, T sarray_rev_in, Genome_T genome_in, Mode_T mode,
Univ_IIT_T chromosome_iit_in, int circular_typeint_in, bool *circularp_in,
Chrpos_T shortsplicedist_in, int splicing_penalty_in,
int max_deletionlength, int max_end_deletions_in,
- int max_middle_insertions, int max_end_insertions,
+ int max_middle_insertions_in, int max_end_insertions,
Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in,
Chrpos_T *splicedists_in, int nsplicesites_in) {
int i;
@@ -479,10 +480,11 @@ Sarray_setup (T sarray_fwd_in, T sarray_rev_in, Genome_T genome_in, Mode_T mode,
max_deletionlen = max_deletionlength;
max_end_deletions = max_end_deletions_in;
- if (max_middle_insertions > max_end_insertions) {
- max_insertionlen = max_middle_insertions;
+ max_middle_insertions_default = max_middle_insertions_in;
+ if (max_middle_insertions_in > max_end_insertions) {
+ max_insertionlen_default = max_middle_insertions_in;
} else {
- max_insertionlen = max_end_insertions;
+ max_insertionlen_default = max_end_insertions;
}
if (shortsplicedist > max_deletionlen) {
@@ -514,6 +516,10 @@ Sarray_setup (T sarray_fwd_in, T sarray_rev_in, Genome_T genome_in, Mode_T mode,
epi32_convert = _mm_set1_epi32(2147483648); /* 2^31 */
#endif
+#if defined(HAVE_AVX2) && !defined(WORDS_BIGENDIAN)
+ epi32_convert_256 = _mm256_set1_epi32(2147483648); /* 2^31 */
+#endif
+
#if defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN) && defined(USE_SHUFFLE_MASK)
/* Used by fill_positions_filtered_first */
shuffle_mask16[0] = _mm_set_epi8(-1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1, -1,-1,-1,-1);
@@ -563,6 +569,7 @@ power (int base, int exponent) {
}
+#if 0
void
Sarray_shmem_remove (char *dir, char *fileroot, char *snps_root, Mode_T mode, bool fwdp) {
char *mode_prefix;
@@ -638,6 +645,7 @@ Sarray_shmem_remove (char *dir, char *fileroot, char *snps_root, Mode_T mode, bo
return;
}
+#endif
#ifdef USE_CSA
@@ -725,9 +733,8 @@ csa_lookup (T sarray, Sarrayptr_T i) {
#endif
-/* Ignores snps_root */
T
-Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_access, Access_mode_T lcp_access,
+Sarray_new (char *dir, char *fileroot, Access_mode_T sarray_access, Access_mode_T lcp_access,
Access_mode_T guideexc_access, Access_mode_T indexij_access, bool sharedp, Mode_T mode, bool fwdp) {
T new;
char *comma1;
@@ -737,20 +744,6 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
bool old_format_p;
char *sarrayfile; /* Old format */
-#ifdef USE_CSA
- char *csafile;
- int shmid;
- int fd, fd0;
- size_t len, len0;
-
- /* New format */
- char *sasamplesfile;
- char *csaA_ptrsfile, *csaA_compfile, *csaC_ptrsfile, *csaC_compfile,
- *csaG_ptrsfile, *csaG_compfile, *csaT_ptrsfile, *csaT_compfile, *csaX_ptrsfile, *csaX_compfile;
- char *filename;
- FILE *fp;
-#endif
-
char *lcpchilddcfile;
char *lcp_guidefile, *lcp_exceptionsfile;
char *child_guidefile, *child_exceptionsfile;
@@ -793,39 +786,6 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
sarrayfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("sarray")+1,sizeof(char));
sprintf(sarrayfile,"%s/%s%ssarray",dir,fileroot,mode_prefix);
-#ifdef USE_CSA
-#ifdef DEBUG3A
- csafile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csa")+1,sizeof(char));
- sprintf(csafile,"%s/%s%scsa",dir,fileroot,mode_prefix);
-#endif
-
- /* New format */
- sasamplesfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("sasamples")+1,sizeof(char));
- sprintf(sasamplesfile,"%s/%s%ssasamples",dir,fileroot,mode_prefix);
-
- csaA_ptrsfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaAmeta")+1,sizeof(char));
- sprintf(csaA_ptrsfile,"%s/%s%scsaAmeta",dir,fileroot,mode_prefix);
- csaA_compfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaAstrm")+1,sizeof(char));
- sprintf(csaA_compfile,"%s/%s%scsaAstrm",dir,fileroot,mode_prefix);
- csaC_ptrsfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaCmeta")+1,sizeof(char));
- sprintf(csaC_ptrsfile,"%s/%s%scsaCmeta",dir,fileroot,mode_prefix);
- csaC_compfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaCstrm")+1,sizeof(char));
- sprintf(csaC_compfile,"%s/%s%scsaCstrm",dir,fileroot,mode_prefix);
- csaG_ptrsfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaGmeta")+1,sizeof(char));
- sprintf(csaG_ptrsfile,"%s/%s%scsaGmeta",dir,fileroot,mode_prefix);
- csaG_compfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaGstrm")+1,sizeof(char));
- sprintf(csaG_compfile,"%s/%s%scsaGstrm",dir,fileroot,mode_prefix);
- csaT_ptrsfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaTmeta")+1,sizeof(char));
- sprintf(csaT_ptrsfile,"%s/%s%scsaTmeta",dir,fileroot,mode_prefix);
- csaT_compfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaTstrm")+1,sizeof(char));
- sprintf(csaT_compfile,"%s/%s%scsaTstrm",dir,fileroot,mode_prefix);
- csaX_ptrsfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaXmeta")+1,sizeof(char));
- sprintf(csaX_ptrsfile,"%s/%s%scsaXmeta",dir,fileroot,mode_prefix);
- csaX_compfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("csaXstrm")+1,sizeof(char));
- sprintf(csaX_compfile,"%s/%s%scsaXstrm",dir,fileroot,mode_prefix);
-#endif
-
-
lcpchilddcfile = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("salcpchilddc")+1,sizeof(char));
sprintf(lcpchilddcfile,"%s/%s%ssalcpchilddc",dir,fileroot,mode_prefix);
@@ -868,11 +828,7 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
sprintf(indexij_compfile,"%s/%s%ssaindex64strm",dir,fileroot,mode_prefix);
#endif
- if (Access_file_exists_p(sarrayfile) == false
-#ifdef USE_CSA
- && Access_file_exists_p(csaA_ptrsfile) == false
-#endif
- ) {
+ if (Access_file_exists_p(sarrayfile) == false) {
fprintf(stderr,"No suffix array for genome\n");
new = (T) NULL;
@@ -884,66 +840,7 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
} else {
new = (T) MALLOC_KEEP(sizeof(*new));
-
-#ifdef USE_CSA
- if (
-#ifdef DEBUG3A
- 0 &&
-#endif
- Access_file_exists_p(sarrayfile) == true) {
- fprintf(stderr,"The genome was built using a non-compressed suffix array: %s\n",sarrayfile);
- old_format_p = true;
-
- } else {
- old_format_p = false;
-
-#ifdef DEBUG3B
- new->csa = (UINT4 *) Access_mmap_and_preload(&fd0,&len0,&npages,&seconds,csafile,sizeof(UINT4));
-#endif
-
- filename = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("saindex0")+1,sizeof(char));
- sprintf(filename,"%s/%s%ssaindex0",dir,fileroot,mode_prefix);
- fp = fopen(filename,"rb");
- FREAD_UINT(&new->indexA,fp);
- FREAD_UINT(&new->indexC,fp);
- FREAD_UINT(&new->indexG,fp);
- FREAD_UINT(&new->indexT,fp);
- FREAD_UINT(&new->indexX,fp);
-
- /* For compressed suffix arrays, cannot rely upon array_len */
- FREAD_UINT(&new->n_plus_one,fp); /* Should be genomiclength + 1 */
- new->n = new->n_plus_one - 1;
-
- /* Needed for SSE2 version of csa_lookup */
- new->index0[0] = new->indexA;
- new->index0[1] = new->indexC;
- new->index0[3] = new->indexG;
- new->index0[7] = new->indexT;
- new->index0[15] = new->indexX;
-
- fclose(fp);
- FREE(filename);
-
-#if defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN)
- new->indices0 = _mm_sub_epi32(_mm_set_epi32(new->indexX,new->indexT,new->indexG,new->indexC),
- _mm_set1_epi32(2147483648) /* 2^31, same as epi_convert */);
- /* because (a >= indices) is equivalent to (a > indices - 1) */
- new->indices0 = _mm_sub_epi32(new->indices0,_mm_set1_epi32(1));
-#endif
-
-
- filename = (char *) CALLOC(strlen(dir)+strlen("/")+strlen(fileroot)+strlen(mode_prefix)+strlen("sasampleq")+1,sizeof(char));
- sprintf(filename,"%s/%s%ssasampleq",dir,fileroot,mode_prefix);
- fp = fopen(filename,"rb");
- FREAD_UINT(&new->sa_sampling,fp);
- fclose(fp);
- FREE(filename);
- }
-
- new->array_samples = (UINT4 *) NULL;
-#else
old_format_p = true;
-#endif
if (sarray_access == USE_MMAP_PRELOAD) {
if (old_format_p == true) {
@@ -956,132 +853,49 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
comma1 = Genomicpos_commafmt(new->array_len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
FREE(comma1);
-
-#ifdef USE_CSA
- } else {
-#ifdef DEBUG3A
- new->array = (UINT4 *) Access_mmap_and_preload(&new->array_fd,&new->array_len,&npages,&seconds,sarrayfile,
- sizeof(UINT4));
- new->array_samples = (UINT4 *) Access_mmap_and_preload(&fd,&len,&npages,&seconds,sasamplesfile,
- sizeof(UINT4));
-#else
- new->array = (UINT4 *) NULL;
- new->array_samples = (UINT4 *) Access_mmap_and_preload(&new->array_fd,&new->array_len,&npages,&seconds,sasamplesfile,
- sizeof(UINT4));
-#endif
- new->csaAptrs = (UINT4 *) Access_mmap_and_preload(&new->csaAptrs_fd,&new->csaAptrs_len,&npages,&seconds,csaA_ptrsfile,
- sizeof(UINT4));
- new->csaAcomp = (UINT4 *) Access_mmap_and_preload(&new->csaAcomp_fd,&new->csaAcomp_len,&npages,&seconds,csaA_compfile,
- sizeof(UINT4));
- new->csaCptrs = (UINT4 *) Access_mmap_and_preload(&new->csaCptrs_fd,&new->csaCptrs_len,&npages,&seconds,csaC_ptrsfile,
- sizeof(UINT4));
- new->csaCcomp = (UINT4 *) Access_mmap_and_preload(&new->csaCcomp_fd,&new->csaCcomp_len,&npages,&seconds,csaC_compfile,
- sizeof(UINT4));
- new->csaGptrs = (UINT4 *) Access_mmap_and_preload(&new->csaGptrs_fd,&new->csaGptrs_len,&npages,&seconds,csaG_ptrsfile,
- sizeof(UINT4));
- new->csaGcomp = (UINT4 *) Access_mmap_and_preload(&new->csaGcomp_fd,&new->csaGcomp_len,&npages,&seconds,csaG_compfile,
- sizeof(UINT4));
- new->csaTptrs = (UINT4 *) Access_mmap_and_preload(&new->csaTptrs_fd,&new->csaTptrs_len,&npages,&seconds,csaT_ptrsfile,
- sizeof(UINT4));
- new->csaTcomp = (UINT4 *) Access_mmap_and_preload(&new->csaTcomp_fd,&new->csaTcomp_len,&npages,&seconds,csaT_compfile,
- sizeof(UINT4));
- new->csaXptrs = (UINT4 *) Access_mmap_and_preload(&new->csaXptrs_fd,&new->csaXptrs_len,&npages,&seconds,csaX_ptrsfile,
- sizeof(UINT4));
- new->csaXcomp = (UINT4 *) Access_mmap_and_preload(&new->csaXcomp_fd,&new->csaXcomp_len,&npages,&seconds,csaX_compfile,
- sizeof(UINT4));
-#endif
- }
- new->sarray_access = MMAPPED;
+ }
+ new->array_access = MMAPPED;
} else if (sarray_access == USE_MMAP_ONLY) {
if (old_format_p == true) {
- new->array = (UINT4 *) Access_mmap(&new->array_fd,&new->array_len,sarrayfile,sizeof(UINT4),/*randomp*/true);
+ new->array = (UINT4 *) Access_mmap(&new->array_fd,&new->array_len,sarrayfile,/*randomp*/true);
new->n_plus_one = new->array_len/sizeof(UINT4); /* Should be genomiclength + 1*/
new->n = new->n_plus_one - 1;
-#ifdef USE_CSA
- } else {
-#ifdef DEBUG3A
- new->array = (UINT4 *) Access_mmap(&new->array_fd,&new->array_len,sarrayfile,sizeof(UINT4),/*randomp*/true);
- new->array_samples = (UINT4 *) Access_mmap(&fd,&len,sasamplesfile,sizeof(UINT4),/*randomp*/true);
-#else
- new->array = (UINT4 *) NULL;
- new->array_samples = (UINT4 *) Access_mmap(&new->array_fd,&new->array_len,sasamplesfile,sizeof(UINT4),/*randomp*/true);
-#endif
- new->csaAptrs = (UINT4 *) Access_mmap(&new->csaAptrs_fd,&new->csaAptrs_len,csaA_ptrsfile,sizeof(UINT4),/*randomp*/true);
- new->csaAcomp = (UINT4 *) Access_mmap(&new->csaAcomp_fd,&new->csaAcomp_len,csaA_compfile,sizeof(UINT4),/*randomp*/true);
- new->csaCptrs = (UINT4 *) Access_mmap(&new->csaCptrs_fd,&new->csaCptrs_len,csaC_ptrsfile,sizeof(UINT4),/*randomp*/true);
- new->csaCcomp = (UINT4 *) Access_mmap(&new->csaCcomp_fd,&new->csaCcomp_len,csaC_compfile,sizeof(UINT4),/*randomp*/true);
- new->csaGptrs = (UINT4 *) Access_mmap(&new->csaGptrs_fd,&new->csaGptrs_len,csaG_ptrsfile,sizeof(UINT4),/*randomp*/true);
- new->csaGcomp = (UINT4 *) Access_mmap(&new->csaGcomp_fd,&new->csaGcomp_len,csaG_compfile,sizeof(UINT4),/*randomp*/true);
- new->csaTptrs = (UINT4 *) Access_mmap(&new->csaTptrs_fd,&new->csaTptrs_len,csaT_ptrsfile,sizeof(UINT4),/*randomp*/true);
- new->csaTcomp = (UINT4 *) Access_mmap(&new->csaTcomp_fd,&new->csaTcomp_len,csaT_compfile,sizeof(UINT4),/*randomp*/true);
- new->csaXptrs = (UINT4 *) Access_mmap(&new->csaXptrs_fd,&new->csaXptrs_len,csaX_ptrsfile,sizeof(UINT4),/*randomp*/true);
- new->csaXcomp = (UINT4 *) Access_mmap(&new->csaXcomp_fd,&new->csaXcomp_len,csaX_compfile,sizeof(UINT4),/*randomp*/true);
-#endif
}
- new->sarray_access = MMAPPED;
+ new->array_access = MMAPPED;
} else if (sarray_access == USE_ALLOCATE) {
if (old_format_p == true) {
fprintf(stderr,"Allocating memory for suffix array...");
- new->array = (UINT4 *) Access_allocate(&new->array_shmid,&new->array_len,&seconds,sarrayfile,sizeof(UINT4),sharedp);
+ if (sharedp == true) {
+ new->array = (UINT4 *) Access_allocate_shared(&new->array_access,&new->array_shmid,&new->array_key,
+ &new->array_fd,&new->array_len,&seconds,sarrayfile,sizeof(UINT4));
+ } else {
+ new->array = (UINT4 *) Access_allocate_private(&new->array_access,&new->array_len,&seconds,sarrayfile,sizeof(UINT4));
+ }
new->n_plus_one = new->array_len/sizeof(UINT4); /* Should be genomiclength + 1*/
new->n = new->n_plus_one - 1;
comma1 = Genomicpos_commafmt(new->array_len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
FREE(comma1);
-#ifdef USE_CSA
- } else {
-#ifdef DEBUG3A
- new->array = (UINT4 *) Access_allocate(&new->array_shmid,&new->array_len,&seconds,sarrayfile,sizeof(UINT4),sharedp);
-#else
- new->array = (UINT4 *) NULL;
-#endif
- new->array_samples = (UINT4 *) Access_allocate(&shmid,&len,&seconds,sasamplesfile,sizeof(UINT4),sharedp);
- new->csaAptrs = (UINT4 *) Access_allocate(&new->csaAptrs_shmid,&new->csaAptrs_len,&seconds,csaA_ptrsfile,sizeof(UINT4),sharedp);
- new->csaAcomp = (UINT4 *) Access_allocate(&new->csaAcomp_shmid,&new->csaAcomp_len,&seconds,csaA_compfile,sizeof(UINT4),sharedp);
- new->csaCptrs = (UINT4 *) Access_allocate(&new->csaCptrs_shmid,&new->csaCptrs_len,&seconds,csaC_ptrsfile,sizeof(UINT4),sharedp);
- new->csaCcomp = (UINT4 *) Access_allocate(&new->csaCcomp_shmid,&new->csaCcomp_len,&seconds,csaC_compfile,sizeof(UINT4),sharedp);
- new->csaGptrs = (UINT4 *) Access_allocate(&new->csaGptrs_shmid,&new->csaGptrs_len,&seconds,csaG_ptrsfile,sizeof(UINT4),sharedp);
- new->csaGcomp = (UINT4 *) Access_allocate(&new->csaGcomp_shmid,&new->csaGcomp_len,&seconds,csaG_compfile,sizeof(UINT4),sharedp);
- new->csaTptrs = (UINT4 *) Access_allocate(&new->csaTptrs_shmid,&new->csaTptrs_len,&seconds,csaT_ptrsfile,sizeof(UINT4),sharedp);
- new->csaTcomp = (UINT4 *) Access_allocate(&new->csaTcomp_shmid,&new->csaTcomp_len,&seconds,csaT_compfile,sizeof(UINT4),sharedp);
- new->csaXptrs = (UINT4 *) Access_allocate(&new->csaXptrs_shmid,&new->csaXptrs_len,&seconds,csaX_ptrsfile,sizeof(UINT4),sharedp);
- new->csaXcomp = (UINT4 *) Access_allocate(&new->csaXcomp_shmid,&new->csaXcomp_len,&seconds,csaX_compfile,sizeof(UINT4),sharedp);
-#endif
- }
-
- if (sharedp == true) {
- new->sarray_access = ALLOCATED_SHARED;
- } else {
- new->sarray_access = ALLOCATED_PRIVATE;
}
}
-#ifdef USE_CSA
- new->csa0ptrs[0] = new->csaAptrs; new->csa0comp[0] = new->csaAcomp;
- new->csa0ptrs[1] = new->csaCptrs; new->csa0comp[1] = new->csaCcomp;
- new->csa0ptrs[3] = new->csaGptrs; new->csa0comp[3] = new->csaGcomp;
- new->csa0ptrs[7] = new->csaTptrs; new->csa0comp[7] = new->csaTcomp;
- new->csa0ptrs[15] = new->csaXptrs; new->csa0comp[15] = new->csaXcomp;
-#endif
-
-
#ifdef DEBUG15
/* 8 is for two DIFFERENTIAL_METAINFO_SIZE words */
- new->indexi_ptrs = (UINT4 *) Access_allocate(&key,&new->indexi_ptrs_len,&seconds,indexi_ptrsfile,sizeof(UINT4),/*sharedp*/false);
- new->indexi_comp = (UINT4 *) Access_allocate(&key,&new->indexi_comp_len,&seconds,indexi_compfile,sizeof(UINT4),/*sharedp*/false);
- new->indexj_ptrs = (UINT4 *) Access_allocate(&key,&new->indexj_ptrs_len,&seconds,indexj_ptrsfile,sizeof(UINT4),/*sharedp*/false);
- new->indexj_comp = (UINT4 *) Access_allocate(&key,&new->indexj_comp_len,&seconds,indexj_compfile,sizeof(UINT4),/*sharedp*/false);
- new->indexij_ptrs = (UINT4 *) Access_allocate(&key,&new->indexij_ptrs_len,&seconds,indexij_ptrsfile,sizeof(UINT4),/*sharedp*/false);
- new->indexij_comp = (UINT4 *) Access_allocate(&key,&new->indexij_comp_len,&seconds,indexij_compfile,sizeof(UINT4),/*sharedp*/false);
+ new->indexi_ptrs = (UINT4 *) Access_allocate_private(&new->indexi_ptrs_len,&seconds,indexi_ptrsfile,sizeof(UINT4));
+ new->indexi_comp = (UINT4 *) Access_allocate_private(&new->indexi_comp_len,&seconds,indexi_compfile,sizeof(UINT4));
+ new->indexj_ptrs = (UINT4 *) Access_allocate_private(&new->indexj_ptrs_len,&seconds,indexj_ptrsfile,sizeof(UINT4));
+ new->indexj_comp = (UINT4 *) Access_allocate_private(&new->indexj_comp_len,&seconds,indexj_compfile,sizeof(UINT4));
+ new->indexij_ptrs = (UINT4 *) Access_allocate_private(&new->indexij_ptrs_len,&seconds,indexij_ptrsfile,sizeof(UINT4));
+ new->indexij_comp = (UINT4 *) Access_allocate_private(&new->indexij_comp_len,&seconds,indexij_compfile,sizeof(UINT4));
new->indexsize = 3 + log4(((new->indexij_ptrs_len - 8)/sizeof(UINT4)/2)/ /*DIFFERENTIAL_METAINFO_SIZE*/2);
#elif defined(USE_SEPARATE_BUCKETS)
/* 8 is for two DIFFERENTIAL_METAINFO_SIZE words */
- new->indexi_ptrs = (UINT4 *) Access_allocate(&key,&new->indexi_ptrs_len,&seconds,indexi_ptrsfile,sizeof(UINT4),/*sharedp*/false);
- new->indexi_comp = (UINT4 *) Access_allocate(&key,&new->indexi_comp_len,&seconds,indexi_compfile,sizeof(UINT4),/*sharedp*/false);
- new->indexj_ptrs = (UINT4 *) Access_allocate(&key,&new->indexj_ptrs_len,&seconds,indexj_ptrsfile,sizeof(UINT4),/*sharedp*/false);
- new->indexj_comp = (UINT4 *) Access_allocate(&key,&new->indexj_comp_len,&seconds,indexj_compfile,sizeof(UINT4),/*sharedp*/false);
+ new->indexi_ptrs = (UINT4 *) Access_allocate_private(&new->indexi_ptrs_access,&new->indexi_ptrs_len,&seconds,indexi_ptrsfile,sizeof(UINT4));
+ new->indexi_comp = (UINT4 *) Access_allocate_private(&new->indexi_comp_access,&new->indexi_comp_len,&seconds,indexi_compfile,sizeof(UINT4));
+ new->indexj_ptrs = (UINT4 *) Access_allocate_private(&new->indexj_ptrs_access,&new->indexj_ptrs_len,&seconds,indexj_ptrsfile,sizeof(UINT4));
+ new->indexj_comp = (UINT4 *) Access_allocate_private(&new->indexj_comp_access,&new->indexj_comp_len,&seconds,indexj_compfile,sizeof(UINT4));
new->indexsize = 3 + log4(((new->indexi_ptrs_len - 8)/sizeof(UINT4))/ /*DIFFERENTIAL_METAINFO_SIZE*/2);
#else
/* 8 is for two DIFFERENTIAL_METAINFO_SIZE words */
@@ -1100,32 +914,45 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
FREE(comma1);
- new->indexij_access = MMAPPED;
+ new->indexij_ptrs_access = MMAPPED;
+ new->indexij_comp_access = MMAPPED;
} else if (indexij_access == USE_MMAP_ONLY) {
- new->indexij_ptrs = (UINT4 *) Access_mmap(&new->indexij_ptrs_fd,&new->indexij_ptrs_len,indexij_ptrsfile,sizeof(UINT4),/*randomp*/true);
- new->indexij_comp = (UINT4 *) Access_mmap(&new->indexij_comp_fd,&new->indexij_comp_len,indexij_compfile,sizeof(UINT4),/*randomp*/true);
+ new->indexij_ptrs = (UINT4 *) Access_mmap(&new->indexij_ptrs_fd,&new->indexij_ptrs_len,indexij_ptrsfile,/*randomp*/true);
+ new->indexij_comp = (UINT4 *) Access_mmap(&new->indexij_comp_fd,&new->indexij_comp_len,indexij_compfile,/*randomp*/true);
- new->indexij_access = MMAPPED;
+ new->indexij_ptrs_access = MMAPPED;
+ new->indexij_comp_access = MMAPPED;
} else if (indexij_access == USE_ALLOCATE) {
- fprintf(stderr,"Allocating memory for indexij ptrs...");
- new->indexij_ptrs = (UINT4 *) Access_allocate(&new->indexij_ptrs_shmid,&new->indexij_ptrs_len,&seconds,indexij_ptrsfile,sizeof(UINT4),sharedp);
- comma1 = Genomicpos_commafmt(new->indexij_ptrs_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
-
- fprintf(stderr,"Allocating memory for indexij comp...");
- new->indexij_comp = (UINT4 *) Access_allocate(&new->indexij_comp_shmid,&new->indexij_comp_len,&seconds,indexij_compfile,sizeof(UINT4),sharedp);
- comma1 = Genomicpos_commafmt(new->indexij_comp_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
-
if (sharedp == true) {
- new->indexij_access = ALLOCATED_SHARED;
+ fprintf(stderr,"Allocating memory for indexij ptrs...");
+ new->indexij_ptrs = (UINT4 *) Access_allocate_shared(&new->indexij_ptrs_access,&new->indexij_ptrs_shmid,&new->indexij_ptrs_key,
+ &new->indexij_ptrs_fd,&new->indexij_ptrs_len,&seconds,indexij_ptrsfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->indexij_ptrs_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
+
+ fprintf(stderr,"Allocating memory for indexij comp...");
+ new->indexij_comp = (UINT4 *) Access_allocate_shared(&new->indexij_comp_access,&new->indexij_comp_shmid,&new->indexij_comp_key,
+ &new->indexij_comp_fd,&new->indexij_comp_len,&seconds,indexij_compfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->indexij_comp_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
} else {
- new->indexij_access = ALLOCATED_PRIVATE;
+ fprintf(stderr,"Allocating memory for indexij ptrs...");
+ new->indexij_ptrs = (UINT4 *) Access_allocate_private(&new->indexij_ptrs_access,&new->indexij_ptrs_len,&seconds,indexij_ptrsfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->indexij_ptrs_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
+
+ fprintf(stderr,"Allocating memory for indexij comp...");
+ new->indexij_comp = (UINT4 *) Access_allocate_private(&new->indexij_comp_access,&new->indexij_comp_len,&seconds,indexij_compfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->indexij_comp_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
}
+
}
new->indexsize = 3 + log4(((new->indexij_ptrs_len - 8)/sizeof(UINT4)/2)/ /*DIFFERENTIAL_METAINFO_SIZE*/2);
@@ -1136,26 +963,24 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
fprintf(stderr,"Pre-loading LCP/child/DC arrays...");
new->lcpchilddc = (unsigned char *) Access_mmap_and_preload(&new->lcpchilddc_fd,&new->lcpchilddc_len,&npages,&seconds,
lcpchilddcfile,sizeof(unsigned char));
- new->lcp_access = MMAPPED;
+ new->lcpchilddc_access = MMAPPED;
comma1 = Genomicpos_commafmt(new->lcpchilddc_len);
fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
FREE(comma1);
} else if (lcp_access == USE_MMAP_ONLY) {
- new->lcpchilddc = (unsigned char *) Access_mmap(&new->lcpchilddc_fd,&new->lcpchilddc_len,lcpchilddcfile,
- sizeof(unsigned char),/*randomp*/true);
- new->lcp_access = MMAPPED;
+ new->lcpchilddc = (unsigned char *) Access_mmap(&new->lcpchilddc_fd,&new->lcpchilddc_len,lcpchilddcfile,/*randomp*/true);
+ new->lcpchilddc_access = MMAPPED;
} else if (lcp_access == USE_ALLOCATE) {
fprintf(stderr,"Allocating memory for lcpchildc...");
- new->lcpchilddc = (unsigned char *) Access_allocate(&new->lcpchilddc_shmid,&new->lcpchilddc_len,&seconds,lcpchilddcfile,sizeof(unsigned char),sharedp);
- comma1 = Genomicpos_commafmt(new->lcpchilddc_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
-
if (sharedp == true) {
- new->lcp_access = ALLOCATED_SHARED;
+ new->lcpchilddc = (unsigned char *) Access_allocate_shared(&new->lcpchilddc_access,&new->lcpchilddc_shmid,&new->lcpchilddc_key,
+ &new->lcpchilddc_fd,&new->lcpchilddc_len,&seconds,lcpchilddcfile,sizeof(unsigned char));
} else {
- new->lcp_access = ALLOCATED_PRIVATE;
+ new->lcpchilddc = (unsigned char *) Access_allocate_private(&new->lcpchilddc_access,&new->lcpchilddc_len,&seconds,lcpchilddcfile,sizeof(unsigned char));
}
+ comma1 = Genomicpos_commafmt(new->lcpchilddc_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
}
if (guideexc_access == USE_MMAP_PRELOAD) {
@@ -1168,49 +993,81 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
child_guidefile,sizeof(UINT4));
new->child_exceptions = (UINT4 *) Access_mmap_and_preload(&new->child_exceptions_fd,&new->child_exceptions_len,&npages,&seconds,
child_exceptionsfile,sizeof(UINT4));
- new->guideexc_access = MMAPPED;
+ new->lcp_guide_access = MMAPPED;
+ new->lcp_exceptions_access = MMAPPED;
+ new->child_guide_access = MMAPPED;
+ new->child_exceptions_access = MMAPPED;
fprintf(stderr,"done\n");
} else if (guideexc_access == USE_MMAP_ONLY) {
new->lcp_guide = (UINT4 *) Access_mmap(&new->lcp_guide_fd,&new->lcp_guide_len,
- lcp_guidefile,sizeof(UINT4),/*randomp*/true);
+ lcp_guidefile,/*randomp*/true);
new->lcp_exceptions = (UINT4 *) Access_mmap(&new->lcp_exceptions_fd,&new->lcp_exceptions_len,
- lcp_exceptionsfile,sizeof(UINT4),/*randomp*/true);
+ lcp_exceptionsfile,/*randomp*/true);
new->child_guide = (UINT4 *) Access_mmap(&new->child_guide_fd,&new->child_guide_len,
- child_guidefile,sizeof(UINT4),/*randomp*/true);
+ child_guidefile,/*randomp*/true);
new->child_exceptions = (UINT4 *) Access_mmap(&new->child_exceptions_fd,&new->child_exceptions_len,
- child_exceptionsfile,sizeof(UINT4),/*randomp*/true);
- new->guideexc_access = MMAPPED;
+ child_exceptionsfile,/*randomp*/true);
+ new->lcp_guide_access = MMAPPED;
+ new->lcp_exceptions_access = MMAPPED;
+ new->child_guide_access = MMAPPED;
+ new->child_exceptions_access = MMAPPED;
} else if (guideexc_access == USE_ALLOCATE) {
fprintf(stderr,"Allocating memory for lcp guide...");
- new->lcp_guide = (UINT4 *) Access_allocate(&new->lcp_guide_shmid,&new->lcp_guide_len,&seconds,lcp_guidefile,sizeof(UINT4),sharedp);
- comma1 = Genomicpos_commafmt(new->lcp_guide_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
+ if (sharedp == true) {
+ new->lcp_guide = (UINT4 *) Access_allocate_shared(&new->lcp_guide_access,&new->lcp_guide_shmid,&new->lcp_guide_key,
+ &new->lcp_guide_fd,&new->lcp_guide_len,&seconds,lcp_guidefile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->lcp_guide_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
- fprintf(stderr,"Allocating memory for lcp exceptions...");
- new->lcp_exceptions = (UINT4 *) Access_allocate(&new->lcp_exceptions_shmid,&new->lcp_exceptions_len,&seconds,lcp_exceptionsfile,sizeof(UINT4),sharedp);
- comma1 = Genomicpos_commafmt(new->lcp_exceptions_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
-
- fprintf(stderr,"Allocating memory for child guide...");
- new->child_guide = (UINT4 *) Access_allocate(&new->child_guide_shmid,&new->child_guide_len,&seconds,child_guidefile,sizeof(UINT4),sharedp);
- comma1 = Genomicpos_commafmt(new->child_guide_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
+ fprintf(stderr,"Allocating memory for lcp exceptions...");
+ new->lcp_exceptions = (UINT4 *) Access_allocate_shared(&new->lcp_exceptions_access,&new->lcp_exceptions_shmid,&new->lcp_exceptions_key,
+ &new->lcp_exceptions_fd,&new->lcp_exceptions_len,&seconds,lcp_exceptionsfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->lcp_exceptions_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
+
+ fprintf(stderr,"Allocating memory for child guide...");
+ new->child_guide = (UINT4 *) Access_allocate_shared(&new->child_guide_access,&new->child_guide_shmid,&new->child_guide_key,
+ &new->child_guide_fd,&new->child_guide_len,&seconds,child_guidefile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->child_guide_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
- fprintf(stderr,"Allocating memory for child exceptions...");
- new->child_exceptions = (UINT4 *) Access_allocate(&new->child_exceptions_shmid,&new->child_exceptions_len,&seconds,child_exceptionsfile,sizeof(UINT4),sharedp);
- comma1 = Genomicpos_commafmt(new->child_exceptions_len);
- fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
- FREE(comma1);
+ fprintf(stderr,"Allocating memory for child exceptions...");
+ new->child_exceptions = (UINT4 *) Access_allocate_shared(&new->child_exceptions_access,&new->child_exceptions_shmid,&new->child_exceptions_key,
+ &new->child_exceptions_fd,&new->child_exceptions_len,&seconds,child_exceptionsfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->child_exceptions_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
- if (sharedp == true) {
- new->guideexc_access = ALLOCATED_SHARED;
} else {
- new->guideexc_access = ALLOCATED_PRIVATE;
+ new->lcp_guide = (UINT4 *) Access_allocate_private(&new->lcp_guide_access,&new->lcp_guide_len,&seconds,lcp_guidefile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->lcp_guide_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
+
+ fprintf(stderr,"Allocating memory for lcp exceptions...");
+ new->lcp_exceptions = (UINT4 *) Access_allocate_private(&new->lcp_exceptions_access,&new->lcp_exceptions_len,&seconds,
+ lcp_exceptionsfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->lcp_exceptions_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
+
+ fprintf(stderr,"Allocating memory for child guide...");
+ new->child_guide = (UINT4 *) Access_allocate_private(&new->child_guide_access,&new->child_guide_len,&seconds,child_guidefile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->child_guide_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
+
+ fprintf(stderr,"Allocating memory for child exceptions...");
+ new->child_exceptions = (UINT4 *) Access_allocate_private(&new->child_exceptions_access,&new->child_exceptions_len,&seconds,
+ child_exceptionsfile,sizeof(UINT4));
+ comma1 = Genomicpos_commafmt(new->child_exceptions_len);
+ fprintf(stderr,"done (%s bytes, %.2f sec)\n",comma1,seconds);
+ FREE(comma1);
}
}
@@ -1244,15 +1101,6 @@ Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_acc
FREE(indexij_ptrsfile);
#endif
-#ifdef USE_CSA
- FREE(csaX_ptrsfile); FREE(csaX_compfile);
- FREE(csaT_ptrsfile); FREE(csaT_compfile);
- FREE(csaG_ptrsfile); FREE(csaG_compfile);
- FREE(csaC_ptrsfile); FREE(csaC_compfile);
- FREE(csaA_ptrsfile); FREE(csaA_compfile);
-
- FREE(sasamplesfile);
-#endif
FREE(sarrayfile);
return new;
@@ -1275,128 +1123,77 @@ Sarray_free (T *old) {
FREE((*old)->indexj_ptrs);
FREE((*old)->indexj_comp);
#else
- if ((*old)->indexij_access == MMAPPED) {
+ if ((*old)->indexij_ptrs_access == MMAPPED) {
munmap((void *) (*old)->indexij_ptrs,(*old)->indexij_ptrs_len);
close((*old)->indexij_ptrs_fd);
+ } else if ((*old)->indexij_ptrs_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->indexij_ptrs);
+ } else if ((*old)->indexij_ptrs_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->indexij_ptrs,(*old)->indexij_ptrs_shmid,(*old)->indexij_ptrs_key);
+ }
+ if ((*old)->indexij_comp_access == MMAPPED) {
munmap((void *) (*old)->indexij_comp,(*old)->indexij_comp_len);
close((*old)->indexij_comp_fd);
- } else if ((*old)->indexij_access == ALLOCATED_PRIVATE) {
- FREE((*old)->indexij_ptrs);
+ } else if ((*old)->indexij_comp_access == ALLOCATED_PRIVATE) {
FREE((*old)->indexij_comp);
- } else if ((*old)->indexij_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->indexij_ptrs,(*old)->indexij_ptrs_shmid);
- Access_deallocate((*old)->indexij_comp,(*old)->indexij_comp_shmid);
+ } else if ((*old)->indexij_comp_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->indexij_comp,(*old)->indexij_comp_shmid,(*old)->indexij_comp_key);
}
#endif
- if ((*old)->guideexc_access == MMAPPED) {
+ if ((*old)->lcp_guide_access == MMAPPED) {
munmap((void *) (*old)->lcp_guide,(*old)->lcp_guide_len);
close((*old)->lcp_guide_fd);
+ } else if ((*old)->lcp_guide_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->lcp_guide);
+ } else if ((*old)->lcp_guide_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->lcp_guide,(*old)->lcp_guide_shmid,(*old)->lcp_guide_key);
+ }
+
+ if ((*old)->lcp_exceptions_access == MMAPPED) {
munmap((void *) (*old)->lcp_exceptions,(*old)->lcp_exceptions_len);
close((*old)->lcp_exceptions_fd);
+ } else if ((*old)->lcp_exceptions_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->lcp_exceptions);
+ } else if ((*old)->lcp_exceptions_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->lcp_exceptions,(*old)->lcp_exceptions_shmid,(*old)->lcp_exceptions_key);
+ }
+
+ if ((*old)->child_guide_access == MMAPPED) {
munmap((void *) (*old)->child_guide,(*old)->child_guide_len);
close((*old)->child_guide_fd);
+ } else if ((*old)->child_guide_access == ALLOCATED_PRIVATE) {
+ FREE((*old)->child_guide);
+ } else if ((*old)->child_guide_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->child_guide,(*old)->child_guide_shmid,(*old)->child_guide_key);
+ }
+
+ if ((*old)->child_exceptions_access == MMAPPED) {
munmap((void *) (*old)->child_exceptions,(*old)->child_exceptions_len);
close((*old)->child_exceptions_fd);
- } else if ((*old)->guideexc_access == ALLOCATED_PRIVATE) {
- FREE((*old)->lcp_exceptions);
- FREE((*old)->lcp_guide);
+ } else if ((*old)->child_exceptions_access == ALLOCATED_PRIVATE) {
FREE((*old)->child_exceptions);
- FREE((*old)->child_guide);
- } else if ((*old)->guideexc_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->lcp_exceptions,(*old)->lcp_exceptions_shmid);
- Access_deallocate((*old)->lcp_guide,(*old)->lcp_guide_shmid);
- Access_deallocate((*old)->child_exceptions,(*old)->child_exceptions_shmid);
- Access_deallocate((*old)->child_guide,(*old)->child_guide_shmid);
+ } else if ((*old)->child_exceptions_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->child_exceptions,(*old)->child_exceptions_shmid,(*old)->child_exceptions_key);
}
- if ((*old)->lcp_access == MMAPPED) {
+ if ((*old)->lcpchilddc_access == MMAPPED) {
munmap((void *) (*old)->lcpchilddc,(*old)->lcpchilddc_len);
close((*old)->lcpchilddc_fd);
- } else if ((*old)->lcp_access == ALLOCATED_PRIVATE) {
+ } else if ((*old)->lcpchilddc_access == ALLOCATED_PRIVATE) {
FREE((*old)->lcpchilddc);
- } else if ((*old)->lcp_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->lcpchilddc,(*old)->lcpchilddc_shmid);
+ } else if ((*old)->lcpchilddc_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->lcpchilddc,(*old)->lcpchilddc_shmid,(*old)->lcpchilddc_key);
}
-#ifndef USE_CSA
- if ((*old)->sarray_access == MMAPPED) {
+ if ((*old)->array_access == MMAPPED) {
munmap((void *) (*old)->array,(*old)->array_len);
close((*old)->array_fd);
- } else if ((*old)->sarray_access == ALLOCATED_PRIVATE) {
+ } else if ((*old)->array_access == ALLOCATED_PRIVATE) {
FREE((*old)->array);
- } else if ((*old)->sarray_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->array,(*old)->array_shmid);
+ } else if ((*old)->array_access == ALLOCATED_SHARED) {
+ Access_deallocate((*old)->array,(*old)->array_shmid,(*old)->array_key);
}
-#else
- if ((*old)->array != NULL) {
- if ((*old)->sarray_access == MMAPPED) {
- munmap((void *) (*old)->array,(*old)->array_len);
- close((*old)->array_fd);
- } else if ((*old)->sarray_access == ALLOCATED_PRIVATE) {
- FREE((*old)->array);
- } else if ((*old)->sarray_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->array,(*old)->array_shmid);
- }
- } else {
- if ((*old)->sarray_access == MMAPPED) {
- munmap((void *) (*old)->array_samples,(*old)->array_len);
- close((*old)->array_fd);
-
- munmap((void *) (*old)->csaAptrs,(*old)->csaAptrs_len);
- close((*old)->csaAptrs_fd);
- munmap((void *) (*old)->csaAcomp,(*old)->csaAcomp_len);
- close((*old)->csaAcomp_fd);
-
- munmap((void *) (*old)->csaCptrs,(*old)->csaCptrs_len);
- close((*old)->csaCptrs_fd);
- munmap((void *) (*old)->csaCcomp,(*old)->csaCcomp_len);
- close((*old)->csaCcomp_fd);
-
- munmap((void *) (*old)->csaGptrs,(*old)->csaGptrs_len);
- close((*old)->csaGptrs_fd);
- munmap((void *) (*old)->csaGcomp,(*old)->csaGcomp_len);
- close((*old)->csaGcomp_fd);
-
- munmap((void *) (*old)->csaTptrs,(*old)->csaTptrs_len);
- close((*old)->csaTptrs_fd);
- munmap((void *) (*old)->csaTcomp,(*old)->csaTcomp_len);
- close((*old)->csaTcomp_fd);
-
- munmap((void *) (*old)->csaXptrs,(*old)->csaXptrs_len);
- close((*old)->csaXptrs_fd);
- munmap((void *) (*old)->csaXcomp,(*old)->csaXcomp_len);
- close((*old)->csaXcomp_fd);
-
- } else if ((*old)->sarray_access == ALLOCATED_PRIVATE) {
- FREE((*old)->array_samples);
- FREE((*old)->csaAptrs);
- FREE((*old)->csaAcomp);
- FREE((*old)->csaCptrs);
- FREE((*old)->csaCcomp);
- FREE((*old)->csaGptrs);
- FREE((*old)->csaGcomp);
- FREE((*old)->csaTptrs);
- FREE((*old)->csaTcomp);
- FREE((*old)->csaXptrs);
- FREE((*old)->csaXcomp);
-
- } else if ((*old)->sarray_access == ALLOCATED_SHARED) {
- Access_deallocate((*old)->array_samples,(*old)->array_shmid);
- Access_deallocate((*old)->csaAptrs,(*old)->csaAptrs_shmid);
- Access_deallocate((*old)->csaAcomp,(*old)->csaAcomp_shmid);
- Access_deallocate((*old)->csaCptrs,(*old)->csaCptrs_shmid);
- Access_deallocate((*old)->csaCcomp,(*old)->csaCcomp_shmid);
- Access_deallocate((*old)->csaGptrs,(*old)->csaGptrs_shmid);
- Access_deallocate((*old)->csaGcomp,(*old)->csaGcomp_shmid);
- Access_deallocate((*old)->csaTptrs,(*old)->csaTptrs_shmid);
- Access_deallocate((*old)->csaTcomp,(*old)->csaTcomp_shmid);
- Access_deallocate((*old)->csaXptrs,(*old)->csaXptrs_shmid);
- Access_deallocate((*old)->csaXcomp,(*old)->csaXcomp_shmid);
- }
- }
-#endif
-
FREE_KEEP(*old);
}
@@ -1440,13 +1237,13 @@ sarray_search_init (char *query, int querylength, int queryoffset, Compress_T qu
fasti = nmatches_mid +
(Univcoord_T) Genome_consecutive_matches_rightward(query_compress,/*left*/Bigendian_convert_uint(sarray->array[mid])-queryoffset,
/*pos5*/queryoffset+nmatches_mid,
- /*pos3*/queryoffset+querylength,plusp,genestrand,first_read_p);
+ /*pos3*/queryoffset+querylength,plusp,genestrand);
pos = Bigendian_convert_uint(sarray->array[mid]) + fasti;
#else
fasti = nmatches_mid +
(Univcoord_T) Genome_consecutive_matches_rightward(query_compress,/*left*/sarray->array[mid]-queryoffset,
/*pos5*/queryoffset+nmatches_mid,
- /*pos3*/queryoffset+querylength,plusp,genestrand,first_read_p);
+ /*pos3*/queryoffset+querylength,plusp,genestrand);
pos = sarray->array[mid] + fasti;
#endif
c = Genome_get_char_lex(genome,pos,sarray->n,chartable);
@@ -1525,13 +1322,13 @@ sarray_search_final (char *query, int querylength, int queryoffset, Compress_T q
fasti = nmatches_mid +
(Univcoord_T) Genome_consecutive_matches_rightward(query_compress,/*left*/Bigendian_convert_uint(sarray->array[mid])-queryoffset,
/*pos5*/queryoffset+nmatches_mid,
- /*pos3*/queryoffset+querylength,plusp,genestrand,first_read_p);
+ /*pos3*/queryoffset+querylength,plusp,genestrand);
pos = Bigendian_convert_uint(sarray->array[mid]) + fasti;
#else
fasti = nmatches_mid +
(Univcoord_T) Genome_consecutive_matches_rightward(query_compress,/*left*/sarray->array[mid]-queryoffset,
/*pos5*/queryoffset+nmatches_mid,
- /*pos3*/queryoffset+querylength,plusp,genestrand,first_read_p);
+ /*pos3*/queryoffset+querylength,plusp,genestrand);
pos = sarray->array[mid] + fasti;
#endif
c = Genome_get_char_lex(genome,pos,sarray->n,chartable);
@@ -1591,9 +1388,9 @@ nt_querylength (char *query, int querylength) {
}
-Storedoligomer_T
+Oligospace_T
nt_oligo (char *query, int indexsize) {
- Storedoligomer_T oligo = 0U;
+ Oligospace_T oligo = 0U;
int i;
for (i = 0; i < indexsize; i++) {
@@ -1613,9 +1410,9 @@ nt_oligo (char *query, int indexsize) {
return oligo;
}
-Storedoligomer_T
+Oligospace_T
nt_oligo_truncate (char *query, int truncsize, int indexsize, int subst_value) {
- Storedoligomer_T oligo = 0U;
+ Oligospace_T oligo = 0U;
int i;
for (i = 0; i < truncsize; i++) {
@@ -1647,9 +1444,11 @@ nt_oligo_truncate (char *query, int truncsize, int indexsize, int subst_value) {
#define decode_down(index,child_bytes,child_guide,child_exceptions,child_guide_interval) Bytecoding_read_wguide(index,child_bytes,child_guide,child_exceptions,child_guide_interval) + index + 1
#define decode_next(index,child_bytes,child_guide,child_exceptions,child_guide_interval) Bytecoding_read_wguide(index,child_bytes,child_guide,child_exceptions,child_guide_interval) + index + 1
+#if 0
/* 0 1 2 3 4 5 6 7 8 9 A B C D E F */
static char discrim_char_before[16] = {'?','$','$','$','$','$','A','A','A','A','C','C','C','G','G','T'};
static char discrim_char_after[16] = {'?','A','C','G','T','X','C','G','T','X','G','T','X','T','X','X'};
+#endif
static bool
get_child_given_first (Sarrayptr_T *l, Sarrayptr_T *r, Sarrayptr_T i, Sarrayptr_T j, char desired_char,
@@ -1748,7 +1547,7 @@ static UINT4
find_longest_match (UINT4 nmatches, Sarrayptr_T *initptr, Sarrayptr_T *finalptr,
Sarrayptr_T i, Sarrayptr_T j, char *query, UINT4 querylength,
int queryoffset, Compress_T query_compress, T sarray, bool plusp,
- int genestrand, bool first_read_p, char conversion[]) {
+ int genestrand, char conversion[]) {
UINT4 lcp_whole, nextl, up;
UINT4 minlength;
UINT4 l, r;
@@ -1762,7 +1561,7 @@ find_longest_match (UINT4 nmatches, Sarrayptr_T *initptr, Sarrayptr_T *finalptr,
nmatches +=
Genome_consecutive_matches_rightward(query_compress,/*left*/SA_i-queryoffset,
/*pos5*/queryoffset+nmatches,/*pos3*/queryoffset+querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
*initptr = i;
*finalptr = j;
return nmatches;
@@ -1793,7 +1592,7 @@ find_longest_match (UINT4 nmatches, Sarrayptr_T *initptr, Sarrayptr_T *finalptr,
nmatches +=
Genome_consecutive_matches_rightward(query_compress,/*left*/SA_i-queryoffset,
/*pos5*/queryoffset+nmatches,/*pos3*/queryoffset+minlength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
if (nmatches < minlength) {
*initptr = i;
*finalptr = j;
@@ -1809,7 +1608,7 @@ find_longest_match (UINT4 nmatches, Sarrayptr_T *initptr, Sarrayptr_T *finalptr,
debug1(printf("nmatches is now %d => desired_char is %c => %c\n",
nmatches,query[nmatches],conversion[query[nmatches]]));
- if (get_child_given_first(&l,&r,i,j,/*desired_char*/conversion[query[nmatches]],
+ if (get_child_given_first(&l,&r,i,j,/*desired_char*/conversion[(int) query[nmatches]],
sarray,sarray->lcpchilddc,lcp_whole,nextl) == false) {
*initptr = i;
*finalptr = j;
@@ -1837,9 +1636,9 @@ static void
sarray_search (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, bool *successp,
UINT4 *nmatches, char *query, UINT4 querylength, int queryoffset,
Compress_T query_compress, T sarray, bool plusp, int genestrand,
- bool first_read_p, char conversion[]) {
+ char conversion[]) {
int effective_querylength; /* length to first N */
- Storedoligomer_T oligo;
+ Oligospace_T oligo;
UINT4 l, r;
#ifdef DEBUG1
@@ -1911,7 +1710,7 @@ sarray_search (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, bool *successp,
} else {
*nmatches = find_longest_match(*nmatches,&(*initptr),&(*finalptr),/*i*/l,/*j*/r,
query,querylength,queryoffset,query_compress,sarray,
- plusp,genestrand,first_read_p,conversion);
+ plusp,genestrand,conversion);
}
/* Search through suffix tree */
@@ -1935,7 +1734,7 @@ sarray_search (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, bool *successp,
SA_i = csa_lookup(sarray,(*initptr)-1);
recount = Genome_consecutive_matches_rightward(query_compress,/*left*/SA_i-queryoffset,
/*pos5*/queryoffset,/*pos3*/queryoffset+querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
printf("%d\t%u\t%u\t",recount,(*initptr)-1,SA_i/*+ 1U*/);
c2 = Bytecoding_lcpchilddc_dc(&c1,(*initptr)-1,sarray->lcpchilddc);
printf("%c%c\t",c1,c2);
@@ -1974,7 +1773,7 @@ sarray_search (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, bool *successp,
SA_i = csa_lookup(sarray,(*initptr)+k);
recount = Genome_consecutive_matches_rightward(query_compress,/*left*/SA_i-queryoffset,
/*pos5*/queryoffset,/*pos3*/queryoffset+querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
printf("%d\t%u\t%u\t",recount,(*initptr)+k,SA_i/*+ 1U*/);
c2 = Bytecoding_lcpchilddc_dc(&c1,(*initptr)+k,sarray->lcpchilddc);
printf("%c%c\t",c1,c2);
@@ -2025,7 +1824,7 @@ sarray_search (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, bool *successp,
hit = csa_lookup(sarray,(*initptr)+k);
recount = Genome_consecutive_matches_rightward(query_compress,/*left*/hit-queryoffset,
/*pos5*/queryoffset,/*pos3*/queryoffset+querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
printf("%d\t%u\t%u\t",recount,(*initptr)+k,hit /*+ 1U*/);
c2 = Bytecoding_lcpchilddc_dc(&c1,(*initptr)+k,sarray->lcpchilddc);
printf("%c%c\t",c1,c2);
@@ -2063,7 +1862,7 @@ sarray_search (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, bool *successp,
printf("\n");
recount = Genome_consecutive_matches_rightward(query_compress,/*left*/SA_i-queryoffset,
/*pos5*/queryoffset,/*pos3*/queryoffset+querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
printf("%d\t%u\t%u\t",recount,(*finalptr)+1,SA_i/*+ 1U*/);
c2 = Bytecoding_lcpchilddc_dc(&c1,(*finalptr)+1,sarray->lcpchilddc);
printf("%c%c\t",c1,c2);
@@ -2174,6 +1973,7 @@ Elt_new (int querypos, int nmatches, Sarrayptr_T initptr, Sarrayptr_T finalptr,
return new;
}
+#if 0
static Elt_T
Elt_new_fillin (int querystart, int queryend, int indexsize, Univcoord_T left) {
Elt_T new = (Elt_T) MALLOC(sizeof(*new));
@@ -2200,7 +2000,9 @@ Elt_new_fillin (int querystart, int queryend, int indexsize, Univcoord_T left) {
return new;
}
+#endif
+#if 0
static void
Elt_replace (Elt_T this, int querypos, int nmatches, Sarrayptr_T initptr, Sarrayptr_T finalptr) {
this->querystart = querypos;
@@ -2227,6 +2029,7 @@ Elt_replace (Elt_T this, int querypos, int nmatches, Sarrayptr_T initptr, Sarray
return;
}
+#endif
static void
@@ -2259,6 +2062,7 @@ Elt_nmatches_cmp (const void *a, const void *b) {
}
#endif
+#if 0
static int
Elt_querypos_ascending_cmp (const void *a, const void *b) {
Elt_T x = * (Elt_T *) a;
@@ -2272,7 +2076,9 @@ Elt_querypos_ascending_cmp (const void *a, const void *b) {
return 0;
}
}
+#endif
+#if 0
static int
Elt_querypos_descending_cmp (const void *a, const void *b) {
Elt_T x = * (Elt_T *) a;
@@ -2286,11 +2092,12 @@ Elt_querypos_descending_cmp (const void *a, const void *b) {
return 0;
}
}
+#endif
static int
Elt_extend_leftward (int *min_leftward, Elt_T elt, Compress_T query_compress,
- bool plusp, int genestrand, bool first_read_p, int skip_left) {
+ bool plusp, int genestrand, int skip_left) {
int max_leftward, nmatches;
int i;
@@ -2300,11 +2107,11 @@ Elt_extend_leftward (int *min_leftward, Elt_T elt, Compress_T query_compress,
} else {
max_leftward = *min_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/elt->positions[0],
/*pos5*/0,/*pos3*/elt->querystart - skip_left,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
for (i = 1; i < elt->npositions; i++) {
if ((nmatches = Genome_consecutive_matches_leftward(query_compress,/*left*/elt->positions[i],
/*pos5*/0,/*pos3*/elt->querystart,
- plusp,genestrand,first_read_p)) > max_leftward) {
+ plusp,genestrand)) > max_leftward) {
max_leftward = nmatches;
} else if (nmatches < *min_leftward) {
*min_leftward = nmatches;
@@ -2460,55 +2267,285 @@ fill_positions_std (int *npositions, Univcoord_T low_adj, Univcoord_T high_adj,
i = GUESS_ALLOCATION; /* Start count with the number stored */
ptr = lastptr; /* One past the last ptr with a result */
- while (i < *npositions) {
- if ((value = CONVERT(array[--ptr])) < low_adj) {
- /* Skip */
- } else if (value > high_adj) {
- /* Skip */
- } else {
- positions[i++] = value - querystart;
+ while (i < *npositions) {
+ if ((value = CONVERT(array[--ptr])) < low_adj) {
+ /* Skip */
+ } else if (value > high_adj) {
+ /* Skip */
+ } else {
+ positions[i++] = value - querystart;
+ }
+ }
+ }
+
+ return positions;
+}
+#endif
+
+
+
+/* Call fill_positions_filtered_first for first time, which is
+ linear in number of entries or O(n), then on second call, do sort with O(n*log n),
+ plus O(log n) for each additional call */
+
+#ifdef HAVE_ALLOCA
+
+#if defined(HAVE_AVX2) && !defined(WORDS_BIGENDIAN)
+
+/* Using pext method, because _mm256_shuffle_epi32 doesn't work well
+because it works only within lanes, and MASTER_CONTROL does not extend
+well to 256 bits */
+
+static void
+fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T low, Univcoord_T high) {
+ int nmatches;
+ Univcoord_T low_adj, high_adj;
+ Univcoord_T *array = sarray->array, value0;
+ Sarrayptr_T *array_stop, *array_end, *array_ptr;
+ Univcoord_T *positions_temp;
+ UINT8 pointer;
+ Univcoord_T *out;
+ __m256i converted, adjusted, match;
+ __m256i floor, ceiling, values, adj, p;
+ unsigned int mask, selector;
+ unsigned int univ_selector = 0x76543210;
+ __m256i _selector, _varshifts;
+#if defined(REQUIRE_ALIGNMENT)
+ int n_prealign, k;
+#endif
+#ifdef DEBUG7
+ int i;
+#endif
+#ifdef DEBUG8
+ Univcoord_T *positions_std;
+ int npositions_std;
+#endif
+
+
+ debug(printf("Entered fill_positions_filtered_first with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+ debug7(printf("Entered fill_positions_filtered_first with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+
+ if (this->positions_allocated != NULL) {
+ /* Filled from a previous call */
+ FREE(this->positions_allocated);
+ }
+
+ if ((this->n_all_positions = this->finalptr - this->initptr + 1) == 0 /*|| this->n_all_positions > EXCESS_SARRAY_HITS*/) {
+ this->all_positions = (Univcoord_T *) NULL;
+
+ } else {
+ positions_temp = out = (Univcoord_T *) MALLOCA((this->finalptr - this->initptr + 1) * sizeof(Univcoord_T));
+
+ low_adj = low + this->querystart;
+ high_adj = high + this->querystart;
+
+ floor = _mm256_set1_epi32(low_adj - 1 - 2147483648);
+ ceiling = _mm256_set1_epi32(high_adj + 1 - 2147483648);
+ adj = _mm256_set1_epi32(this->querystart);
+ _varshifts = _mm256_set_epi32(28,24,20,16,12,8,4,0);
+
+ this->npositions_allocated = this->npositions = 0;
+#if defined(REQUIRE_ALIGNMENT)
+ array_ptr = &(array[this->initptr]);
+
+ /* Initial part */
+ n_prealign = ((32 - ((UINT8) array_ptr & 0x1F))/4) & 0x7;
+ debug7(printf("Initial ptr is at location %p. Need %d to get to 256-bit boundary\n",pointer,n_prealign));
+
+ debug7(printf("Initial part:\n"));
+ if (n_prealign > this->finalptr - this->initptr + 1) {
+ n_prealign = this->finalptr - this->initptr + 1;
+ }
+ for (k = 0; k < n_prealign; k++) {
+ debug7a(printf("Looking at value %u, relative to low %u and high %u\n",CONVERT(array[ptr]),low_adj,high_adj));
+ if ((value0 = *array_ptr++) >= low_adj && value0 <= high_adj) {
+ *out++ = value0 - this->querystart;
+ }
+ }
+#else
+ array_ptr = &(array[this->initptr]);
+#endif /* REQUIRE_ALIGNMENT */
+
+
+ /* Aligned part */
+ if (this->finalptr < 8) {
+ array_stop = &(array[0]);
+ } else {
+ array_stop = &(array[this->finalptr - 8]);
+ }
+ array_end = &(array[this->finalptr]);
+
+ while (array_ptr < array_stop) {
+
+#if defined(REQUIRE_ALIGNMENT)
+ /* Use stream_load to avoid polluting the cache with suffix array entries */
+ values = _mm256_stream_load_si256((__m256i *) array_ptr);
+#else
+ /* It looks like loadu is just as fast as load */
+ values = _mm256_loadu_si256((__m256i *) array_ptr);
+#endif
+ debug7b(print_vector_uint_256(values));
+
+ converted = _mm256_sub_epi32(values,epi32_convert_256);
+ /* match = _mm256_andnot_si256(_mm256_cmpgt_epi32(floor,converted),_mm256_cmpgt_epi32(ceiling,converted)); -- This is off by 1 at floor */
+ match = _mm256_and_si256(_mm256_cmpgt_epi32(converted,floor),_mm256_cmpgt_epi32(ceiling,converted));
+ /* Example:
+ {0xFFFFFFFF, 0x00000000, 0xFFFFFFFF, 0x00000000, 0xFFFFFFFF, 0x00000000, 0xFFFFFFFF, 0x00000000} (8 x 32-bit ints) */
+ debug7b(print_vector_hex_256(match));
+
+ /* Get most significant from each byte from each byte to obtain a mask in terms of 4-bit nibbles */
+ mask = (unsigned int) _mm256_movemask_epi8(match);
+ /* 11110000 11110000 11110000 11110000 (32-bit int) */
+
+ if (mask) {
+ adjusted = _mm256_sub_epi32(values,adj);
+
+ selector = _pext_u32(univ_selector,mask);
+ /* 01110110 01010100 00110010 00010000 (32-bit int, univ_selector) */
+ /* 00000000 00000000 01110101 00110001 (32-bit int, selector), equiv to 0x00007531 */
+ debug7b(printf("selector: %08X\n",selector));
+
+ _selector = _mm256_set1_epi32(selector);
+ /* {0x00007531, 0x00007531, 0x00007531, 0x00007531, 0x00007531, 0x00007531, 0x00007531, 0x00007531} */
+
+ _selector = _mm256_srlv_epi32(_selector,_varshifts);
+ /* {0x00000000, 0x00000000, 0x00000000, 0x00000000, 0x00000007, 0x00000075, 0x00000753, 0x00007531} */
+ debug7b(print_vector_hex_256(_selector));
+
+ p = _mm256_permutevar8x32_epi32(adjusted,_selector);
+ _mm256_storeu_si256((__m256i *) out, p);
+
+ /* Divide popcount(mask) by 4 to get number of matches */
+#ifdef HAVE_POPCNT
+ out += _popcnt32(mask)/4;
+ debug7b(printf("mask: %08X (%d ones)\n",mask,_popcnt32(mask)/4));
+#elif defined HAVE_MM_POPCNT
+ out += _mm_popcnt_u32(mask)/4;
+ debug7b(printf("mask: %08X (%d ones)\n",mask,_mm_popcnt_u32(mask)/4));
+#else
+ out += __builtin_popcount(mask)/4;
+ debug7b(printf("mask: %08X (%d ones)\n",mask,__builtin_popcount(mask)/4));
+#endif
+ debug7b(print_vector_uint_256(p));
+ }
+
+ array_ptr += 8;
+ }
+
+ /* Partial block at end; do scalar */
+ debug7(printf("\nFinal part:\n"));
+ while (array_ptr <= array_end) {
+ if ((value0 = *array_ptr++) >= low_adj && value0 <= high_adj) {
+ *out++ = value0 - this->querystart;
+ }
+ }
+
+ this->npositions_allocated = this->npositions = out - positions_temp;
+ debug7(printf("SIMD method found %d positions\n",this->npositions));
+
+ /* Copy the positions into heap from temp in stack */
+ if (this->npositions == 0) {
+ this->positions_allocated = this->positions = (Univcoord_T *) NULL;
+ } else {
+ debug7(printf("Sorting %d positions\n",this->npositions));
+ qsort(positions_temp,this->npositions,sizeof(Univcoord_T),Univcoord_compare);
+
+ /* Need to copy positions before the goal */
+ this->positions_allocated = this->positions = MALLOC(this->npositions * sizeof(Univcoord_T));
+ memcpy(this->positions,positions_temp,this->npositions * sizeof(Univcoord_T));
+#ifdef DEBUG7
+ for (i = 0; i < this->npositions; i++) {
+ printf("%u\n",this->positions[i]);
}
+#endif
+
+#if 0
+ /* Not sure why we were doing this. We will find collinear set of diagonals later. */
+ /* Advance pointer to goal (note: do not want goal_adj, since we have already subtracted this->querystart) */
+ /* Have tested positions[i] <= goal, but want positions[-1] to be < goal, or positions[0] >= goal */
+ /* ? Replace with a binary search */
+ i = 0;
+ while (i < this->npositions && positions_temp[i] < goal) {
+ debug7(printf("1 Skipping position %u (%u) < goal %u (%u)\n",
+ positions_temp[i],positions_temp[i] - chroffset,goal,goal - chroffset));
+ i++;
+ }
+ this->positions += i;
+ this->npositions -= i;
+ debug7(printf("Remaining: %d positions\n",this->npositions));
+#endif
}
+
+ FREEA(positions_temp);
}
- return positions;
+ return;
}
-#endif
+#elif defined(HAVE_SSSE3) && !defined(WORDS_BIGENDIAN)
+/* SSSE3 needed for _mm_shuffle_epi8 */
-/* Call fill_positions_filtered_first for first time, which is
- linear in number of entries or O(n), then on second call, do sort with O(n*log n),
- plus O(log n) for each additional call */
+/* Prefer shuffle_mask, because MASTER_CONTROL requires AVX command
+ _mm_permutevar_ps. Cannot use pext approach, because that requires
+ BMI2. */
-#ifdef HAVE_ALLOCA
+/* Nevertheless, here is an explanation of MASTER_CONTROL:
+
+ For blocks of 128 bits:
+
+ MASTER_CONTROL =
+ _mm_set_epi8(0x10, 0x12, 0x13, 0x12, 0x40, 0x68, 0x7C, 0x6B,
+ 0x00, 0x80, 0xC0, 0xBC, 0x00, 0x00, 0x00, 0xC0);
+
+ matchbits = _mm_movemask_ps(_mm_castsi128_ps(match));
+ p = _mm_permutevar_ps(input,_mm_srli_epi32(MASTER_CONTROL,matchbits*2));
+
+ These values come from rotating the control values horizontally, like this:
+
+ 15 14 13 12 11 10 09 08 07 06 05 04 03 02 01 00 (matchbits)
+
+ 00 01 00 10 00 01 00 11 00 01 00 10 00 01 00 XX (control 15 downto 0, bits 1 and 0)
+ 01 10 10 11 01 11 11 XX 01 10 10 XX 01 XX XX XX (control 15 downto 0, bits 3 and 2)
+ 10 11 11 XX 11 XX XX XX 10 XX XX XX XX XX XX XX (control 15 downto 0, bits 5 and 4)
+ 11 XX XX XX XX XX XX XX XX XX XX XX XX XX XX XX (control 15 downto 0, bits 7 and 6)
+
+ and then reading in bytes from right to left for each row.
+
+ Alternatively, create the following table, and read in bits upward
+ starting from the rightmost column:
+
+ matchbits 00: XX XX XX XX ^
+ matchbits 01: XX XX XX 00 |
+ matchbits 02: XX XX XX 01 |
+ matchbits 03: XX XX 01 00 _
+ matchbits 04: XX XX XX 10 ^
+ matchbits 05: XX XX 10 00 |
+ matchbits 06: XX XX 10 01 |
+ matchbits 07: XX 10 01 00 _
+ matchbits 08: XX XX XX 11 .
+ matchbits 09: XX XX 11 00 .
+ matchbits 10: XX XX 11 01 .
+ matchbits 11: XX 11 01 00
+ matchbits 12: XX XX 11 10
+ matchbits 13: XX 11 10 00
+ matchbits 14: XX 11 10 01
+ matchbits 15: 11 10 01 00
+*/
-#if defined(HAVE_SSSE3) && defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN)
-/* SSSE3 needed for _mm_shuffle_epi8 */
static void
-fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T low, Univcoord_T high,
- Compress_T query_compress, bool plusp, int genestrand, bool first_read_p) {
- int nmatches;
+fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T low, Univcoord_T high) {
Univcoord_T low_adj, high_adj;
-#ifdef USE_CSA
- Univcoord_T value3, value2, value1, value0, *all;
- Sarrayptr_T ptri, stopi, endi;
-#else
Univcoord_T *array = sarray->array, value0;
Sarrayptr_T *array_stop, *array_end, *array_ptr;
-#endif
Univcoord_T *positions_temp;
-#ifdef HAVE_64_BIT
- UINT8 pointer;
-#else
- UINT4 pointer;
-#endif
Univcoord_T *out;
__m128i converted, adjusted, match;
__m128i floor, ceiling, values, adj, p;
int matchbits;
-#ifdef USE_CSA
-#elif defined(REQUIRE_ALIGNMENT)
+#if defined(REQUIRE_ALIGNMENT)
int n_prealign, k;
#endif
#ifndef USE_SHUFFLE_MASK
@@ -2523,10 +2560,10 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
#endif
- debug(printf("Entered fill_positions_filtered_first with goal %u, low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
- goal,low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
- debug7(printf("Entered fill_positions_filtered_first with goal %u, low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
- goal,low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+ debug(printf("Entered fill_positions_filtered_first with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+ debug7(printf("Entered fill_positions_filtered_first with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
if (this->positions_allocated != NULL) {
/* Filled from a previous call */
@@ -2537,13 +2574,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->all_positions = (Univcoord_T *) NULL;
} else {
-#ifdef USE_CSA
- all = this->all_positions = (Univcoord_T *) CALLOC(this->n_all_positions,sizeof(Univcoord_T));
-#else
- /* For non-CSA, done by calling procedure */
-#endif
-
-
positions_temp = out = (Univcoord_T *) MALLOCA((this->finalptr - this->initptr + 1) * sizeof(Univcoord_T));
low_adj = low + this->querystart;
@@ -2554,9 +2584,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
adj = _mm_set1_epi32(this->querystart);
this->npositions_allocated = this->npositions = 0;
-#ifdef USE_CSA
- ptri = this->initptr;
-#elif defined(REQUIRE_ALIGNMENT)
+#if defined(REQUIRE_ALIGNMENT)
array_ptr = &(array[this->initptr]);
/* Initial part */
@@ -2573,53 +2601,38 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
}
for (k = 0; k < n_prealign; k++) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",CONVERT(array[ptr]),low_adj,high_adj));
- if ((value = *array_ptr++) >= low_adj && value <= high_adj) {
- *out++ = value - this->querystart;
+ if ((value0 = *array_ptr++) >= low_adj && value0 <= high_adj) {
+ *out++ = value0 - this->querystart;
}
}
#else
array_ptr = &(array[this->initptr]);
-#endif /* USE_CSA */
+#endif /* REQUIRE_ALIGNMENT */
/* Aligned part */
-#ifdef USE_CSA
- if (this->finalptr < 4) {
- stopi = 0;
- } else {
- stopi = this->finalptr - 4;
- }
- endi = this->finalptr;
-#else
if (this->finalptr < 4) {
array_stop = &(array[0]);
} else {
array_stop = &(array[this->finalptr - 4]);
}
array_end = &(array[this->finalptr]);
-#endif
#ifndef USE_SHUFFLE_MASK
MASTER_CONTROL = _mm_setr_epi8(0x10, 0x12, 0x13, 0x12, 0x40, 0x68, 0x7C, 0x6B,
0x00, 0x80, 0xC0, 0xBC, 0x00, 0x00, 0x00, 0xC0);
#endif
- while (
-#ifdef USE_CSA
- ptri < stopi
+ while (array_ptr < array_stop) {
+#if defined(REQUIRE_ALIGNMENT)
+
+#ifdef HAVE_SSE4_1
+ /* Use stream_load to avoid polluting the cache with suffix array entries */
+ values = _mm_stream_load_si128((__m128i *) array_ptr);
#else
- array_ptr < array_stop
+ values = _mm_load_si128((__m128i *) array_ptr);
#endif
- ) {
-#ifdef USE_CSA
- value3 = *all++ = csa_lookup(sarray,ptri);
- value2 = *all++ = csa_lookup(sarray,ptri+1);
- value1 = *all++ = csa_lookup(sarray,ptri+2);
- value0 = *all++ = csa_lookup(sarray,ptri+3);
- values = _mm_set_epi32(value3,value2,value1,value0);
-#elif defined(REQUIRE_ALIGNMENT)
- values = _mm_load_si128((__m128i *) array_ptr);
#else
/* It looks like loadu is just as fast as load */
values = _mm_loadu_si128((__m128i *) array_ptr);
@@ -2641,7 +2654,10 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
#endif
_mm_storeu_si128((__m128i *) out, p);
-#ifdef HAVE_POPCNT
+#if !defined(HAVE_SSE4_2)
+ out += __builtin_popcount(matchbits);
+ debug7b(printf("matchbits: %08X (%d ones)\n",matchbits,__builtin_popcount(matchbits)));
+#elif defined(HAVE_POPCNT)
out += _popcnt32(matchbits);
debug7b(printf("matchbits: %08X (%d ones)\n",matchbits,_popcnt32(matchbits)));
#elif defined HAVE_MM_POPCNT
@@ -2651,30 +2667,20 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
out += __builtin_popcount(matchbits);
debug7b(printf("matchbits: %08X (%d ones)\n",matchbits,__builtin_popcount(matchbits)));
#endif
+ debug7b(print_vector_hex(shuffle_mask16[matchbits]));
+ debug7b(print_vector_uint(p));
}
-#ifdef USE_CSA
- ptri += 4;
-#else
array_ptr += 4;
-#endif
}
/* Partial block at end; do scalar */
debug7(printf("\nFinal part:\n"));
-#ifdef USE_CSA
- while (ptri <= endi) {
- if ((value0 = *all++ = csa_lookup(sarray,ptri++)) >= low_adj && value0 <= high_adj) {
- *out++ = value0 - this->querystart;
- }
- }
-#else
while (array_ptr <= array_end) {
if ((value0 = *array_ptr++) >= low_adj && value0 <= high_adj) {
*out++ = value0 - this->querystart;
}
}
-#endif
this->npositions_allocated = this->npositions = out - positions_temp;
debug7(printf("SIMD method found %d positions\n",this->npositions));
@@ -2720,19 +2726,14 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
#else
-/* Bigendian or missing SSSE3 or SSE2 */
+/* Bigendian or missing SSSE3 */
static void
-fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T low, Univcoord_T high,
- Compress_T query_compress, bool plusp, int genestrand, bool first_read_p) {
- Sarrayptr_T ptr, lastptr;
- int nmatches;
- int i;
+fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T low, Univcoord_T high) {
+ Sarrayptr_T ptr;
Univcoord_T low_adj, high_adj;
- Univcoord_T value3, value2, value1, value0;
-#ifndef USE_CSA
Univcoord_T *array = sarray->array;
-#endif
+ Univcoord_T value3, value2, value1, value0;
Univcoord_T *positions_temp;
#if defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN)
#ifdef HAVE_64_BIT
@@ -2745,8 +2746,8 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
#endif
- debug7(printf("Entered fill_positions_filtered_first with goal %u, low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
- goal,low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+ debug7(printf("Entered fill_positions_filtered_first with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
if (this->positions_allocated != NULL) {
/* Filled from a previous call */
@@ -2757,13 +2758,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->all_positions = (Univcoord_T *) NULL;
} else {
-#ifdef USE_CSA
- all = this->all_positions = (Univcoord_T *) CALLOC(this->n_all_positions,sizeof(Univcoord_T));
-#else
- /* For non-CSA, done by calling procedure */
-#endif
-
-
positions_temp = (Univcoord_T *) MALLOCA((this->finalptr - this->initptr + 1) * sizeof(Univcoord_T));
low_adj = low + this->querystart;
@@ -2777,11 +2771,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
debug7(printf("Small batch, because %u + 3 <= %u\n",ptr,this->finalptr));
while (ptr <= this->finalptr) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",csa_lookup(sarray,ptr),low_adj,high_adj));
- if ((value0 =
-#ifdef USE_CSA
- *all++ =
-#endif
- csa_lookup(sarray,ptr++)) < low_adj) {
+ if ((value0 = csa_lookup(sarray,ptr++)) < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
/* Skip */
@@ -2792,7 +2782,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
}
} else {
-#ifndef USE_CSA
#ifdef HAVE_64_BIT
pointer = (UINT8) &(array[ptr]);
#else
@@ -2815,7 +2804,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
positions_temp[this->npositions++] = value0 - this->querystart;
}
}
-#endif
/* Aligned part */
debug7(printf("\nAligned part:\n"));
@@ -2824,15 +2812,8 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
floor = _mm_set1_epi32(low_adj - 1 - 2147483648);
ceiling = _mm_set1_epi32(high_adj + 1 - 2147483648);
while (ptr + 3 <= this->finalptr) { /* ptr + 4 < this->finalptr + 1 */
-#ifdef USE_CSA
- value3 = *all++ = csa_lookup(sarray,ptr);
- value2 = *all++ = csa_lookup(sarray,ptr+1);
- value1 = *all++ = csa_lookup(sarray,ptr+2);
- value0 = *all++ = csa_lookup(sarray,ptr+3);
- values = _mm_set_epi32(value3,value2,value1,value0);
-#else
+ /* Missing SSSE3 so cannot do stream load */
values = _mm_load_si128((__m128i *) &(array[ptr]));
-#endif
debug7a(print_vector_looking(values,low_adj,high_adj));
values = _mm_sub_epi32(values,epi32_convert);
compare = _mm_and_si128(_mm_cmpgt_epi32(values,floor),_mm_cmplt_epi32(values,ceiling));
@@ -2840,9 +2821,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
/* All results are false, indicating no values between low_adj and high_adj (most common case) */
ptr += 4;
} else {
-#ifndef USE_CSA
value3 = CONVERT(array[ptr++]);
-#endif
if (value3 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value3,low_adj));
@@ -2854,9 +2833,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
positions_temp[this->npositions++] = value3 - this->querystart;
}
-#ifndef USE_CSA
value2 = CONVERT(array[ptr++]);
-#endif
if (value2 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value2,low_adj));
@@ -2868,9 +2845,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
positions_temp[this->npositions++] = value2 - this->querystart;
}
-#ifndef USE_CSA
value1 = CONVERT(array[ptr++]);
-#endif
if (value1 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value1,low_adj));
@@ -2882,9 +2857,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
positions_temp[this->npositions++] = value1 - this->querystart;
}
-#ifndef USE_CSA
value0 = CONVERT(array[ptr++]);
-#endif
if (value0 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value0,low_adj));
@@ -2895,9 +2868,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
debug7(printf("Found position %u between low %u and high %u, and within allocation\n",value0,low_adj,high_adj));
positions_temp[this->npositions++] = value0 - this->querystart;
}
-#ifdef USE_CSA
- ptr += 4;
-#endif
}
}
@@ -2905,11 +2875,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
debug7(printf("\nFinal part:\n"));
while (ptr <= this->finalptr) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",csa_lookup(sarray,ptr),low_adj,high_adj));
- if ((value0 =
-#ifdef USE_CSA
- *all++ =
-#endif
- csa_lookup(sarray,ptr++)) < low_adj) {
+ if ((value0 = csa_lookup(sarray,ptr++)) < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
/* Skip */
@@ -2924,11 +2890,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
while (ptr <= this->finalptr) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",csa_lookup(sarray,ptr),low_adj,high_adj));
- if ((value0 =
-#ifdef USE_CSA
- *all++ =
-#endif
- csa_lookup(sarray,ptr++)) < low_adj) {
+ if ((value0 = csa_lookup(sarray,ptr++)) < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
/* Skip */
@@ -2980,18 +2942,13 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
/* Non-ALLOCA version */
static void
-fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T low, Univcoord_T high,
- Compress_T query_compress, bool plusp, int genestrand, bool first_read_p) {
+fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T low, Univcoord_T high) {
Sarrayptr_T ptr, lastptr;
int nmatches;
int i;
Univcoord_T low_adj, high_adj;
Univcoord_T value3, value2, value1, value0;
-#ifdef USE_CSA
- Sarrayptr_T stopi, endi, ptri, *all;
-#else
Univcoord_T *array = sarray->array;
-#endif
Univcoord_T *more_positions;
#if defined(HAVE_SSE2) && !defined(WORDS_BIGENDIAN)
#ifdef HAVE_64_BIT
@@ -3004,8 +2961,8 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
#endif
- debug7(printf("Entered fill_positions_filtered_first with goal %u, low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
- goal,low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+ debug7(printf("Entered fill_positions_filtered_first with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
if (this->positions_allocated != NULL) {
/* Filled from a previous call */
@@ -3016,13 +2973,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->all_positions = (Univcoord_T *) NULL;
} else {
-#ifdef USE_CSA
- all = this->all_positions = (Univcoord_T *) CALLOC(this->n_all_positions,sizeof(Univcoord_T));
-#else
- /* For non-CSA, done by calling procedure */
-#endif
-
-
/* Guess at allocation size */
this->positions_allocated = this->positions = (Univcoord_T *) CALLOC(GUESS_ALLOCATION,sizeof(Univcoord_T));
@@ -3037,11 +2987,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
debug7(printf("Small batch, because %u + 3 <= %u\n",ptr,this->finalptr));
while (ptr <= this->finalptr) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",csa_lookup(sarray,ptr),low_adj,high_adj));
- if ((value0 =
-#ifdef USE_CSA
- *all++ =
-#endif
- csa_lookup(sarray,ptr++)) < low_adj) {
+ if ((value0 = csa_lookup(sarray,ptr++)) < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
/* Skip */
@@ -3056,7 +3002,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
}
} else {
-#ifndef USE_CSA
#ifdef HAVE_64_BIT
pointer = (UINT8) &(array[ptr]);
#else
@@ -3083,7 +3028,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
lastptr = ptr; /* saves us from going through the entire sarray below */
}
}
-#endif
/* Aligned part */
debug7(printf("\nAligned part:\n"));
@@ -3092,15 +3036,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
floor = _mm_set1_epi32(low_adj - 1 - 2147483648);
ceiling = _mm_set1_epi32(high_adj + 1 - 2147483648);
while (ptr + 3 <= this->finalptr) { /* ptr + 4 < this->finalptr + 1 */
-#ifdef USE_CSA
- value3 = *all++ = csa_lookup(sarray,ptr);
- value2 = *all++ = csa_lookup(sarray,ptr+1);
- value1 = *all++ = csa_lookup(sarray,ptr+2);
- value0 = *all++ = csa_lookup(sarray,ptr+3);
- values = _mm_set_epi32(value3,value2,value1,value0);
-#else
values = _mm_load_si128((__m128i *) &(array[ptr]));
-#endif
debug7a(print_vector_looking(values,low_adj,high_adj));
values = _mm_sub_epi32(values,epi32_convert);
compare = _mm_and_si128(_mm_cmpgt_epi32(values,floor),_mm_cmplt_epi32(values,ceiling));
@@ -3108,9 +3044,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
/* All results are false, indicating no values between low_adj and high_adj (most common case) */
ptr += 4;
} else {
-#ifndef USE_CSA
value3 = CONVERT(array[ptr++]);
-#endif
if (value3 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value3,low_adj));
@@ -3126,9 +3060,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
lastptr = ptr; /* saves us from going through the entire sarray below */
}
-#ifndef USE_CSA
value2 = CONVERT(array[ptr++]);
-#endif
if (value2 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value2,low_adj));
@@ -3144,9 +3076,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
lastptr = ptr; /* saves us from going through the entire sarray below */
}
-#ifndef USE_CSA
value1 = CONVERT(array[ptr++]);
-#endif
if (value1 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value1,low_adj));
@@ -3162,9 +3092,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
lastptr = ptr; /* saves us from going through the entire sarray below */
}
-#ifndef USE_CSA
value0 = CONVERT(array[ptr++]);
-#endif
if (value0 < low_adj) {
/* Skip */
debug7(printf("Skipping position %u < low %u\n",value0,low_adj));
@@ -3179,9 +3107,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->npositions++;
lastptr = ptr; /* saves us from going through the entire sarray below */
}
-#ifdef USE_CSA
- ptr += 4;
-#endif
}
}
@@ -3189,11 +3114,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
debug7(printf("\nFinal part:\n"));
while (ptr <= this->finalptr) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",csa_lookup(sarray,ptr),low_adj,high_adj));
- if ((value0 =
-#ifdef USE_CSA
- *all++ =
-#endif
- csa_lookup(sarray,ptr++)) < low_adj) {
+ if ((value0 = csa_lookup(sarray,ptr++)) < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
/* Skip */
@@ -3212,11 +3133,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
while (ptr <= this->finalptr) {
debug7a(printf("Looking at value %u, relative to low %u and high %u\n",csa_lookup(sarray,ptr),low_adj,high_adj));
- if ((value0 =
-#ifdef USE_CSA
- *all++ =
-#endif
- csa_lookup(sarray,ptr++)) < low_adj) {
+ if ((value0 = csa_lookup(sarray,ptr++)) < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
/* Skip */
@@ -3256,7 +3173,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
}
} else {
-#ifndef USE_CSA
#ifdef HAVE_64_BIT
pointer = (UINT8) &(array[ptr]);
#else
@@ -3276,28 +3192,17 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->positions[i++] = value0 - this->querystart;
}
}
-#endif
/* Aligned part */
while (i < this->npositions && this->initptr + 4 < ptr) {
-#ifdef USE_CSA
- value3 = csa_lookup(sarray,ptr-4);
- value2 = csa_lookup(sarray,ptr-3);
- value1 = csa_lookup(sarray,ptr-2);
- value0 = csa_lookup(sarray,ptr-1);
- values = _mm_set_epi32(value3,value2,value1,value0);
-#else
values = _mm_load_si128((__m128i *) &(array[ptr-4]));
-#endif
values = _mm_sub_epi32(values,epi32_convert);
compare = _mm_and_si128(_mm_cmpgt_epi32(values,floor),_mm_cmplt_epi32(values,ceiling));
if (/*cmp*/_mm_movemask_epi8(compare) == 0x0000) {
/* All results are false, indicating no values between low_adj and high_adj (most common case) */
ptr -= 4;
} else {
-#ifndef USE_CSA
value0 = CONVERT(array[--ptr]);
-#endif
if (value0 < low_adj) {
/* Skip */
} else if (value0 > high_adj) {
@@ -3306,9 +3211,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->positions[i++] = value0 - this->querystart;
}
-#ifndef USE_CSA
value1 = CONVERT(array[--ptr]);
-#endif
if (value1 < low_adj) {
/* Skip */
} else if (value1 > high_adj) {
@@ -3317,9 +3220,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->positions[i++] = value1 - this->querystart;
}
-#ifndef USE_CSA
value2 = CONVERT(array[--ptr]);
-#endif
if (value2 < low_adj) {
/* Skip */
} else if (value2 > high_adj) {
@@ -3328,9 +3229,7 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
this->positions[i++] = value2 - this->querystart;
}
-#ifndef USE_CSA
value3 = CONVERT(array[--ptr]);
-#endif
if (value3 < low_adj) {
/* Skip */
} else if (value3 > high_adj) {
@@ -3338,10 +3237,6 @@ fill_positions_filtered_first (Elt_T this, T sarray, Univcoord_T goal, Univcoord
} else {
this->positions[i++] = value3 - this->querystart;
}
-
-#ifdef USE_CSA
- ptr -= 4;
-#endif
}
}
@@ -3425,13 +3320,12 @@ binary_search (int lowi, int highi, Univcoord_T *positions, Univcoord_T goal) {
/* Used upon second call to Elt_fill_positions_filtered */
static void
-fill_positions_filtered_again (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T low, Univcoord_T high,
- Compress_T query_compress, bool plusp, int genestrand, bool first_read_p) {
+fill_positions_filtered_again (Elt_T this, Univcoord_T low, Univcoord_T high) {
int lowi, highi, i;
- debug(printf("Entered fill_positions_filtered_again with goal %u, low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
- goal,low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
+ debug(printf("Entered fill_positions_filtered_again with low %u and high %u, initptr %u and finalptr %u (n = %d), nmatches %d\n",
+ low,high,this->initptr,this->finalptr,this->finalptr - this->initptr + 1,this->nmatches));
if (this->positions_allocated != NULL) {
/* Filled from a previous call */
@@ -3465,20 +3359,21 @@ fill_positions_filtered_again (Elt_T this, T sarray, Univcoord_T goal, Univcoord
static void
Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T low, Univcoord_T high,
- Compress_T query_compress, bool plusp, int genestrand, bool first_read_p,
- bool multiplep) {
+ Compress_T query_compress, bool plusp, int genestrand, bool multiplep) {
int nmatches;
#ifdef DEBUG8
Univcoord_T *positions_std;
int npositions_std;
#endif
+#ifdef WORDS_BIGENDIAN
int i;
+#endif
if (this->nmatches == 0 || this->finalptr - this->initptr + 1 > EXCESS_SARRAY_HITS) {
/* Check for an extension */
nmatches = Genome_consecutive_matches_rightward(query_compress,/*left*/goal,/*pos5*/this->querystart,
- /*pos3*/this->queryend + 1,plusp,genestrand,first_read_p);
+ /*pos3*/this->queryend + 1,plusp,genestrand);
debug7(printf("rightward at goal %u from %d to %d shows %d matches (want %d)\n",goal,this->querystart,this->queryend,
nmatches,this->queryend - this->querystart + 1));
@@ -3498,20 +3393,15 @@ Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T
}
return; /* Don't even try other methods */
-#ifndef USE_CSA
} else if (multiplep == true) {
if (this->status == ELT_VIRGIN) {
/* Just go directly to sorting method, and skip SIMD filtering method */
this->status = ELT_UNSORTED;
}
-#endif
}
if (this->status == ELT_VIRGIN) {
- fill_positions_filtered_first(this,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
-#if USE_CSA
- this->status = ELT_UNSORTED;
-#else
+ fill_positions_filtered_first(this,sarray,low,high);
if (this->finalptr - this->initptr + 1 > EXCESS_SARRAY_HITS) {
/* Just keep filtering using SIMD method */
this->all_positions = (Univcoord_T *) NULL;
@@ -3519,14 +3409,8 @@ Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T
} else {
this->status = ELT_UNSORTED;
}
-#endif
} else if (this->status == ELT_UNSORTED) {
-#ifdef USE_CSA
- if (this->n_all_positions > 0) {
- qsort(this->all_positions,this->n_all_positions,sizeof(Univcoord_T),Univcoord_compare);
- }
-#else
if ((this->n_all_positions = this->finalptr - this->initptr + 1) == 0 /*|| this->npositions > EXCESS_SARRAY_HITS*/) {
this->all_positions = (Univcoord_T *) NULL;
this->n_all_positions = 0;
@@ -3541,7 +3425,6 @@ Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T
#endif
qsort(this->all_positions,this->n_all_positions,sizeof(Univcoord_T),Univcoord_compare);
}
-#endif
#ifdef DEBUG10
for (i = 0; i < this->n_all_positions; i++) {
printf("%d: %u\n",i,this->all_positions[i]);
@@ -3549,12 +3432,12 @@ Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T
printf("\n");
#endif
- fill_positions_filtered_again(this,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ fill_positions_filtered_again(this,low,high);
this->status = ELT_SORTED;
} else {
/* ELT_SORTED */
- fill_positions_filtered_again(this,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ fill_positions_filtered_again(this,low,high);
}
#ifdef DEBUG8
@@ -3569,6 +3452,7 @@ Elt_fill_positions_filtered (Elt_T this, T sarray, Univcoord_T goal, Univcoord_T
}
+#if 0
static void
Elt_dump_list (List_T list) {
List_T p;
@@ -3597,7 +3481,9 @@ Elt_dump_list (List_T list) {
return;
}
+#endif
+#ifdef DEBUG
static void
Elt_dump (Elt_T elt) {
int k;
@@ -3611,6 +3497,7 @@ Elt_dump (Elt_T elt) {
return;
}
+#endif
@@ -3618,6 +3505,7 @@ Elt_dump (Elt_T elt) {
#define subtract_bounded(x,minusterm,lowbound) ((x < lowbound + (minusterm)) ? lowbound : x - (minusterm))
+#if 0
/* Copied to stage1hr.c */
static int
donor_match_length_cmp (const void *a, const void *b) {
@@ -3635,7 +3523,10 @@ donor_match_length_cmp (const void *a, const void *b) {
return 0;
}
}
+#endif
+
+#if 0
/* Copied to stage1hr.c */
static int
acceptor_match_length_cmp (const void *a, const void *b) {
@@ -3653,6 +3544,7 @@ acceptor_match_length_cmp (const void *a, const void *b) {
return 0;
}
}
+#endif
/* Also defined in stage1hr.c */
@@ -3814,7 +3706,7 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
/* sub */
debug7(printf(" Testing in entire query\n"));
nmismatches = Genome_count_mismatches_substring(query_compress,left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug7(printf("nmismatches = %d (vs %d misses allowed)\n",nmismatches,nmisses_allowed));
if (nmismatches > nmisses_allowed) {
@@ -3955,17 +3847,17 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
} else {
#if 0
nmismatches1 = Genome_count_mismatches_substring(query_compress,left1,/*pos5*/0,/*pos3*/indel_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
nmismatches2 = Genome_count_mismatches_substring(query_compress,left2,/*pos5*/indel_pos,
- /*pos3*/querylength,plusp,genestrand,first_read_p);
+ /*pos3*/querylength,plusp,genestrand);
if (plusp == true) {
query_indel_pos = indel_pos;
} else {
query_indel_pos = querylength - indel_pos;
}
+ /* genomiclength = querylength+nindels; */
if ((hit = Stage3end_new_deletion(&(*found_score),nindels,query_indel_pos,
- nmismatches1,nmismatches2,
- left1,/*genomiclength*/querylength+nindels,
+ nmismatches1,nmismatches2,left1,
query_compress,querylength,plusp,genestrand,first_read_p,
chrnum,chroffset,chrhigh,chrlength,
/*indel_penalty*/2,/*sarrayp*/true)) != NULL) {
@@ -3977,8 +3869,7 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
*indels = Indel_solve_middle_deletion(&foundp,&(*found_score),&nhits,*indels,
/*left*/left1,chrnum,chroffset,chrhigh,chrlength,
/*indels*/-nindels,query_compress,querylength,
- nmisses_allowed,
- plusp,genestrand,first_read_p,/*sarray*/true);
+ nmisses_allowed,plusp,genestrand,/*sarray*/true);
debug7(
if (foundp == true) {
printf("successful");
@@ -3996,17 +3887,17 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
debug7(printf("C insertion of %d bp (nmisses allowed %d)...",nindels,nmisses_allowed));
#if 0
nmismatches1 = Genome_count_mismatches_substring(query_compress,left1,/*pos5*/0,/*pos3*/indel_pos-nindels,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
nmismatches2 = Genome_count_mismatches_substring(query_compress,left2,/*pos5*/indel_pos+nindels,
- /*pos3*/querylength,plusp,genestrand,first_read_p);
+ /*pos3*/querylength,plusp,genestrand);
if (plusp == true) {
query_indel_pos = indel_pos;
} else {
query_indel_pos = querylength - indel_pos - nindels;
}
+ /* genomiclength = querylength-nindels; */
if ((hit = Stage3end_new_insertion(&(*found_score),nindels,query_indel_pos,
- nmismatches1,nmismatches2,
- left1,/*genomiclength*/querylength-nindels,
+ nmismatches1,nmismatches2,left1,
query_compress,querylength,plusp,genestrand,first_read_p,
chrnum,chroffset,chrhigh,chrlength,
/*indel_penalty*/2,/*sarrayp*/true)) != NULL) {
@@ -4018,7 +3909,7 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
*indels = Indel_solve_middle_insertion(&foundp,&(*found_score),&nhits,*indels,
/*left*/left1,chrnum,chroffset,chrhigh,chrlength,
/*indels*/+nindels,query_compress,querylength,nmisses_allowed,
- plusp,genestrand,first_read_p,/*sarrayp*/true);
+ plusp,genestrand,/*sarrayp*/true);
debug7(
if (foundp == true) {
printf("successful");
@@ -4168,7 +4059,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -4232,7 +4122,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -4403,7 +4292,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -4467,7 +4355,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -4616,17 +4503,17 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
} else {
#if 0
nmismatches1 = Genome_count_mismatches_substring(query_compress,left1,/*pos5*/0,/*pos3*/indel_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
nmismatches2 = Genome_count_mismatches_substring(query_compress,left2,/*pos5*/indel_pos,
- /*pos3*/querylength,plusp,genestrand,first_read_p);
+ /*pos3*/querylength,plusp,genestrand);
if (plusp == true) {
query_indel_pos = indel_pos;
} else {
query_indel_pos = querylength - indel_pos;
}
+ /* genomiclength = querylength+nindels; */
if ((hit = Stage3end_new_deletion(&(*found_score),nindels,query_indel_pos,
- nmismatches1,nmismatches2,
- left1,/*genomiclength*/querylength+nindels,
+ nmismatches1,nmismatches2,left1,
query_compress,querylength,plusp,genestrand,first_read_p,
chrnum,chroffset,chrhigh,chrlength,
/*indel_penalty*/2,/*sarrayp*/true)) != NULL) {
@@ -4638,8 +4525,7 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
*indels = Indel_solve_middle_deletion(&foundp,&(*found_score),&nhits,*indels,
/*left*/left1,chrnum,chroffset,chrhigh,chrlength,
/*indels*/-nindels,query_compress,querylength,
- nmisses_allowed,
- plusp,genestrand,first_read_p,/*sarray*/true);
+ nmisses_allowed,plusp,genestrand,/*sarray*/true);
debug7(
if (foundp == true) {
printf("successful");
@@ -4657,17 +4543,17 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
debug7(printf("C insertion of %d bp (nmisses allowed %d)...",nindels,nmisses_allowed));
#if 0
nmismatches1 = Genome_count_mismatches_substring(query_compress,left1,/*pos5*/0,/*pos3*/indel_pos-nindels,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
nmismatches2 = Genome_count_mismatches_substring(query_compress,left2,/*pos5*/indel_pos+nindels,
- /*pos3*/querylength,plusp,genestrand,first_read_p);
+ /*pos3*/querylength,plusp,genestrand);
if (plusp == true) {
query_indel_pos = indel_pos;
} else {
query_indel_pos = querylength - indel_pos - nindels;
}
+ /*genomiclength = querylength-nindels; */
if ((hit = Stage3end_new_insertion(&(*found_score),nindels,query_indel_pos,
- nmismatches1,nmismatches2,
- left1,/*genomiclength*/querylength-nindels,
+ nmismatches1,nmismatches2,left1,
query_compress,querylength,plusp,genestrand,first_read_p,
chrnum,chroffset,chrhigh,chrlength,
/*indel_penalty*/2,/*sarrayp*/true)) != NULL) {
@@ -4679,7 +4565,7 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
*indels = Indel_solve_middle_insertion(&foundp,&(*found_score),&nhits,*indels,
/*left*/left1,chrnum,chroffset,chrhigh,chrlength,
/*indels*/+nindels,query_compress,querylength,nmisses_allowed,
- plusp,genestrand,first_read_p,/*sarrayp*/true);
+ plusp,genestrand,/*sarrayp*/true);
debug7(
if (foundp == true) {
printf("successful");
@@ -4831,7 +4717,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -4896,7 +4781,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -5065,7 +4949,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -5129,7 +5012,6 @@ solve_twopart (int *found_score, List_T *subs, List_T *indels, List_T *ambiguous
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_nmatches*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -5182,15 +5064,13 @@ static int
get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T *best_left_diagonals,
List_T *all_right_diagonals, List_T *all_left_diagonals,
T sarray, char *queryptr, int querylength, Compress_T query_compress,
- Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
+ Univcoord_T chroffset, Univcoord_T chrhigh,
Univcoord_T goal, Elt_T *original_elt_array, int best_i, int nelts,
- bool plusp, int genestrand, bool first_read_p, char conversion[],
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool) {
+ bool plusp, int genestrand, char conversion[]) {
int best_score_right, best_score_left, best_score, score;
Elt_T elt, right_elt;
List_T *elt_tree;
Univcoord_T low, high;
- Chrpos_T low_chrpos, high_chrpos;
int max_leftward, min_leftward, skip_left;
int querystart, queryend;
@@ -5202,22 +5082,30 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
List_T p;
Univdiag_T *diagonal_array, diagonal, prev_diagonal;
- List_T sub_diagonals;
- Diag_T sub_diagonal;
int querypos;
int ndiagonals;
- int nfound;
- bool *coveredp;
+#ifdef SUBDIVIDE_NOMATCHES
+ Chrpos_T low_chrpos, high_chrpos;
+ List_T sub_diagonals;
+ Diag_T sub_diagonal;
+ int nfound;
Univcoord_T mappingstart, mappingend;
- Chrpos_T **mappings, chrstart, chrend;
- int *npositions, totalpositions = 0;
int maxnconsecutive = 0;
+
Oligoindex_T oligoindex;
- bool oned_matrix_p;
- int indexsize;
+ Chrpos_T **mappings, chrstart, chrend;
+ bool *coveredp;
+ int *npositions, totalpositions = 0;
+#endif
+ int max_insertionlen;
+ if (max_middle_insertions_default >= 0) {
+ max_insertionlen = max_insertionlen_default;
+ } else {
+ max_insertionlen = querylength;
+ }
debug13(printf("\n***Entered get_diagonals, plusp %d, with goal %u\n",plusp,goal));
@@ -5229,13 +5117,13 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
/* Compute leftward extensions for right side */
- debug13(printf("Performing leftward extensions for right side\n"));
+ debug13(printf("Performing leftward extensions for right side. Subtracting %d and adding %d\n",
+ max_insertionlen,overall_max_distance));
low = subtract_bounded(goal,/*minusterm*/max_insertionlen,chroffset);
high = add_bounded(goal,/*plusterm*/overall_max_distance,chrhigh);
for (i = best_i + 1; i < nelts; i++) {
elt = (Elt_T) elt_tree[i]->first;
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p,
- /*multiplep*/false);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
if (elt->npositions > 0) {
/* Success: Update low and high for next search */
low = subtract_bounded(elt->positions[0],/*minusterm*/max_insertionlen,chroffset);
@@ -5246,10 +5134,9 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
if (i + 1 < nelts) {
/* A. Try moving boundary to the left */
right_elt = (Elt_T) elt_tree[i+1]->first;
- Elt_fill_positions_filtered(right_elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p,
- /*multiplep*/false);
+ Elt_fill_positions_filtered(right_elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
if ((max_leftward = Elt_extend_leftward(&min_leftward,right_elt,query_compress,
- plusp,genestrand,first_read_p,/*skip_left*/0)) > 0) {
+ plusp,genestrand,/*skip_left*/0)) > 0) {
debug13(printf("Can extend %d..%d leftward by max %d, min %d\n",
right_elt->querystart,right_elt->queryend,max_leftward,min_leftward));
right_elt->querystart_leftward -= min_leftward; /* Using min_leftward is conservative */
@@ -5269,15 +5156,14 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
/* queryend was computed above */
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querystart]),
/*querylength*/(queryend + 1) - querystart,/*queryoffset*/querystart,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt_tree[j] = List_pop(elt_tree[j],(void **) &elt);
if (elt->temporaryp == true) {
Elt_free(&elt);
}
elt = Elt_new(querystart,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[j] = List_push(NULL,(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p,
- /*multiplep*/false);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
}
}
}
@@ -5292,13 +5178,13 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
/* Compute leftward extensions for left side */
- debug13(printf("Performing leftward extensions for left side\n"));
+ debug13(printf("Performing leftward extensions for left side. Subtracting %d and adding %d\n",
+ overall_max_distance,max_insertionlen));
low = subtract_bounded(goal,/*minusterm*/overall_max_distance,chroffset);
high = add_bounded(goal,/*plusterm*/max_insertionlen,chrhigh);
for (i = best_i - 1; i >= 0; --i) {
elt = (Elt_T) elt_tree[i]->first;
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p,
- /*multiplep*/false);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
if (elt->npositions > 0) {
/* Success: Update low and high for next search */
low = subtract_bounded(elt->positions[0],/*minusterm*/overall_max_distance,chroffset);
@@ -5311,10 +5197,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
right_elt = (Elt_T) elt_tree[i+1]->first;
skip_left = 0;
if ((max_leftward = Elt_extend_leftward(&min_leftward,right_elt,query_compress,
- plusp,genestrand,first_read_p,/*skip_left*/0)) == 0) {
+ plusp,genestrand,/*skip_left*/0)) == 0) {
skip_left = 1;
max_leftward = Elt_extend_leftward(&min_leftward,right_elt,query_compress,
- plusp,genestrand,first_read_p,skip_left);
+ plusp,genestrand,skip_left);
debug13(printf("On second try, min_leftward is %d, max_leftward is %d\n",min_leftward,max_leftward));
}
@@ -5338,15 +5224,14 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
/* queryend was computed above */
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querystart]),
/*querylength*/(queryend + 1) - querystart,/*queryoffset*/querystart,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt_tree[j] = List_pop(elt_tree[j],(void **) &elt);
if (elt->temporaryp == true) {
Elt_free(&elt);
}
elt = Elt_new(querystart,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[j] = List_push(NULL,(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p,
- /*multiplep*/false);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
}
}
}
@@ -5397,10 +5282,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
for (querypos = queryend - 16; querypos >= querystart; querypos -= 8) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querypos]),
/*querylength*/16,/*queryoffset*/querypos,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt = Elt_new(querypos,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[i] = List_push(elt_tree[i],(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
nfound += elt->npositions;
debug13(printf("Subelt at %d..%d has %d matching positions\n",elt->querystart,elt->queryend,elt->npositions));
}
@@ -5411,10 +5296,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
for (querypos = queryend - 16; querypos >= querystart; querypos -= 1) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querypos]),
/*querylength*/16,/*queryoffset*/querypos,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt = Elt_new(querypos,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[i] = List_push(elt_tree[i],(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
nfound += elt->npositions;
debug13(printf("Subelt at %d..%d has %d matching positions\n",elt->querystart,elt->queryend,elt->npositions));
}
@@ -5426,10 +5311,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
for (querypos = queryend - 8; querypos >= querystart; querypos -= 1) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querypos]),
/*querylength*/8,/*queryoffset*/querypos,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt = Elt_new(querypos,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[i] = List_push(elt_tree[i],(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
nfound += elt->npositions;
debug13(printf("Subelt at %d..%d has %d matching positions\n",elt->querystart,elt->queryend,elt->npositions));
}
@@ -5495,10 +5380,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
for (querypos = queryend - 16; querypos >= querystart; querypos -= 8) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querystart]),
/*querylength*/16,/*queryoffset*/querystart,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt = Elt_new(querystart,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[i] = List_push(elt_tree[i],(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
nfound += elt->npositions;
debug13(printf("Subelt at %d..%d has %d matching positions\n",elt->querystart,elt->queryend,elt->npositions));
}
@@ -5509,10 +5394,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
for (querypos = queryend - 16; querypos >= querystart; querypos -= 1) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querypos]),
/*querylength*/16,/*queryoffset*/querypos,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt = Elt_new(querypos,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[i] = List_push(elt_tree[i],(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
nfound += elt->npositions;
debug13(printf("Subelt at %d..%d has %d matching positions\n",elt->querystart,elt->queryend,elt->npositions));
}
@@ -5524,10 +5409,10 @@ get_diagonals (Univdiag_T *middle_diagonal, List_T *best_right_diagonals, List_T
for (querypos = queryend - 8; querypos >= querystart; querypos -= 1) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryptr[querypos]),
/*querylength*/8,/*queryoffset*/querypos,
- query_compress,sarray,plusp,genestrand,first_read_p,conversion);
+ query_compress,sarray,plusp,genestrand,conversion);
elt = Elt_new(querypos,nmatches,initptr,finalptr,/*temporaryp*/true);
elt_tree[i] = List_push(elt_tree[i],(void *) elt);
- Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,first_read_p);
+ Elt_fill_positions_filtered(elt,sarray,goal,low,high,query_compress,plusp,genestrand,/*multiplep*/false);
nfound += elt->npositions;
debug13(printf("Subelt at %d..%d has %d matching positions\n",elt->querystart,elt->queryend,elt->npositions));
}
@@ -5886,30 +5771,31 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
Univdiag_T middle_diagonal, List_T best_right_diagonals, List_T best_left_diagonals,
- char *queryptr, int querylength, Compress_T query_compress,
- Univcoord_T chroffset, Univcoord_T chrhigh,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, bool plusp, int genestrand,
- bool first_read_p, int max_mismatches_allowed) {
+ int querylength, Compress_T query_compress, Univcoord_T chroffset,
+ bool plusp, int genestrand, int max_mismatches_allowed) {
List_T middle_path;
List_T p;
List_T diagonal_path, ambig_path;
Univdiag_T diagonal, common_diagonal, prev_diagonal, right_indel_diagonal = NULL, left_indel_diagonal = NULL;
- Diag_T sub_diagonal;
int nbest;
- List_T sub_diagonals;
- int querystart, queryend;
- bool *coveredp;
- Univcoord_T mappingstart, mappingend, left, prev_left, ambig_left;
+#ifdef SUBDIVIDE_ENDS
+ int indexsize;
+ bool oned_matrix_p;
Chrpos_T **mappings, chrstart, chrend;
- int *npositions, totalpositions = 0;
int maxnconsecutive = 0;
+ int *npositions, totalpositions = 0;
+ bool *coveredp;
+ int querystart, queryend;
+ Univcoord_T mappingstart, mappingend;
+ List_T sub_diagonals;
+ Diag_T sub_diagonal;
Oligoindex_T oligoindex;
- bool oned_matrix_p;
- int indexsize;
+#endif
+ Univcoord_T left, prev_left;
- Chrpos_T splice_distance;
+ /* Chrpos_T splice_distance; */
int splice_pos;
int best_knowni_i, best_knowni_j, best_nmismatches_i, best_nmismatches_j;
double best_prob_i, best_prob_j;
@@ -5936,12 +5822,13 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
debug13(printf("***Entered find_best_path\n"));
- coveredp = (bool *) CALLOCA(querylength,sizeof(bool));
+#ifdef SUBDIVIDE_ENDS
mappings = (Chrpos_T **) MALLOCA(querylength * sizeof(Chrpos_T *));
+ indexsize = Oligoindex_indexsize(oligoindex);
+ coveredp = (bool *) CALLOCA(querylength,sizeof(bool));
npositions = (int *) CALLOCA(querylength,sizeof(int));
oligoindex = Oligoindex_array_elt(oligoindices_minor,/*source*/0);
- indexsize = Oligoindex_indexsize(oligoindex);
-
+#endif
/* A3. Traceback for dynamic programming */
*right_endpoints_sense = *right_endpoints_antisense = (Intlist_T) NULL;
@@ -5957,13 +5844,13 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
if ((nbest = List_length(best_right_diagonals)) == 0) {
common_diagonal = (Univdiag_T) NULL;
- querystart = middle_diagonal->queryend + 1;
+ /* querystart = middle_diagonal->queryend + 1; */
left = middle_diagonal->univdiagonal;
} else if (nbest == 1) {
common_diagonal = (Univdiag_T) List_head(best_right_diagonals);
- querystart = common_diagonal->queryend + 1;
+ /* querystart = common_diagonal->queryend + 1; */
left = common_diagonal->univdiagonal;
} else {
@@ -5995,11 +5882,11 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
if (common_diagonal == NULL) {
/* All paths connect directly to the middle diagonal, so there is no common diagonal */
prev_diagonal = middle_diagonal;
- querystart = middle_diagonal->queryend + 1;
+ /* querystart = middle_diagonal->queryend + 1; */
prev_left = middle_diagonal->univdiagonal;
} else {
prev_diagonal = common_diagonal;
- querystart = common_diagonal->queryend + 1;
+ /* querystart = common_diagonal->queryend + 1; */
prev_left = common_diagonal->univdiagonal;
}
@@ -6020,7 +5907,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
if (right_indel_diagonal != NULL) {
/* Push onto middle path later */
- querystart = right_indel_diagonal->queryend + 1;
+ /* querystart = right_indel_diagonal->queryend + 1; */
left = right_indel_diagonal->univdiagonal;
} else {
@@ -6069,7 +5956,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength + 100;
segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength + 100;
- splice_distance = left - prev_left;
+ /* splice_distance = left - prev_left; */
#if 0
max_mismatches_allowed = (diagonal->querystart - prev_diagonal->queryend - 1);
debug13(printf("max_mismatches %d = %d - %d - 1\n",max_mismatches_allowed,diagonal->querystart,prev_diagonal->queryend));
@@ -6091,8 +5978,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
segmentj_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,
- plusp,genestrand,first_read_p)) >= 0) {
+ max_mismatches_allowed,plusp,genestrand)) >= 0) {
*right_endpoints_sense = Intlist_push(*right_endpoints_sense,splice_pos);
*right_queryends_sense = Intlist_push(*right_queryends_sense,diagonal->queryend + 1);
*right_ambcoords_sense = Uintlist_push(*right_ambcoords_sense,left + splice_pos);
@@ -6113,8 +5999,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
segmentj_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,
- plusp,genestrand,first_read_p)) >= 0) {
+ max_mismatches_allowed,plusp,genestrand)) >= 0) {
*right_endpoints_antisense = Intlist_push(*right_endpoints_antisense,splice_pos);
*right_queryends_antisense = Intlist_push(*right_queryends_antisense,diagonal->queryend + 1);
*right_ambcoords_antisense = Uintlist_push(*right_ambcoords_antisense,left + splice_pos);
@@ -6128,9 +6013,10 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
}
}
- sub_diagonals = (List_T) NULL;
#ifdef SUBDIVIDE_ENDS
+ sub_diagonals = (List_T) NULL;
+
if (querystart + MIN_ENDLENGTH >= querylength) {
} else {
/* Run oligoindex here to right of common_diagonal */
@@ -6253,13 +6139,13 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
if ((nbest = List_length(best_left_diagonals)) == 0) {
common_diagonal = (Univdiag_T) NULL;
- queryend = middle_diagonal->querystart;
+ /* queryend = middle_diagonal->querystart; */
left = middle_diagonal->univdiagonal;
} else if (nbest == 1) {
common_diagonal = (Univdiag_T) List_head(best_left_diagonals);
- queryend = common_diagonal->querystart;
+ /* queryend = common_diagonal->querystart; */
left = common_diagonal->univdiagonal;
} else {
@@ -6291,11 +6177,11 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
if (common_diagonal == NULL) {
/* All paths connect directly to the middle diagonal, so there is no common diagonal */
diagonal = middle_diagonal;
- queryend = middle_diagonal->querystart;
+ /* queryend = middle_diagonal->querystart; */
left = middle_diagonal->univdiagonal;
} else {
diagonal = common_diagonal;
- queryend = common_diagonal->querystart;
+ /* queryend = common_diagonal->querystart; */
left = common_diagonal->univdiagonal;
}
@@ -6317,7 +6203,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
if (left_indel_diagonal != NULL) {
/* Push onto middle path later */
left = left_indel_diagonal->univdiagonal;
- queryend = left_indel_diagonal->querystart;
+ /* queryend = left_indel_diagonal->querystart; */
} else {
for (p = *left_paths; p != NULL; p = List_next(p)) {
@@ -6365,7 +6251,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
segmentj_acceptor_knownpos[segmentj_acceptor_nknown] = querylength + 100;
segmentj_antidonor_knownpos[segmentj_antidonor_nknown] = querylength + 100;
- splice_distance = left - prev_left;
+ /* splice_distance = left - prev_left; */
#if 0
max_mismatches_allowed = (diagonal->querystart - prev_diagonal->queryend - 1);
debug13(printf("max_mismatches %d = %d - %d - 1\n",max_mismatches_allowed,diagonal->querystart,prev_diagonal->queryend));
@@ -6387,8 +6273,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
segmentj_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,
- plusp,genestrand,first_read_p)) >= 0) {
+ max_mismatches_allowed,plusp,genestrand)) >= 0) {
*left_endpoints_sense = Intlist_push(*left_endpoints_sense,splice_pos);
*left_querystarts_sense = Intlist_push(*left_querystarts_sense,prev_diagonal->querystart);
*left_ambcoords_sense = Uintlist_push(*left_ambcoords_sense,prev_left + splice_pos);
@@ -6409,8 +6294,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
segmentj_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,
- plusp,genestrand,first_read_p)) >= 0) {
+ max_mismatches_allowed,plusp,genestrand)) >= 0) {
*left_endpoints_antisense = Intlist_push(*left_endpoints_antisense,splice_pos);
*left_querystarts_antisense = Intlist_push(*left_querystarts_antisense,prev_diagonal->querystart);
*left_ambcoords_antisense = Uintlist_push(*left_ambcoords_antisense,prev_left + splice_pos);
@@ -6425,9 +6309,9 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
}
+#ifdef SUBDIVIDE_ENDS
sub_diagonals = (List_T) NULL;
-#ifdef SUBDIVIDE_ENDS
/* Run oligoindex here to left of common_diagonal */
if (queryend < MIN_ENDLENGTH) {
} else {
@@ -6505,6 +6389,12 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
debug13(printf("***Exiting find_best_path\n"));
+#ifdef SUBDIVIDE_ENDS
+ FREEA(npositions);
+ FREEA(coveredp);
+ FREEA(mappings);
+#endif
+
return middle_path;
}
@@ -6514,6 +6404,7 @@ find_best_path (List_T *right_paths, Intlist_T *right_endpoints_sense, Intlist_T
end paths to get stage2. Would be better to run oligoindex_hr to get
a better stage2, or to run GMAP from GSNAP or pairsearch */
+#if 0
static List_T
run_gmap_plus (List_T gmap, List_T middle_path, List_T start_paths, List_T end_paths,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
@@ -6671,7 +6562,7 @@ run_gmap_plus (List_T gmap, List_T middle_path, List_T start_paths, List_T end_p
if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
ambig_end_length_5,ambig_end_length_3,
ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
+ min_splice_prob,
pairarray,npairs,nsegments,nintrons,nindelbreaks,
/*left*/start,/*genomiclength*/end - start + 1,
/*plusp*/true,genestrand,first_read_p,
@@ -6688,8 +6579,10 @@ run_gmap_plus (List_T gmap, List_T middle_path, List_T start_paths, List_T end_p
return gmap;
}
+#endif
+#if 0
static List_T
run_gmap_minus (List_T gmap, List_T middle_path, List_T start_paths, List_T end_paths,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
@@ -6851,7 +6744,7 @@ run_gmap_minus (List_T gmap, List_T middle_path, List_T start_paths, List_T end_
if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
ambig_end_length_5,ambig_end_length_3,
ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
+ min_splice_prob,
pairarray,npairs,nsegments,nintrons,nindelbreaks,
/*left*/end,/*genomiclength*/start - end + 1,
/*plusp*/false,genestrand,first_read_p,
@@ -6868,8 +6761,10 @@ run_gmap_minus (List_T gmap, List_T middle_path, List_T start_paths, List_T end_
return gmap;
}
+#endif
+#if 0
static bool
find_sense (int *sensedir, List_T sense_junctions, List_T antisense_junctions,
Intlist_T sense_endpoints, Intlist_T antisense_endpoints) {
@@ -6937,6 +6832,7 @@ find_sense (int *sensedir, List_T sense_junctions, List_T antisense_junctions,
return true;
}
}
+#endif
static bool
@@ -7022,21 +6918,19 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Chrpos_T chrlength, int querylength, Compress_T query_compress,
- bool plusp, int genestrand, bool first_read_p, int max_mismatches_allowed) {
- List_T super_path, ambig_path;
+ bool plusp, int genestrand, int max_mismatches_allowed) {
+ List_T super_path;
Stage3end_T hit;
int sensedir, sense_sensedir, antisense_sensedir;
- List_T substrings = NULL;
List_T p;
Univdiag_T diagonal, prev_diagonal, new_diagonal;
Chrpos_T splice_distance;
int querystart_for_merge, querystart, queryend, ignore;
- int max_leftward, skip_left;
+ int max_leftward;
int nmismatches;
bool fillin_p;
- Junction_T junction;
int indel_pos;
int nindels;
Univcoord_T deletionpos;
@@ -7046,11 +6940,10 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
bool sense_acceptable_p, antisense_acceptable_p, sense_intronp, antisense_intronp;
Univcoord_T left, prev_left;
- Uintlist_T sense_lefts = NULL, antisense_lefts = NULL, q;
- Intlist_T sense_nmismatches = NULL, antisense_nmismatches = NULL, x;
- Intlist_T sense_endpoints = NULL, antisense_endpoints = NULL, r;
+ Uintlist_T sense_lefts = NULL, antisense_lefts = NULL;
+ Intlist_T sense_nmismatches = NULL, antisense_nmismatches = NULL;
+ Intlist_T sense_endpoints = NULL, antisense_endpoints = NULL;
List_T sense_junctions = NULL, antisense_junctions = NULL;
- Substring_T substring;
int best_knowni_i, best_knowni_j, best_nmismatches_i, best_nmismatches_j;
double best_prob_i, best_prob_j;
@@ -7059,7 +6952,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
left_ambig_sense, left_ambig_antisense;
int segmenti_donor_nknown, segmentj_acceptor_nknown,
segmentj_antidonor_nknown, segmenti_antiacceptor_nknown;
- int i, j;
+ int j;
#ifdef HAVE_ALLOCA
int *segmenti_donor_knownpos = (int *) ALLOCA((querylength+1)*sizeof(int));
@@ -7194,7 +7087,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((indel_pos = Indel_resolve_middle_insertion(&best_nmismatches_i,&best_nmismatches_j,
/*left*/prev_left,/*indels*/+nindels,query_compress,
prev_diagonal->querystart,diagonal->queryend,querylength,
- max_mismatches_allowed,/*plusp:true*/true,genestrand,first_read_p)) < 0) {
+ max_mismatches_allowed,/*plusp:true*/true,genestrand)) < 0) {
sense_junctions = List_push(sense_junctions,NULL);
antisense_junctions = List_push(antisense_junctions,NULL);
} else {
@@ -7233,7 +7126,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((indel_pos = Indel_resolve_middle_deletion(&best_nmismatches_i,&best_nmismatches_j,
/*left*/prev_left,/*indels*/-nindels,query_compress,
prev_diagonal->querystart,diagonal->queryend,querylength,
- max_mismatches_allowed,/*plusp:true*/true,genestrand,first_read_p)) < 0) {
+ max_mismatches_allowed,/*plusp:true*/true,genestrand)) < 0) {
sense_junctions = List_push(sense_junctions,NULL);
antisense_junctions = List_push(antisense_junctions,NULL);
} else {
@@ -7321,8 +7214,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
segmentj_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,
- plusp,genestrand,first_read_p)) < 0) {
+ max_mismatches_allowed,plusp,genestrand)) < 0) {
sense_endpoints = Intlist_push(sense_endpoints,-1); /* Mark as invalid */
sense_junctions = List_push(sense_junctions,NULL);
} else if (plusp == true) {
@@ -7350,8 +7242,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
segmentj_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,
- plusp,genestrand,first_read_p)) < 0) {
+ max_mismatches_allowed,plusp,genestrand)) < 0) {
antisense_endpoints = Intlist_push(antisense_endpoints,-1); /* Mark as invalid */
antisense_junctions = List_push(antisense_junctions,NULL);
} else if (plusp == true) {
@@ -7436,8 +7327,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if (plusp == true) {
right_ambig_sense = Substring_new_ambig(/*querystart*/splice_pos,queryend,
/*splice_pos*/splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
right_ambcoords_sense,right_amb_knowni_sense,
right_amb_nmismatchesj_sense,right_amb_probsj_sense,
/*amb_common_prob*/Doublelist_head(right_amb_probsi_sense),
@@ -7445,8 +7335,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
} else {
right_ambig_sense = Substring_new_ambig(/*querystart*/querylength - queryend,querylength - splice_pos,
/*splice_pos*/querylength - splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
right_ambcoords_sense,right_amb_knowni_sense,
right_amb_nmismatchesj_sense,right_amb_probsj_sense,
/*amb_common_prob*/Doublelist_head(right_amb_probsi_sense),
@@ -7513,8 +7402,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if (plusp == true) {
right_ambig_antisense = Substring_new_ambig(/*querystart*/splice_pos,queryend,
/*splice_pos*/splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
right_ambcoords_antisense,right_amb_knowni_antisense,
right_amb_nmismatchesj_antisense,right_amb_probsj_antisense,
/*amb_common_prob*/Doublelist_head(right_amb_probsi_antisense),
@@ -7522,8 +7410,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
} else {
right_ambig_antisense = Substring_new_ambig(/*querystart*/querylength - queryend,querylength - splice_pos,
/*splice_pos*/querylength - splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
right_ambcoords_antisense,right_amb_knowni_antisense,
right_amb_nmismatchesj_antisense,right_amb_probsj_antisense,
/*amb_common_prob*/Doublelist_head(right_amb_probsi_antisense),
@@ -7577,10 +7464,10 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if (Intlist_head(sense_endpoints) > 0) {
sense_endpoints = Intlist_pop(sense_endpoints,&querystart);
if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(sense_lefts),
- /*pos5*/0,/*pos3*/querystart,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart,plusp,genestrand)) > 0) {
sense_endpoints = Intlist_push(sense_endpoints,querystart - max_leftward);
} else if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(sense_lefts),
- /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand)) > 0) {
sense_endpoints = Intlist_push(sense_endpoints,querystart - max_leftward - 1);
} else {
sense_endpoints = Intlist_push(sense_endpoints,querystart);
@@ -7617,10 +7504,10 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
/* Skip, but extend leftward */
sense_endpoints = Intlist_pop(sense_endpoints,&querystart);
if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(sense_lefts),
- /*pos5*/0,/*pos3*/querystart,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart,plusp,genestrand)) > 0) {
sense_endpoints = Intlist_push(sense_endpoints,querystart - max_leftward);
} else if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(sense_lefts),
- /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand)) > 0) {
sense_endpoints = Intlist_push(sense_endpoints,querystart - max_leftward - 1);
} else {
sense_endpoints = Intlist_push(sense_endpoints,querystart);
@@ -7638,8 +7525,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if (plusp == true) {
left_ambig_sense = Substring_new_ambig(querystart,/*queryend*/splice_pos,
/*splice_pos*/splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
left_ambcoords_sense,left_amb_knowni_sense,
left_amb_nmismatchesi_sense,left_amb_probsi_sense,
/*amb_common_prob*/Doublelist_head(left_amb_probsj_sense),
@@ -7647,8 +7533,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
} else {
left_ambig_sense = Substring_new_ambig(querylength - splice_pos,/*queryend*/querylength - querystart,
/*splice_pos*/querylength - splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
left_ambcoords_sense,left_amb_knowni_sense,
left_amb_nmismatchesi_sense,left_amb_probsi_sense,
/*amb_common_prob*/Doublelist_head(left_amb_probsj_sense),
@@ -7678,10 +7563,10 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if (Intlist_head(antisense_endpoints) > 0) {
antisense_endpoints = Intlist_pop(antisense_endpoints,&querystart);
if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(antisense_lefts),
- /*pos5*/0,/*pos3*/querystart,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart,plusp,genestrand)) > 0) {
antisense_endpoints = Intlist_push(antisense_endpoints,querystart - max_leftward);
} else if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(antisense_lefts),
- /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand)) > 0) {
antisense_endpoints = Intlist_push(antisense_endpoints,querystart - max_leftward - 1);
} else {
antisense_endpoints = Intlist_push(antisense_endpoints,querystart);
@@ -7718,10 +7603,10 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
/* Skip, but extend leftward */
antisense_endpoints = Intlist_pop(antisense_endpoints,&querystart);
if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(antisense_lefts),
- /*pos5*/0,/*pos3*/querystart,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart,plusp,genestrand)) > 0) {
antisense_endpoints = Intlist_push(antisense_endpoints,querystart - max_leftward);
} else if ((max_leftward = Genome_consecutive_matches_leftward(query_compress,/*left*/Uintlist_head(antisense_lefts),
- /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand,first_read_p)) > 0) {
+ /*pos5*/0,/*pos3*/querystart-1,plusp,genestrand)) > 0) {
antisense_endpoints = Intlist_push(antisense_endpoints,querystart - max_leftward - 1);
} else {
antisense_endpoints = Intlist_push(antisense_endpoints,querystart);
@@ -7739,8 +7624,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if (plusp == true) {
left_ambig_antisense = Substring_new_ambig(querystart,/*queryend*/splice_pos,
/*splice_pos*/splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
left_ambcoords_antisense,left_amb_knowni_antisense,
left_amb_nmismatchesi_antisense,left_amb_probsi_antisense,
/*amb_common_prob*/Doublelist_head(left_amb_probsj_antisense),
@@ -7748,8 +7632,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
} else {
left_ambig_antisense = Substring_new_ambig(querylength - splice_pos,/*queryend*/querylength - querystart,
/*splice_pos*/querylength - splice_pos,querylength,
- chrnum,chroffset,chrhigh,chrlength,
- /*genomiclength*/querylength,plusp,genestrand,first_read_p,
+ chrnum,chroffset,chrhigh,chrlength,plusp,genestrand,
left_ambcoords_antisense,left_amb_knowni_antisense,
left_amb_nmismatchesi_antisense,left_amb_probsi_antisense,
/*amb_common_prob*/Doublelist_head(left_amb_probsj_antisense),
@@ -7812,7 +7695,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((hit = Stage3end_new_substrings(&(*found_score),sense_endpoints,sense_lefts,
sense_nmismatches,sense_junctions,querylength,query_compress,
/*right_ambig*/NULL,/*left_ambig*/NULL,plusp,genestrand,/*sensedir*/SENSE_NULL,
- first_read_p,chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
+ chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
Substring_free(&right_ambig_sense);
Substring_free(&left_ambig_sense);
/* Junction_gc(&sense_junctions); -- Done by Stage3end_new_substrings */
@@ -7832,7 +7715,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((hit = Stage3end_new_substrings(&(*found_score),sense_endpoints,sense_lefts,
sense_nmismatches,sense_junctions,querylength,query_compress,
right_ambig_sense,left_ambig_sense,plusp,genestrand,sense_sensedir,
- first_read_p,chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
+ chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
Substring_free(&right_ambig_sense);
Substring_free(&left_ambig_sense);
/* Junction_gc(&sense_junctions); -- Done by Stage3end_new_substrings */
@@ -7847,7 +7730,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((hit = Stage3end_new_substrings(&(*found_score),antisense_endpoints,antisense_lefts,
antisense_nmismatches,antisense_junctions,querylength,query_compress,
right_ambig_antisense,left_ambig_antisense,plusp,genestrand,antisense_sensedir,
- first_read_p,chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
+ chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
Substring_free(&right_ambig_antisense);
Substring_free(&left_ambig_antisense);
/* Junction_gc(&antisense_junctions); -- Done by Stage3end_new_substrings */
@@ -7869,7 +7752,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((hit = Stage3end_new_substrings(&(*found_score),sense_endpoints,sense_lefts,
sense_nmismatches,sense_junctions,querylength,query_compress,
right_ambig_sense,left_ambig_sense,plusp,genestrand,sensedir,
- first_read_p,chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
+ chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
Substring_free(&right_ambig_sense);
Substring_free(&left_ambig_sense);
/* Junction_gc(&sense_junctions); -- Done by Stage3end_new_substrings */
@@ -7894,7 +7777,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
if ((hit = Stage3end_new_substrings(&(*found_score),antisense_endpoints,antisense_lefts,
antisense_nmismatches,antisense_junctions,querylength,query_compress,
right_ambig_antisense,left_ambig_antisense,plusp,genestrand,sensedir,
- first_read_p,chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
+ chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/true)) == NULL) {
Substring_free(&right_ambig_antisense);
Substring_free(&left_ambig_antisense);
/* Junction_gc(&antisense_junctions); -- Done by Stage3end_new_substrings */
@@ -7944,9 +7827,7 @@ solve_via_segments (int *found_score, bool *completep, List_T hits, List_T middl
List_T
Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int querylength,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
- int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
- int nmisses_allowed, int genestrand, bool first_read_p) {
+ int nmisses_allowed, int genestrand) {
List_T hits = NULL;
List_T plus_set, minus_set, p;
List_T rightward_set_plus = NULL, leftward_set_plus = NULL, rightward_set_minus = NULL, leftward_set_minus = NULL;
@@ -7954,7 +7835,7 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
UINT4 best_plus_nmatches, best_minus_nmatches, nmatches;
Sarrayptr_T initptr, finalptr;
bool successp, completep;
- int plus_querypos, minus_querypos, halfwaypos;
+ int plus_querypos, minus_querypos;
int i;
Chrnum_T chrnum;
Univcoord_T chroffset, chrhigh, left;
@@ -7965,7 +7846,6 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
int nseeds_plus, nseeds_minus;
int *scores_plus = NULL, *scores_minus = NULL;
int niter, best_plus_i, best_minus_i, nplus, nminus;
- int best_score;
List_T *middle_path_plus = NULL, *right_paths_plus = NULL, *left_paths_plus = NULL,
*middle_path_minus = NULL, *right_paths_minus = NULL, *left_paths_minus = NULL;
Univdiag_T *middle_diagonals_plus = NULL, *middle_diagonals_minus = NULL;
@@ -7993,17 +7873,15 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
left_amb_probsj_sense, left_amb_probsj_antisense;
List_T diagonal_path;
- bool twopartp = false;
-
- Univdiag_T first_diagonal, last_diagonal, diagonal;
- List_T low_diagonals, high_diagonals;
+ Univdiag_T diagonal;
+#if 0
bool *coveredp;
- Chrpos_T **mappings, chrstart, chrend;
- int *npositions, totalpositions = 0;
- int querystart, queryend, maxnconsecutive = 0;
+ Chrpos_T **mappings;
+ int *npositions;
Oligoindex_T oligoindex;
- bool oned_matrix_p;
int indexsize;
+ int best_score;
+#endif
if (nmisses_allowed < 0) {
@@ -8037,7 +7915,7 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
while (niter < nmisses_allowed && plus_querypos < querylength && minus_querypos < querylength) {
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryuc_ptr[plus_querypos]),
querylength - plus_querypos,/*queryoffset*/plus_querypos,
- query_compress_fwd,plus_sarray,/*plusp*/true,genestrand,first_read_p,plus_conversion);
+ query_compress_fwd,plus_sarray,/*plusp*/true,genestrand,plus_conversion);
elt = Elt_new(plus_querypos,nmatches,initptr,finalptr,/*temporaryp*/false);
if (nmatches > best_plus_nmatches && elt->nptr <= MAX_HITS_FOR_BEST_ELT) {
best_plus_elt = elt;
@@ -8050,7 +7928,7 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
sarray_search(&initptr,&finalptr,&successp,&nmatches,&(queryrc[minus_querypos]),
querylength - minus_querypos,/*queryoffset*/minus_querypos,
- query_compress_rev,minus_sarray,/*plusp*/false,genestrand,first_read_p,minus_conversion);
+ query_compress_rev,minus_sarray,/*plusp*/false,genestrand,minus_conversion);
elt = Elt_new(minus_querypos,nmatches,initptr,finalptr,/*temporaryp*/false);
if (nmatches > best_minus_nmatches && elt->nptr < MAX_HITS_FOR_BEST_ELT) {
best_minus_elt = elt;
@@ -8145,9 +8023,8 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
&(best_right_diagonals_plus[i]),&(best_left_diagonals_plus[i]),
&(all_right_diagonals_plus[i]),&(all_left_diagonals_plus[i]),
plus_sarray,/*queryptr*/queryuc_ptr,querylength,query_compress_fwd,
- chroffset,chrhigh,chrlength,/*goal*/left,plus_elt_array,
- best_plus_i,nplus,/*plusp*/true,genestrand,first_read_p,
- plus_conversion,oligoindices_minor,diagpool);
+ chroffset,chrhigh,/*goal*/left,plus_elt_array,
+ best_plus_i,nplus,/*plusp*/true,genestrand,plus_conversion);
debug(printf("Got plus score %d\n",scores_plus[i]));
}
@@ -8215,9 +8092,8 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
&(best_right_diagonals_minus[i]),&(best_left_diagonals_minus[i]),
&(all_right_diagonals_minus[i]),&(all_left_diagonals_minus[i]),
minus_sarray,/*queryptr*/queryrc,querylength,query_compress_rev,
- chroffset,chrhigh,chrlength,/*goal*/left,minus_elt_array,
- best_minus_i,nminus,/*plusp*/false,genestrand,first_read_p,
- minus_conversion,oligoindices_minor,diagpool);
+ chroffset,chrhigh,/*goal*/left,minus_elt_array,
+ best_minus_i,nminus,/*plusp*/false,genestrand,minus_conversion);
debug(printf("Got minus score %d\n",scores_minus[i]));
}
@@ -8242,11 +8118,13 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
debug(printf("Have %d nseeds_plus and %d nseeds_minus\n",nseeds_plus,nseeds_minus));
+#if 0
coveredp = (bool *) CALLOCA(querylength,sizeof(bool));
mappings = (Chrpos_T **) MALLOCA(querylength * sizeof(Chrpos_T *));
npositions = (int *) CALLOCA(querylength,sizeof(int));
oligoindex = Oligoindex_array_elt(oligoindices_minor,/*source*/0);
indexsize = Oligoindex_indexsize(oligoindex);
+#endif
/* *sarray_gmap = (List_T) NULL; */
@@ -8278,9 +8156,8 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
&left_amb_probsi_sense,&left_amb_probsi_antisense,
&left_amb_probsj_sense,&left_amb_probsj_antisense,
&(fillin_diagonals_plus[i]),diagonal,best_right_diagonals_plus[i],best_left_diagonals_plus[i],
- /*queryptr*/queryuc_ptr,querylength,query_compress_fwd,chroffset,chrhigh,
- oligoindices_minor,diagpool,/*plusp*/true,genestrand,first_read_p,
- /*nmismatches_allowed*/nmisses_allowed);
+ querylength,query_compress_fwd,chroffset,
+ /*plusp*/true,genestrand,/*nmismatches_allowed*/nmisses_allowed);
hits = solve_via_segments(&(*found_score),&completep,hits,middle_path_plus[i],
right_endpoints_sense,right_endpoints_antisense,
@@ -8302,7 +8179,7 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
left_amb_probsj_sense,left_amb_probsj_antisense,
chrnum,chroffset,chrhigh,chrlength,
- querylength,query_compress_fwd,/*plusp*/true,genestrand,first_read_p,
+ querylength,query_compress_fwd,/*plusp*/true,genestrand,
/*max_mismatches_allowed*/nmisses_allowed);
#if 0
@@ -8362,9 +8239,8 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
&left_amb_probsi_sense,&left_amb_probsi_antisense,
&left_amb_probsj_sense,&left_amb_probsj_antisense,
&(fillin_diagonals_minus[i]),diagonal,best_right_diagonals_minus[i],best_left_diagonals_minus[i],
- /*queryptr*/queryrc,querylength,query_compress_rev,chroffset,chrhigh,
- oligoindices_minor,diagpool,/*plusp*/false,genestrand,first_read_p,
- /*nmismatches_allowed*/nmisses_allowed);
+ querylength,query_compress_rev,chroffset,
+ /*plusp*/false,genestrand,/*nmismatches_allowed*/nmisses_allowed);
hits = solve_via_segments(&(*found_score),&completep,hits,middle_path_minus[i],
right_endpoints_sense,right_endpoints_antisense,
@@ -8386,7 +8262,7 @@ Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int qu
left_amb_probsj_sense,left_amb_probsj_antisense,
chrnum,chroffset,chrhigh,chrlength,
- querylength,query_compress_rev,/*plusp*/false,genestrand,first_read_p,
+ querylength,query_compress_rev,/*plusp*/false,genestrand,
/*max_mismatches_allowed*/nmisses_allowed);
#if 0
diff --git a/src/sarray-read.h b/src/sarray-read.h
index ac10803..b799ee0 100644
--- a/src/sarray-read.h
+++ b/src/sarray-read.h
@@ -1,4 +1,4 @@
-/* $Id: sarray-read.h 181923 2016-01-08 00:43:56Z twu $ */
+/* $Id: sarray-read.h 184464 2016-02-18 00:09:13Z twu $ */
#ifndef SARRAY_READ_INCLUDED
#define SARRAY_READ_INCLUDED
#include "access.h"
@@ -23,15 +23,17 @@ Sarray_setup (T sarray_fwd_in, T sarray_rev_in, Genome_T genome_in, Mode_T mode,
Univ_IIT_T chromosome_iit_in, int circular_typeint_in, bool *circularp_in,
Chrpos_T shortsplicedist_in, int splicing_penalty_in,
int max_deletionlength, int max_end_deletions,
- int max_middle_insertions, int max_end_insertions,
+ int max_middle_insertions_in, int max_end_insertions,
Univcoord_T *splicesites_in, Splicetype_T *splicetypes_in,
Chrpos_T *splicedists_in, int nsplicesites_in);
+#if 0
extern void
Sarray_shmem_remove (char *dir, char *fileroot, char *snps_root, Mode_T mode, bool fwdp);
+#endif
extern T
-Sarray_new (char *dir, char *fileroot, char *snps_root, Access_mode_T sarray_access, Access_mode_T lcp_access,
+Sarray_new (char *dir, char *fileroot, Access_mode_T sarray_access, Access_mode_T lcp_access,
Access_mode_T guideexc_access, Access_mode_T indexij_access, bool sharedp, Mode_T mode, bool fwdp);
extern void
Sarray_free (T *old);
@@ -39,10 +41,7 @@ Sarray_free (T *old);
extern List_T
Sarray_search_greedy (int *found_score, char *queryuc_ptr, char *queryrc, int querylength,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
- int maxpeelback, Pairpool_T pairpool,
- Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
- int nmisses_allowed, int genestrand, bool first_read_p);
+ int nmisses_allowed, int genestrand);
#undef T
#endif
diff --git a/src/sarray-write.c b/src/sarray-write.c
index 30418b9..25c0553 100644
--- a/src/sarray-write.c
+++ b/src/sarray-write.c
@@ -1,11 +1,11 @@
-static char rcsid[] = "$Id: sarray-write.c 170326 2015-07-22 17:49:55Z twu $";
+static char rcsid[] = "$Id: sarray-write.c 184473 2016-02-18 00:12:38Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "sarray-write.h"
-#include <stdlib.h>
+#include <stdlib.h> /* For qsort */
#include <stdio.h>
#include <string.h>
#include <sys/mman.h> /* For munmap */
@@ -25,6 +25,7 @@ static char rcsid[] = "$Id: sarray-write.c 170326 2015-07-22 17:49:55Z twu $";
#include "saca-k.h"
#include "genome128_hr.h"
#include "uintlist.h"
+#include "list.h"
#include "intlist.h"
@@ -171,6 +172,7 @@ power (int base, int exponent) {
}
+#if 0
static void
sarray_search_char (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, char desired_char,
Genome_T genomecomp, UINT4 *SA, int n, char *chartable) {
@@ -227,13 +229,10 @@ sarray_search_char (Sarrayptr_T *initptr, Sarrayptr_T *finalptr, char desired_ch
*finalptr = high;
return;
}
+#endif
#define LOW_TWO_BITS 0x3
-#define RIGHT_A 0
-#define RIGHT_C 1
-#define RIGHT_G 2
-#define RIGHT_T 3
static void
@@ -352,7 +351,7 @@ make_index_separate (Sarrayptr_T *saindexi, Sarrayptr_T *saindexj,
UINT4 noccupied = 0;
char *queryuc_ptr;
UINT4 oligo;
- char *comma;
+ /* char *comma; */
queryuc_ptr = (char *) CALLOC(querylength+1,sizeof(char));
@@ -387,7 +386,7 @@ make_index_interleaved (Sarrayptr_T *saindex,
UINT4 noccupied = 0;
char *queryuc_ptr;
UINT4 oligo;
- char *comma;
+ /* char *comma; */
Sarrayptr_T indexi, indexj;
queryuc_ptr = (char *) CALLOC(querylength+1,sizeof(char));
@@ -508,9 +507,10 @@ Sarray_write_index_separate (char *indexiptrsfile, char *indexicompfile, char *i
char *sarrayfile, Genome_T genomecomp, UINT4 genomelength, bool compressp,
char chartable[]) {
UINT4 n = genomelength;
- Oligospace_T oligospace, prev_oligospace, noccupied;
+ Oligospace_T oligospace, noccupied;
/* Oligospace_T prev_noccupied; */
- Sarrayptr_T *saindexi_new, *saindexj_new, *saindexi_old, *saindexj_old;
+ /* Sarrayptr_T *saindexi_new, *saindexj_new; */
+ Sarrayptr_T *saindexi_old, *saindexj_old;
UINT4 *SA;
int sa_fd;
size_t sa_len;
@@ -518,7 +518,7 @@ Sarray_write_index_separate (char *indexiptrsfile, char *indexicompfile, char *i
FILE *fp;
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/true);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/true);
indexsize = MIN_INDEXSIZE;
oligospace = power(4,/*querylength*/indexsize);
@@ -527,7 +527,7 @@ Sarray_write_index_separate (char *indexiptrsfile, char *indexicompfile, char *i
/* prev_noccupied = 0; */
noccupied = make_index_separate(saindexi_old,saindexj_old,
oligospace,/*querylength*/indexsize,genomecomp,SA,n,chartable);
- fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace);
+ fprintf(stderr,"For indexsize %d, occupied %llu/%llu\n",indexsize,(unsigned long long) noccupied,(unsigned long long) oligospace);
#if 0
indexsize++;
@@ -613,9 +613,9 @@ Sarray_write_index_interleaved (char *indexptrsfile, char *indexcompfile,
char *sarrayfile, Genome_T genomecomp, UINT4 genomelength, bool compressp,
char chartable[]) {
UINT4 n = genomelength;
- Oligospace_T oligospace, prev_oligospace, noccupied;
+ Oligospace_T oligospace, noccupied;
/* Oligospace_T prev_noccupied; */
- Sarrayptr_T *saindex_new, *saindex_old;
+ Sarrayptr_T *saindex_old;
UINT4 *SA;
int sa_fd;
size_t sa_len;
@@ -623,7 +623,7 @@ Sarray_write_index_interleaved (char *indexptrsfile, char *indexcompfile,
FILE *fp;
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/true);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/true);
indexsize = MIN_INDEXSIZE;
oligospace = power(4,/*querylength*/indexsize);
@@ -631,7 +631,7 @@ Sarray_write_index_interleaved (char *indexptrsfile, char *indexcompfile,
/* prev_noccupied = 0; */
noccupied = make_index_interleaved(saindex_old,
oligospace,/*querylength*/indexsize,genomecomp,SA,n,chartable);
- fprintf(stderr,"For indexsize %d, occupied %u/%u\n",indexsize,noccupied,oligospace);
+ fprintf(stderr,"For indexsize %d, occupied %llu/%llu\n",indexsize,(unsigned long long) noccupied,(unsigned long long) oligospace);
#if 0
indexsize++;
@@ -713,12 +713,11 @@ Sarray_write_csa (char **csaptrfiles, char **csacompfiles, char *sasampleqfile,
FILE *fp, *sa_fp, *samples_fp;
/* FILE *csa_fp; */
UINT4 n = genomelength, n_plus_one, ii, i, b;
- int chari, k;
- Sarrayptr_T saindexi[5], saindexj[5], saindexn, indexX;
+ int chari;
+ Sarrayptr_T saindexi[5], saindexj[5], saindexn;
int sa_fd, rank_fd;
size_t sa_len, rank_len;
- int indexsize;
- UINT4 *read_buffer, *write_buffer, ignore;
+ UINT4 *read_buffer;
char *queryuc_ptr;
int csa_sampling;
@@ -731,7 +730,7 @@ Sarray_write_csa (char **csaptrfiles, char **csacompfiles, char *sasampleqfile,
/* Determine sizes of each csa */
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/true);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/true);
queryuc_ptr = (char *) CALLOC(/*querylength*/1+1,sizeof(char));
/* A */
@@ -782,7 +781,7 @@ Sarray_write_csa (char **csaptrfiles, char **csacompfiles, char *sasampleqfile,
/* Process suffix array */
read_buffer = (UINT4 *) MALLOC(RW_BATCH * sizeof(UINT4));
- SA_inv = (UINT4 *) Access_mmap(&rank_fd,&rank_len,rankfile,sizeof(UINT4),/*randomp*/true);
+ SA_inv = (UINT4 *) Access_mmap(&rank_fd,&rank_len,rankfile,/*randomp*/true);
/* csa_fp = fopen(csafile,"wb");*/
sa_fp = fopen(sarrayfile,"rb");
samples_fp = fopen(sasamplesfile,"wb");
@@ -1041,7 +1040,7 @@ Sarray_compute_lcp (char *rankfile, char *permuted_sarray_file, char *sarrayfile
write_buffer = (UINT4 *) MALLOC(RW_BATCH * sizeof(UINT4));
fp = fopen(rankfile,"rb");
permsa_fp = fopen(permuted_sarray_file,"wb");
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/false);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
for (ii = 0; ii + RW_BATCH <= n; ii += RW_BATCH) {
FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
@@ -1138,6 +1137,247 @@ Sarray_compute_lcp (char *rankfile, char *permuted_sarray_file, char *sarrayfile
}
+struct Cell_T {
+ UINT4 index;
+ UINT4 timestamp;
+ UINT4 value;
+ bool validp;
+};
+
+typedef struct Cell_T *Cell_T;
+
+static Cell_T
+Cell_new (UINT4 index, UINT4 timestamp, UINT4 value, bool validp) {
+ Cell_T new = (Cell_T) MALLOC(sizeof(*new));
+
+ new->index = index;
+ new->timestamp = timestamp;
+ new->value = value;
+ new->validp = validp;
+ return new;
+}
+
+static void
+Cell_free (Cell_T *old) {
+ FREE(*old);
+ return;
+}
+
+static int
+Cell_compare (const void *a, const void *b) {
+ Cell_T x = * (Cell_T *) a;
+ Cell_T y = * (Cell_T *) b;
+
+ if (x->index < y->index) {
+ return -1;
+ } else if (y->index < x->index) {
+ return +1;
+ } else if (x->timestamp > y->timestamp) {
+ return -1;
+ } else if (y->timestamp > x->timestamp) {
+ return +1;
+ } else {
+ return 0;
+ }
+}
+
+
+/* Puts rank and permuted suffix array in file, to save on memory even further */
+/* Rank file is the same as the inverted suffix array, needed to compute the compressed suffix array */
+unsigned char *
+Sarray_compute_lcp_bytes (UINT4 **lcp_exceptions, UINT4 *nexceptions,
+ char *rankfile, char *permuted_sarray_file,
+ char *sarrayfile, UINT4 n) {
+ unsigned char *lcp_bytes;
+ List_T exceptions_list = NULL;
+ Cell_T *array;
+ UINT4 *SA, SA_i, zero = 0;
+ UINT4 *rank, rank_i, h;
+ UINT4 i, ii, b, j, k;
+ char *comma;
+ UINT4 *read_buffer_1, *read_buffer_2, *write_buffer;
+ void *p;
+
+ int sa_fd;
+ size_t sa_len;
+ FILE *fp, *permsa_fp;
+
+
+ read_buffer_1 = (UINT4 *) MALLOC(RW_BATCH * sizeof(UINT4));
+
+ /* Compute rank */
+ fp = fopen(sarrayfile,"rb");
+ rank = (UINT4 *) MALLOC((n+1)*sizeof(UINT4));
+
+ for (ii = 0; ii + RW_BATCH <= n; ii += RW_BATCH) {
+ FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
+ for (b = 0, i = ii; b < RW_BATCH; b++, i++) {
+ rank[read_buffer_1[b]] = i; /* rank[SA_i] = i; */
+ }
+ if (ii % MONITOR_INTERVAL == 0) {
+ comma = Genomicpos_commafmt(ii);
+ fprintf(stderr,"Computing rank %s\n",comma);
+ FREE(comma);
+ }
+ }
+ for (i = ii; i <= n; i++) { /* final partial batch */
+ FREAD_UINT(&SA_i,fp);
+ rank[SA_i] = i;
+ }
+
+ fclose(fp); /* sarrayfile */
+
+
+ /* Store rank in temporary file */
+ fprintf(stderr,"Writing temporary file for rank...");
+ fp = fopen(rankfile,"wb");
+ for (ii = 0; ii + RW_BATCH <= n; ii += RW_BATCH) {
+ p = (void *) &(rank[ii]);
+ FWRITE_UINTS(p,RW_BATCH,fp);
+ }
+ if (ii <= n) {
+ p = (void *) &(rank[ii]);
+ FWRITE_UINTS(p,n - ii + 1,fp);
+ }
+ fclose(fp); /* rankfile */
+ FREE(rank);
+ fprintf(stderr,"done\n");
+
+
+ /* Write permuted sarray */
+ fprintf(stderr,"Writing temporary file for permuted sarray...");
+ write_buffer = (UINT4 *) MALLOC(RW_BATCH * sizeof(UINT4));
+ fp = fopen(rankfile,"rb");
+ permsa_fp = fopen(permuted_sarray_file,"wb");
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
+
+ for (ii = 0; ii + RW_BATCH <= n; ii += RW_BATCH) {
+ FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
+ for (b = 0, i = ii; b < RW_BATCH; b++, i++) {
+ rank_i = read_buffer_1[b];
+ if (rank_i > 0) {
+#ifdef WORDS_BIGENDIAN
+ write_buffer[b] = Bigendian_convert_uint(SA[rank_i - 1]);
+#else
+ write_buffer[b] = SA[rank_i - 1];
+#endif
+ } else {
+ write_buffer[b] = 0; /* Will be ignored */
+ }
+ }
+ FWRITE_UINTS(write_buffer,RW_BATCH,permsa_fp);
+ }
+ for (i = ii; i <= n; i++) { /* final partial batch */
+ FREAD_UINT(&rank_i,fp);
+ if (rank_i > 0) {
+#ifdef WORDS_BIGENDIAN
+ FWRITE_UINT(Bigendian_convert_uint(SA[rank_i - 1]),permsa_fp);
+#else
+ FWRITE_UINT(SA[rank_i - 1],permsa_fp);
+#endif
+ } else {
+ FWRITE_UINT(zero,permsa_fp); /* Will be ignored */
+ }
+ }
+
+ munmap((void *) SA,sa_len);
+ close(sa_fd);
+ fclose(permsa_fp); /* permuted_sarray_file */
+ fclose(fp); /* rankfile */
+ FREE(write_buffer);
+ fprintf(stderr,"done\n");
+
+
+ /* Now allocate memory for lcp and compute */
+ read_buffer_2 = (UINT4 *) MALLOC(RW_BATCH * sizeof(UINT4));
+ fp = fopen(rankfile,"rb");
+ permsa_fp = fopen(permuted_sarray_file,"rb");
+
+ lcp_bytes = (unsigned char *) MALLOC((n+1)*sizeof(unsigned char));
+
+ lcp_bytes[0] = 0; /* -1 ? */
+ h = 0;
+ k = 0;
+ for (ii = 0; ii + RW_BATCH <= n; ii += RW_BATCH) {
+ FREAD_UINTS(read_buffer_1,RW_BATCH,fp);
+ FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp);
+ for (b = 0, i = ii; b < RW_BATCH; b++, i++) {
+ rank_i = read_buffer_1[b];
+ j = read_buffer_2[b]; /* j = SA[rank_i - 1] */
+ if (rank_i > 0) {
+ h += Genome_consecutive_matches_pair(i+h,j+h,/*genomelength*/n);
+ if (h >= 255) {
+ lcp_bytes[rank_i] = 255;
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(/*index*/rank_i,/*timestamp*/0,/*value*/h,/*validp*/true));
+ k++;
+ } else {
+ lcp_bytes[rank_i] = (unsigned char) h;
+ }
+ if (h > 0) {
+ h--;
+ }
+ }
+ }
+
+ if (ii % MONITOR_INTERVAL == 0) {
+ comma = Genomicpos_commafmt(ii);
+ fprintf(stderr,"Computing lcp index %s\n",comma);
+ FREE(comma);
+ }
+ }
+
+ for (i = ii; i <= n; i++) { /* final partial batch */
+ FREAD_UINT(&rank_i,fp);
+ FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */
+ if (rank_i > 0) {
+ h += Genome_consecutive_matches_pair(i+h,j+h,/*genomelength*/n);
+ if (h >= 255) {
+ lcp_bytes[rank_i] = 255;
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(/*index*/rank_i,/*timestamp*/0,/*value*/h,/*validp*/true));
+ k++;
+ } else {
+ lcp_bytes[rank_i] = (unsigned char) h;
+ }
+ if (h > 0) {
+ h--;
+ }
+ }
+ }
+
+ fclose(permsa_fp); /* permuted_sarray_file */
+ fclose(fp); /* rankfile */
+ FREE(read_buffer_2);
+ FREE(read_buffer_1);
+ remove(permuted_sarray_file);
+#ifndef USE_CSA
+ remove(rankfile);
+#endif
+
+ printf("Found %u exceptions\n",k);
+ *nexceptions = k;
+
+
+ /* Create exceptions array */
+ if (*nexceptions == 0) {
+ *lcp_exceptions = (UINT4 *) NULL;
+ } else {
+ array = (Cell_T *) List_to_array(exceptions_list,NULL);
+ List_free(&exceptions_list);
+ qsort(array,*nexceptions,sizeof(Cell_T),Cell_compare);
+ *lcp_exceptions = (UINT4 *) MALLOC(2 * (*nexceptions) * sizeof(UINT4));
+ k = 0;
+ for (i = 0; i < *nexceptions; i++) {
+ (*lcp_exceptions)[k++] = array[i]->index;
+ (*lcp_exceptions)[k++] = array[i]->value;
+ Cell_free(&(array[i]));
+ }
+ FREE(array);
+ }
+
+ return lcp_bytes;
+}
+
+
#if 0
/* Based on Manzini, 2004 */
/* eos_pos: end-of-string pos? */
@@ -1276,6 +1516,163 @@ Sarray_compute_lcp_from_genome (UINT4 *SA, unsigned char *gbuffer, UINT4 n) {
return lcp;
}
+#if 0
+/* Used by cmetindex and atoiindex. Requires memory usage of a table */
+unsigned char *
+Sarray_compute_lcp_bytes_from_genome_table (Uinttableuint_T *lcp_exceptions_table, UINT4 *SA, unsigned char *gbuffer, UINT4 n) {
+ unsigned char *lcp_bytes;
+ UINT4 *rank, h;
+ UINT4 i, j;
+ char *comma;
+ /* UINT4 horig; */
+
+ lcp_bytes = (unsigned char *) MALLOC((n+1)*sizeof(unsigned char));
+ *lcp_exceptions_table = Uinttableuint_new(/*hint*/(int) (n/10));
+
+ rank = (UINT4 *) CALLOC(n+1,sizeof(UINT4));
+ for (i = 0; i <= n; i++) {
+ rank[SA[i]] = i;
+ }
+
+ lcp_bytes[0] = 0; /* -1 ? */
+ h = 0;
+ for (i = 0; i <= n; i++) {
+ if (rank[i] > 0) {
+ j = SA[rank[i] - 1];
+ /* horig = h; */
+ while (i + h < n && j + h < n && gbuffer[i+h] == gbuffer[j+h]) {
+ h++;
+ }
+ if (h >= 255) {
+ lcp_bytes[rank[i]] = 255;
+ Uinttableuint_put(*lcp_exceptions_table,rank[i],h);
+ } else {
+ lcp_bytes[rank[i]] = (unsigned char) h;
+ }
+ if (h > 0) {
+ h--;
+ }
+ }
+ if (i % MONITOR_INTERVAL == 0) {
+ comma = Genomicpos_commafmt(i);
+ fprintf(stderr,"Computing lcp index %s\n",comma);
+ FREE(comma);
+ }
+ }
+
+ FREE(rank);
+
+ return lcp_bytes;
+}
+#endif
+
+
+#if 0
+void
+binary_store_exception (UINT4 key, UINT4 value, UINT4 *exceptions, int nexceptions) {
+ UINT4 lowi, middlei, highi;
+
+ lowi = 0;
+ highi = nexceptions;
+ /* debug10(printf("entered binary search with lowi=%d, highi=%d, goal=%u\n",lowi,highi,key)); */
+
+ while (lowi < highi) {
+ middlei = lowi + ((highi - lowi) / 2);
+ /* debug10(printf(" binary: %d:%u %d:%u %d:%u vs. %u\n",
+ lowi,exceptions[2*lowi],middlei,exceptions[2*middlei],
+ highi,exceptions[2*highi],key)); */
+ if (key < exceptions[2*middlei]) {
+ highi = middlei;
+ } else if (key > exceptions[2*middlei]) {
+ lowi = middlei + 1;
+ } else {
+ /* debug10(printf("binary search returns %d => %u\n",middlei,exceptions[2*middlei+1])); */
+ exceptions[2*middlei+1] = value;
+ }
+ }
+
+ fprintf(stderr,"binary_store_exceptions should have found index %u as an exception, but failed\n",key);
+ abort();
+}
+#endif
+
+
+
+/* Used by cmetindex and atoiindex. Minimizes memory usage */
+unsigned char *
+Sarray_compute_lcp_bytes_from_genome (UINT4 **lcp_exceptions, UINT4 *nexceptions,
+ UINT4 *SA, unsigned char *gbuffer, UINT4 n) {
+ unsigned char *lcp_bytes;
+ List_T exceptions_list = NULL;
+ Cell_T *array;
+ UINT4 *rank, h;
+ UINT4 i, j, k;
+ char *comma;
+ /* UINT4 horig; */
+
+ lcp_bytes = (unsigned char *) MALLOC((n+1)*sizeof(unsigned char));
+
+ rank = (UINT4 *) CALLOC(n+1,sizeof(UINT4));
+ for (i = 0; i <= n; i++) {
+ rank[SA[i]] = i;
+ }
+
+ lcp_bytes[0] = 0; /* -1 ? */
+ h = 0;
+ k = 0;
+ for (i = 0; i <= n; i++) {
+ if (rank[i] > 0) {
+ j = SA[rank[i] - 1];
+ /* horig = h; */
+ while (i + h < n && j + h < n && gbuffer[i+h] == gbuffer[j+h]) {
+ h++;
+ }
+ if (h >= 255) {
+ lcp_bytes[rank[i]] = 255;
+ /* Uinttableuint_put(*lcp_exceptions_table,rank[i],h); */
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(/*index*/rank[i],/*timestamp*/0,/*value*/h,/*validp*/true));
+ k++;
+ } else {
+ lcp_bytes[rank[i]] = (unsigned char) h;
+ }
+ if (h > 0) {
+ h--;
+ }
+ }
+ if (i % MONITOR_INTERVAL == 0) {
+ comma = Genomicpos_commafmt(i);
+ fprintf(stderr,"Computing lcp index %s\n",comma);
+ FREE(comma);
+ }
+ }
+
+ printf("Found %u exceptions\n",k);
+ *nexceptions = k;
+
+
+ /* Create exceptions array */
+ if (*nexceptions == 0) {
+ *lcp_exceptions = (UINT4 *) NULL;
+ } else {
+ array = (Cell_T *) List_to_array(exceptions_list,NULL);
+ List_free(&exceptions_list);
+ qsort(array,*nexceptions,sizeof(Cell_T),Cell_compare);
+ *lcp_exceptions = (UINT4 *) MALLOC(2 * (*nexceptions) * sizeof(UINT4));
+ k = 0;
+ for (i = 0; i < *nexceptions; i++) {
+ (*lcp_exceptions)[k++] = array[i]->index;
+ (*lcp_exceptions)[k++] = array[i]->value;
+ Cell_free(&(array[i]));
+ }
+ FREE(array);
+ }
+
+ FREE(rank);
+
+ return lcp_bytes;
+}
+
+
/* Computes permuted lcp (Karkkainen, CPM 2009) */
/* Two methods for storing plcp as a cumulative sum: (1) Cum value at k is
@@ -1404,11 +1801,12 @@ get_all_children (bool *filledp, Sarrayptr_T *l, Sarrayptr_T *r, Sarrayptr_T i,
void
Sarray_write_plcp (char *plcpptrsfile, char *plcpcompfile, UINT4 *SA, UINT4 genomelength) {
UINT4 *plcp;
- UINT4 *ramp, *p;
+ UINT4 *ramp;
UINT4 n = genomelength, i;
- UINT4 ii;
- FILE *fp;
+ /* UINT4 *p; */
+ /* UINT4 ii; */
+ /* FILE *fp; */
plcp = (UINT4 *) MALLOC((n+1)*sizeof(UINT4));
ramp = plcp;
@@ -1454,12 +1852,88 @@ Sarray_write_plcp (char *plcpptrsfile, char *plcpcompfile, UINT4 *SA, UINT4 geno
}
-
/* Without encoding, would be child[index] = value */
#define encode_up(child,index,value) child[index-1] = (index - 1) - (value)
#define encode_down(child,index,value) child[index] = (value) - 1 - (index)
#define encode_next(child,index,value) child[index] = (value) - 1 - (index)
+#if 0
+
+/* Uses a table, which requires much memory */
+
+#define encode_bytes_up(child_bytes,child_exceptions_table,index,value,encoding) \
+ if ((encoding = (index - 1) - (value)) >= 255) { \
+ child_bytes[index-1] = 255; \
+ Uinttableuint_put(child_exceptions_table,index-1,encoding); \
+ } else if (child_bytes[index-1] == 255) { \
+ Uinttableuint_remove(child_exceptions_table,index-1); \
+ child_bytes[index-1] = (unsigned char) encoding; \
+ } else { \
+ child_bytes[index-1] = (unsigned char) encoding; \
+ }
+
+#define encode_bytes_down(child_bytes,child_exceptions_table,index,value,encoding) \
+ if ((encoding = (value) - 1 - (index)) >= 255) { \
+ child_bytes[index] = 255; \
+ Uinttableuint_put(child_exceptions_table,index,encoding); \
+ } else if (child_bytes[index] == 255) { \
+ Uinttableuint_remove(child_exceptions_table,index); \
+ child_bytes[index] = (unsigned char) encoding; \
+ } else { \
+ child_bytes[index] = (unsigned char) encoding; \
+ }
+
+#define encode_bytes_next(child_bytes,child_exceptions_table,index,value,encoding) \
+ if ((encoding = (value) - 1 - (index)) >= 255) { \
+ child_bytes[index] = 255; \
+ Uinttableuint_put(child_exceptions_table,index,encoding); \
+ } else if (child_bytes[index] == 255) { \
+ Uinttableuint_remove(child_exceptions_table,index); \
+ child_bytes[index] = (unsigned char) encoding; \
+ } else { \
+ child_bytes[index] = (unsigned char) encoding; \
+ }
+
+#else
+
+/* Uses a list, which requires less memory */
+
+#define encode_bytes_up(child_bytes,exceptions_list,index,timestamp,value,encoding) \
+ if ((encoding = (index - 1) - (value)) >= 255) { \
+ child_bytes[index-1] = 255; \
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(index-1,timestamp++,encoding,/*validp*/true)); \
+ } else if (child_bytes[index-1] == 255) { \
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(index-1,timestamp++,/*encoding*/0,/*validp*/false)); \
+ child_bytes[index-1] = (unsigned char) encoding; \
+ } else { \
+ child_bytes[index-1] = (unsigned char) encoding; \
+ }
+
+#define encode_bytes_down(child_bytes,exceptions_list,index,timestamp,value,encoding) \
+ if ((encoding = (value) - 1 - (index)) >= 255) { \
+ child_bytes[index] = 255; \
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(index,timestamp++,encoding,/*validp*/true)); \
+ } else if (child_bytes[index] == 255) { \
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(index,timestamp++,/*encoding*/0,/*validp*/false)); \
+ child_bytes[index] = (unsigned char) encoding; \
+ } else { \
+ child_bytes[index] = (unsigned char) encoding; \
+ }
+
+#define encode_bytes_next(child_bytes,exceptions_list,index,timestamp,value,encoding) \
+ if ((encoding = (value) - 1 - (index)) >= 255) { \
+ child_bytes[index] = 255; \
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(index,timestamp++,encoding,/*validp*/true)); \
+ } else if (child_bytes[index] == 255) { \
+ exceptions_list = List_push(exceptions_list,(void *) Cell_new(index,timestamp++,/*encoding*/0,/*validp*/false)); \
+ child_bytes[index] = (unsigned char) encoding; \
+ } else { \
+ child_bytes[index] = (unsigned char) encoding; \
+ }
+
+#endif
+
+
/* For child[index+1].up, just calling child[index] */
#define decode_up(child_i,index) index - child_i
#define decode_down(child_i,index) child_i + index + 1
@@ -2183,6 +2657,199 @@ Sarray_compute_child (unsigned char *lcp_bytes, UINT4 *lcp_guide, UINT4 *lcp_exc
}
+/* Onepass method */
+unsigned char *
+Sarray_compute_child_bytes (UINT4 **child_exceptions, UINT4 *nexceptions,
+ unsigned char *lcp_bytes, UINT4 *lcp_guide, UINT4 *lcp_exceptions, UINT4 n) {
+ unsigned char *child_bytes;
+ List_T exceptions_list = NULL, p;
+ Cell_T *array;
+ UINT4 timestamp = 0;
+ int ncells, l, j;
+ UINT4 k;
+
+ UINT4 child_at_1;
+ UINT4 encoding;
+ UINT4 lastindex, i;
+ Uintlist_T indexstack;
+ Uintlist_T lcpstack;
+ UINT4 lcp_i, lcp_lastindex;
+ char *comma;
+
+ child_bytes = (unsigned char *) CALLOC(n+1,sizeof(unsigned char));
+
+ /* Allocate based on two nibbles per byte */
+ /* We consider 0 and (n+1) to be at lcp -1, and 1 at lcp 0 */
+
+ i = 1;
+ lastindex = 1;
+ lcp_i = 0;
+ indexstack = Uintlist_push(NULL,i);
+ lcpstack = Uintlist_push(NULL,lcp_i);
+
+ for (i = 2; i <= n; i++) {
+ lcp_i = Bytecoding_read_wguide(i,lcp_bytes,lcp_guide,lcp_exceptions,/*lcp_guide_interval*/1024);
+ debug2(printf("index %d, lcp %u\n",i,lcp_i));
+
+ while (lcp_i < Uintlist_head(lcpstack)) {
+ indexstack = Uintlist_pop(indexstack,&lastindex);
+ lcpstack = Uintlist_pop(lcpstack,&lcp_lastindex);
+ /* Mark as a right child. Either down or next, which are
+ treated the same. Therefore, the next conditional is not
+ really necessary. */
+ if (lcp_lastindex == Uintlist_head(lcpstack)) {
+#if 0
+ debug2(printf("Encoding next %u at %u\n",lastindex,Uintlist_head(indexstack)));
+ encode_bytes_next(child_bytes,exceptions_list,Uintlist_head(indexstack),timestamp,lastindex,encoding);
+#endif
+ } else {
+ debug2(printf("Encoding down %u at %u\n",lastindex,Uintlist_head(indexstack)));
+ encode_bytes_down(child_bytes,exceptions_list,Uintlist_head(indexstack),timestamp,lastindex,encoding);
+ }
+ }
+
+ if (lastindex != 0) {
+ debug2(printf("Encoding up %u at %u\n",lastindex,i));
+ encode_bytes_up(child_bytes,exceptions_list,i,timestamp,lastindex,encoding);
+ lastindex = 0;
+ }
+
+ /* This check is still necessary, even if we handle "next" within the previous loop */
+ if (lcp_i == Uintlist_head(lcpstack)) {
+ /* This is a right sibling, so mark previous index as having a right sibling */
+ debug2(printf("Encoding next %u at %u\n",i,Uintlist_head(indexstack)));
+ encode_bytes_next(child_bytes,exceptions_list,Uintlist_head(indexstack),timestamp,i,encoding);
+ }
+
+ indexstack = Uintlist_push(indexstack,i);
+ lcpstack = Uintlist_push(lcpstack,lcp_i);
+
+ if (i % MONITOR_INTERVAL == 0) {
+ comma = Genomicpos_commafmt(i);
+ fprintf(stderr,"Computing child index %s\n",comma);
+ FREE(comma);
+ }
+ debug2(printf("\n"));
+ }
+
+ /* Previously, thought there was no need to clean out stack, because
+ all of the next links have been written. However, skipping the
+ section below gave rise to an incorrect child array in the T section */
+ debug2(printf("stack still has %d entries\n",Uintlist_length(lcpstack)));
+#if 1
+ lcp_i = 0;
+ while (lcp_i < Uintlist_head(lcpstack)) {
+ indexstack = Uintlist_pop(indexstack,&lastindex);
+ lcpstack = Uintlist_pop(lcpstack,&lcp_lastindex);
+ /* Mark as a right child. Either down or next, which are
+ treated the same. Therefore, the next conditional is not
+ really necessary. */
+ if (lcp_lastindex == Uintlist_head(lcpstack)) {
+#if 0
+ debug2(printf("Final: Encoding next %u at %u\n",lastindex,Uintlist_head(indexstack)));
+ encode_bytes_next(child_bytes,exceptions_list,Uintlist_head(indexstack),timestamp,lastindex,encoding);
+#endif
+ } else {
+ debug2(printf("Final: Encoding down %u at %u\n",lastindex,Uintlist_head(indexstack)));
+ encode_bytes_down(child_bytes,exceptions_list,Uintlist_head(indexstack),timestamp,lastindex,encoding);
+ }
+ }
+#endif
+
+
+ /* Two choices for final value for up at n+1 (stored at n). If we
+ want it to fail the test (1 < up && up <= n), we could use 0, 1,
+ or n+1. The value n+1 causes -1 to be encoded. If we want it to
+ succeed, then the correct value should be already stored as
+ child[1] as a next value. */
+
+ if ((child_at_1 = child_bytes[1]) == 255) {
+ p = exceptions_list;
+ while (p != NULL && ((Cell_T) List_head(p))->index != 1) {
+ p = List_next(p);
+ }
+ if (p == NULL) {
+ fprintf(stderr,"Expected a cell for index 1\n");
+ abort();
+ } else if (((Cell_T) List_head(p))->validp == false) {
+ fprintf(stderr,"Expected cell for index 1 to be valid\n");
+ abort();
+ } else {
+ child_at_1 = ((Cell_T) List_head(p))->value;
+ }
+ }
+ debug2(printf("Final: Encoding up %u at %u\n",child_at_1+1+1,n+1));
+ encode_bytes_up(child_bytes,exceptions_list,n+1,timestamp,child_at_1 + /*index*/1 + 1,encoding);
+
+
+#if 0
+ if (lastindex != 0) {
+ debug2(printf("Final: Encoding up %u at %u\n",lastindex,i));
+ encode_bytes_up(child_bytes,exceptions_list,/*i*/n+1,timestamp,1,encoding);
+ lastindex = 0;
+ }
+
+ /* Top-level siblings, at lcp_i == 0. This conditional should always be true. */
+ /* This check is still necessary, even if we handle "next" within the previous loop */
+ i = n+1;
+ if (lcp_i == Uintlist_head(lcpstack)) {
+ /* This is a right sibling, so mark previous index as having a right sibling */
+ debug2(printf("Final: Encoding next %u at %u\n",i,Uintlist_head(indexstack)));
+ encode_bytes_next(child_bytes,exceptions_list,Uintlist_head(indexstack),timestamp,i,encoding);
+ }
+#endif
+
+
+ Uintlist_free(&lcpstack);
+ Uintlist_free(&indexstack);
+
+ /* Create child_exceptions */
+ if (exceptions_list == NULL) {
+ *child_exceptions = (UINT4 *) NULL;
+ *nexceptions = 0;
+ } else {
+ array = (Cell_T *) List_to_array_n(&ncells,exceptions_list);
+ List_free(&exceptions_list);
+ qsort(array,ncells,sizeof(Cell_T),Cell_compare);
+
+ /* Pass 1 */
+ l = j = k = 0;
+ while (l < ncells) {
+ while (j < ncells && array[j]->index == array[l]->index) {
+ j++;
+ }
+ if (array[l]->validp == true) {
+ k++;
+ }
+ l = j;
+ }
+ *nexceptions = k;
+ *child_exceptions = (UINT4 *) MALLOC(2 * (*nexceptions) * sizeof(UINT4));
+
+ /* Pass 2 */
+ l = j = k = 0;
+ while (l < ncells) {
+ while (j < ncells && array[j]->index == array[l]->index) {
+ j++;
+ }
+ if (array[l]->validp == true) {
+ (*child_exceptions)[k++] = array[l]->index;
+ (*child_exceptions)[k++] = array[l]->value;
+ }
+ l = j;
+ }
+
+ for (l = 0; l < ncells; l++) {
+ Cell_free(&(array[l]));
+ }
+ FREE(array);
+ }
+
+ return child_bytes;
+}
+
+
+
#if 0
/* Modeled after Kasai */
UINT4 *
@@ -2256,12 +2923,12 @@ Sarray_traverse_lcp_intervals (unsigned char *lcp_bytes, UINT4 *lcp_exceptions,
void
Sarray_array_uncompress (Genome_T genomecomp, char *sarrayfile, char *plcpptrsfile, char *plcpcompfile,
UINT4 genomelength, UINT4 start, UINT4 end) {
- UINT4 n = genomelength, pos, match, h;
- unsigned char *gbuffer;
+ UINT4 n = genomelength, pos, h;
+ char *gbuffer;
- int shmid;
UINT4 *SA, *plcpptrs, *plcpcomp;
+ Access_T plcpptrs_access;
int sa_fd, plcpcomp_fd;
size_t sa_len, plcpptrs_len, plcpcomp_len;
@@ -2269,7 +2936,7 @@ Sarray_array_uncompress (Genome_T genomecomp, char *sarrayfile, char *plcpptrsfi
UINT4 sa_i, lcp_i, sa_nexti, lcp_nexti;
- gbuffer = (unsigned char *) CALLOC(n+1,sizeof(unsigned char));
+ gbuffer = (char *) CALLOC(n+1,sizeof(char));
Genome_fill_buffer_simple(genomecomp,/*left*/0,/*length*/n,gbuffer);
gbuffer[n] = 0; /* '\0', terminator */
@@ -2278,12 +2945,10 @@ Sarray_array_uncompress (Genome_T genomecomp, char *sarrayfile, char *plcpptrsfi
end = n;
}
- SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,sizeof(UINT4),/*randomp*/false);
- plcpptrs = (UINT4 *) Access_allocate(&shmid,&plcpptrs_len,&seconds,plcpptrsfile,sizeof(UINT4),/*sharedp*/false);
- plcpcomp = (UINT4 *) Access_mmap(&plcpcomp_fd,&plcpcomp_len,plcpcompfile,sizeof(UINT4),
- /*randomp*/true);
- plcpcomp = (UINT4 *) Access_mmap(&plcpcomp_fd,&plcpcomp_len,plcpcompfile,sizeof(UINT4),
- /*randomp*/true);
+ SA = (UINT4 *) Access_mmap(&sa_fd,&sa_len,sarrayfile,/*randomp*/false);
+ plcpptrs = (UINT4 *) Access_allocate_private(&plcpptrs_access,&plcpptrs_len,&seconds,plcpptrsfile,sizeof(UINT4));
+ plcpcomp = (UINT4 *) Access_mmap(&plcpcomp_fd,&plcpcomp_len,plcpcompfile,/*randomp*/true);
+ plcpcomp = (UINT4 *) Access_mmap(&plcpcomp_fd,&plcpcomp_len,plcpcompfile,/*randomp*/true);
/* Bitpack64_read_setup(); */
@@ -2382,12 +3047,13 @@ Sarray_child_uncompress (Genome_T genomecomp, unsigned char *lcpchilddc, UINT4 *
int n_lcp_exceptions, UINT4 *child_guide, UINT4 *child_exceptions, int n_child_exceptions,
UINT4 *SA, UINT4 genomelength, UINT4 start, UINT4 end) {
UINT4 n = genomelength, pos, h;
- unsigned char *gbuffer;
- UINT4 sa_i, lcp_i, child_i, sa_nexti, lcp_nexti, child_nexti;
+ char *gbuffer;
+ UINT4 sa_i, lcp_i, lcp_nexti;
+ /* UINT4 child_i, sa_nexti, child_nexti; */
char c1, c2;
- gbuffer = (unsigned char *) CALLOC(n+1,sizeof(unsigned char));
+ gbuffer = (char *) CALLOC(n+1,sizeof(char));
Genome_fill_buffer_simple(genomecomp,/*left*/0,/*length*/n,gbuffer);
gbuffer[n] = 0; /* '\0', terminator */
diff --git a/src/sarray-write.h b/src/sarray-write.h
index 75ecf94..d9f9265 100644
--- a/src/sarray-write.h
+++ b/src/sarray-write.h
@@ -1,4 +1,4 @@
-/* $Id: sarray-write.h 165971 2015-05-20 00:20:26Z twu $ */
+/* $Id: sarray-write.h 179284 2015-11-20 00:30:33Z twu $ */
#ifndef SARRAY_WRITE_INCLUDED
#define SARRAY_WRITE_INCLUDED
#include "types.h"
@@ -26,8 +26,16 @@ Sarray_write_csa (char **csaptrfiles, char **csacompfiles, char *sasampleqfile,
extern UINT4 *
Sarray_compute_lcp (char *rankfile, char *permuted_sarray_file, char *sarrayfile, UINT4 n);
+extern unsigned char *
+Sarray_compute_lcp_bytes (UINT4 **lcp_exceptions, UINT4 *nexceptions,
+ char *rankfile, char *permuted_sarray_file,
+ char *sarrayfile, UINT4 n);
+
extern UINT4 *
Sarray_compute_lcp_from_genome (UINT4 *SA, unsigned char *gbuffer, UINT4 n);
+extern unsigned char *
+Sarray_compute_lcp_bytes_from_genome (UINT4 **lcp_exceptions, UINT4 *nexceptions,
+ UINT4 *SA, unsigned char *gbuffer, UINT4 n);
extern unsigned char *
Sarray_discriminating_chars (UINT4 *nbytes, char *sarrayfile, Genome_T genome,
@@ -36,7 +44,9 @@ Sarray_discriminating_chars (UINT4 *nbytes, char *sarrayfile, Genome_T genome,
extern UINT4 *
Sarray_compute_child (unsigned char *lcp_bytes, UINT4 *lcp_guide, UINT4 *lcp_exceptions, UINT4 n);
-
+extern unsigned char *
+Sarray_compute_child_bytes (UINT4 **child_exceptions, UINT4 *nexceptions,
+ unsigned char *lcp_bytes, UINT4 *lcp_guide, UINT4 *lcp_exceptions, UINT4 n);
extern void
Sarray_array_uncompress (Genome_T genomecomp, char *sarrayfile, char *plcpptrsfile, char *plcpcompfile,
diff --git a/src/semaphore.c b/src/semaphore.c
new file mode 100644
index 0000000..ab4be21
--- /dev/null
+++ b/src/semaphore.c
@@ -0,0 +1,104 @@
+static char rcsid[] = "$Id: semaphore.c 183989 2016-02-09 18:07:52Z twu $";
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "semaphore.h"
+#include <stdlib.h>
+#include <stdio.h>
+
+#include <sys/ipc.h>
+#include <sys/sem.h> /* For semaphores */
+
+
+int
+Semaphore_create (key_t key, int nsems, ushort *values) {
+ int semid;
+ union semun {
+ int val;
+ struct semid_ds *buf;
+ ushort *array;
+ } arg;
+
+ if ((semid = semget(key,nsems,IPC_CREAT | IPC_EXCL | 0666)) == -1) {
+ return -1;
+ } else {
+ arg.array = values;
+ semctl(semid,/*semno*/0,SETALL,arg);
+ return semid;
+ }
+}
+
+int
+Semaphore_find (key_t key) {
+ return semget(key,/*nsems*/0,/*flags*/0);
+}
+
+
+void
+Semaphore_delete (int semid) {
+ if (semctl(semid,0,IPC_RMID,NULL) == -1) {
+ fprintf(stderr,"Error releasing semaphore %d\n",semid);
+ /* abort(); */
+ }
+ return;
+}
+
+
+void
+Semaphore_set_value (int semid, int semno, int value) {
+ union semun {
+ int val;
+ struct semid_ds *buf;
+ ushort *array;
+ } arg;
+
+ arg.val = value;
+ semctl(semid,semno,SETVAL,arg);
+ return;
+}
+
+int
+Semaphore_get_value (int semid, int semno) {
+ /* printf("Value of semno %d is %d\n",semno,semctl(semid,semno,GETVAL,NULL)); */
+ return semctl(semid,semno,GETVAL,/*arg*/NULL);
+}
+
+
+int
+Semaphore_nwaiting (int semid, int semno) {
+ printf("nwaiting = %d\n",semctl(semid,semno,GETNCNT,NULL));
+ return semctl(semid,semno,GETNCNT,/*arg*/NULL);
+}
+
+
+/* If already locked, then puts process to sleep */
+void
+Semaphore_lock (int semid, int semno) {
+ struct sembuf op;
+
+ /* printf("Process %d locking semaphore %d\n",getpid(),semid); */
+ op.sem_num = semno;
+ op.sem_op = -1;
+ op.sem_flg = SEM_UNDO;
+ semop(semid,&op,1);
+
+ return;
+}
+
+void
+Semaphore_unlock (int semid, int semno) {
+ struct sembuf op;
+
+ /* printf("Process %d unlocking semaphore %d\n",getpid(),semid); */
+ op.sem_num = semno;
+ op.sem_op = +1;
+ op.sem_flg = SEM_UNDO;
+ semop(semid,&op,1);
+
+ /* return semctl(semid,SEMAPHORE_CREATION,GETNCNT,NULL); */
+ return;
+ /* printf("%d processes still waiting\n",semctl(semid,SEMAPHORE_CREATION,GETNCNT,NULL)); */
+}
+
+
diff --git a/src/semaphore.h b/src/semaphore.h
new file mode 100644
index 0000000..bce15b1
--- /dev/null
+++ b/src/semaphore.h
@@ -0,0 +1,45 @@
+/* $Id: semaphore.h 183951 2016-02-09 01:00:57Z twu $ */
+#ifndef SEMAPHORE_INCLUDED
+#define SEMAPHORE_INCLUDED
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <sys/types.h> /* For key_t and ushort */
+
+
+#define NSEMAPHORES 2
+#define SEMNO_NA 0
+#define SEMNO_LOCK 0
+#define SEMNO_KEEP 1
+
+#define SEMAPHORE_RESIDENT 99
+#define SEMAPHORE_FREEABLE 1
+
+
+extern int
+Semaphore_create (key_t key, int nsems, ushort *vals);
+
+extern int
+Semaphore_find (key_t key);
+
+extern void
+Semaphore_delete (int semid);
+
+extern void
+Semaphore_set_value (int semid, int semno, int value);
+
+extern int
+Semaphore_get_value (int semid, int semno);
+
+extern int
+Semaphore_nwaiting (int semid, int semno);
+
+extern void
+Semaphore_lock (int semid, int semno);
+
+extern void
+Semaphore_unlock (int semid, int semno);
+
+#endif
+
diff --git a/src/sequence.c b/src/sequence.c
index beb2d8f..b657ee3 100644
--- a/src/sequence.c
+++ b/src/sequence.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: sequence.c 170023 2015-07-17 16:47:21Z twu $";
+static char rcsid[] = "$Id: sequence.c 184174 2016-02-12 19:48:42Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -978,6 +978,7 @@ make_complement_uppercase (char *sequence, unsigned int length) {
#endif
+#if 0
static void
make_complement_buffered (char *complement, char *sequence, unsigned int length) {
int i, j;
@@ -989,6 +990,7 @@ make_complement_buffered (char *complement, char *sequence, unsigned int length)
complement[length] = '\0';
return;
}
+#endif
static void
diff --git a/src/shortread.c b/src/shortread.c
index 10f624c..a4d6b99 100644
--- a/src/shortread.c
+++ b/src/shortread.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: shortread.c 160871 2015-03-13 00:14:41Z twu $";
+static char rcsid[] = "$Id: shortread.c 183889 2016-02-05 20:34:55Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -314,16 +314,17 @@ Shortread_find_read (FILE *fp) {
unsigned long long **
Shortread_input_divide (bool *fastq_format_p, char **files, int nfiles, int naliquots) {
- unsigned long long **aliquots, ptr, filesize1, filesize2, filestep1, filestep2;
+ size_t filesize1, filesize2, filestep1, filestep2;
+ size_t **aliquots, ptr;
FILE *input1, *input2;
int c;
int workeri, filei;
Header[0] = '\0';
- aliquots = (unsigned long long **) CALLOC(naliquots+1,sizeof(unsigned long long *));
+ aliquots = (size_t **) CALLOC(naliquots+1,sizeof(size_t *));
for (workeri = 0; workeri <= naliquots; workeri++) {
- aliquots[workeri] = (unsigned long long *) CALLOC(nfiles,sizeof(unsigned long long));
+ aliquots[workeri] = (size_t *) CALLOC(nfiles,sizeof(size_t));
}
diff --git a/src/smooth.c b/src/smooth.c
index 3737fc6..f87ce26 100644
--- a/src/smooth.c
+++ b/src/smooth.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: smooth.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: smooth.c 184474 2016-02-18 00:12:53Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -149,16 +149,16 @@ static void
get_exonmatches (int *total_matches, int *total_denominator, int **exonmatches, int **exon_denominator,
int *nexons, List_T pairs) {
Intlist_T matchlist = NULL, denominatorlist = NULL;
- Pair_T firstpair, pair;
- int querypos, nmatches = 0, nmismatches = 0;
+ Pair_T pair;
+ int nmatches = 0, nmismatches = 0;
#ifdef DEBUG
int i;
#endif
*total_matches = *total_denominator = 0;
- firstpair = List_head(pairs);
- querypos = firstpair->querypos;
+ /* firstpair = List_head(pairs); */
+ /* querypos = firstpair->querypos; */
while (pairs != NULL) {
pair = List_head(pairs);
@@ -170,12 +170,12 @@ get_exonmatches (int *total_matches, int *total_denominator, int **exonmatches,
pairs = List_next(pairs);
if (pairs != NULL) {
- firstpair = List_head(pairs);
- querypos = firstpair->querypos;
+ /* firstpair = List_head(pairs); */
+ /* querypos = firstpair->querypos; */
nmatches = nmismatches = 0;
}
} else {
- querypos = pair->querypos;
+ /* querypos = pair->querypos; */
if (pair->comp == MATCH_COMP || pair->comp == DYNPROG_MATCH_COMP) {
nmatches++;
} else {
@@ -363,6 +363,7 @@ compute_prob (int exonlen, int intronlen, int indexsize) {
return prob;
}
+#if 0
static bool
short_exon_byprob (int exonlen, int intronlen, int indexsize, double prob_threshold) {
double prob;
@@ -374,7 +375,9 @@ short_exon_byprob (int exonlen, int intronlen, int indexsize, double prob_thresh
return true;
}
}
+#endif
+#if 0
static bool
short_exon_bylength (int exonlen, int length_threshold) {
@@ -384,6 +387,7 @@ short_exon_bylength (int exonlen, int length_threshold) {
return true;
}
}
+#endif
static void
zero_net_gap (int *starti, int *startj, int i, int j, int *intronlengths) {
@@ -572,14 +576,14 @@ find_internal_bads_by_prob (bool *deletep, int *exonstatus, int *exonmatches, in
int *intron_matches_right, int *intron_denominator_right,
int total_matches, int total_denominator) {
struct Smoothcell_T *cells;
- int starti, startj, i, j;
- int exonlen;
- double theta_1, theta0, theta1;
- int numerator_1, denominator_1, numerator0, denominator0, numerator1, denominator1;
+ int i;
+ double theta0;
+ int numerator0, denominator0;
bool intron1_bad_p, intron2_bad_p;
- double worst_exon_pvalue = 1.0, pvalue;
- int worst_exoni = -1;
+ double pvalue;
+ /* double worst_exon_pvalue = 1.0; */
+ /* int worst_exoni = -1; */
*deletep = false;
cells = (struct Smoothcell_T *) MALLOCA(nexons * sizeof(struct Smoothcell_T));
@@ -635,6 +639,7 @@ find_internal_bads_by_prob (bool *deletep, int *exonstatus, int *exonmatches, in
+#if 0
/* For ends, we turn off the indexsize parameter */
static void
find_end_shorts (bool *deletep, int *exonstatus, int *exonmatches, int nexons, int *intronlengths) {
@@ -674,6 +679,7 @@ find_end_shorts (bool *deletep, int *exonstatus, int *exonmatches, int nexons, i
return;
}
+#endif
#ifdef DEBUG
@@ -964,7 +970,7 @@ List_T
Smooth_pairs_by_size (bool *shortp, bool *deletep, List_T pairs, Pairpool_T pairpool, int stage2_indexsize) {
int *exonstatus;
int *exonlengths, *exonmatches, *exonprotects, *intronlengths, nexons, nintrons;
- bool delete1p, delete2p;
+ bool delete2p;
#ifdef DEBUG
int i;
#endif
diff --git a/src/snpindex.c b/src/snpindex.c
index a54704b..77706cd 100644
--- a/src/snpindex.c
+++ b/src/snpindex.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: snpindex.c 168395 2015-06-26 17:13:13Z twu $";
+static char rcsid[] = "$Id: snpindex.c 184165 2016-02-12 19:14:32Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -67,11 +67,22 @@ static char rcsid[] = "$Id: snpindex.c 168395 2015-06-26 17:13:13Z twu $";
#include "indexdb.h"
#include "indexdb-write.h"
#include "bitpack64-write.h"
+#include "bitpack64-read.h"
+#include "bitpack64-readtwo.h"
+#include "bitpack64-access.h"
+#include "bitpack64-incr.h"
#include "getopt.h"
#define POSITIONS8_HIGH_SHIFT 32
#define POSITIONS8_LOW_MASK 0xFFFFFFFF
+#define DIFFERENTIAL_METAINFO_SIZE 2
+#define BLOCKSIZE 64
+#define BUFFER_SIZE 1000000
+
+#define MONITOR_INTERVAL 10000000
+
+
#ifdef DEBUG
#define debug(x) x
#else
@@ -158,20 +169,14 @@ power (int base, int exponent) {
}
-/* 87654321 */
-#define RIGHT_A 0x00000000
-#define RIGHT_C 0x00000001
-#define RIGHT_G 0x00000002
-#define RIGHT_T 0x00000003
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
static char *
-shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
+shortoligo_nt (Oligospace_T oligo, int oligosize) {
char *nt;
int i, j;
- Storedoligomer_T lowbits;
+ Oligospace_T lowbits;
nt = (char *) CALLOC(oligosize+1,sizeof(char));
j = oligosize-1;
@@ -191,7 +196,7 @@ shortoligo_nt (Storedoligomer_T oligo, int oligosize) {
}
static char
-check_acgt (char nt, IIT_T snps_iit, int divno, char *divstring,
+check_acgt (char nt, IIT_T snps_iit, char *divstring,
int origindex, Interval_T interval) {
char *label;
bool allocp;
@@ -212,8 +217,8 @@ check_acgt (char nt, IIT_T snps_iit, int divno, char *divstring,
}
-static Storedoligomer_T
-revise_oligomer (Storedoligomer_T oligo, char nt) {
+static Oligospace_T
+revise_oligomer (Oligospace_T oligo, char nt) {
switch (nt) {
case 'A': return (oligo << 2);
case 'C': return (oligo << 2) | 1U;
@@ -275,13 +280,14 @@ Labeled_interval_cmp (const void *a, const void *b) {
+/* Same procedure used for writing offsets and writing positions, depending on whether positions4/positions8 is NULL */
static int
-process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, UINT8 *positions8,
- Labeled_interval_T *intervals, int nintervals,
+process_snp_block (int *nwarnings, char *packsizes, UINT4 **bitpacks,
+ UINT4 *snponly_offsetsmeta, UINT4 *snponly_offsetsstrm, UINT4 *countermeta, UINT4 *counterstrm,
+ UINT4 *positions4, UINT8 *positions8, Labeled_interval_T *intervals, int nintervals,
Univcoord_T chroffset, Genome_T genome,
- Genomecomp_T *snp_blocks, int divno, char *divstring, int intervali,
- IIT_T snps_iit, Univ_IIT_T chromosome_iit, int index1part,
- bool coord_values_8p) {
+ Genomecomp_T *snp_blocks, char *divstring,
+ IIT_T snps_iit, int index1part, bool coord_values_8p) {
int nerrors = 0;
bool *snpp;
char *refstring;
@@ -290,19 +296,18 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
char *nt;
#endif
- int index, length;
+ int length;
int nsnps, stringi, starti, shift, i, k;
char *snptype, *label, refnt, altnt;
Univcoord_T ptr;
Univcoord_T snpposition, startposition, endposition, first_snppos, last_snppos, position;
Chrpos_T chrpos;
- Chrnum_T chrnum;
Interval_T interval;
- int nunknowns;
bool badcharp, allocp;
Uintlist_T oligomers, newoligomers, p;
- Storedoligomer_T oligo;
+ Oligospace_T oligo, bmer;
+ UINT4 offset;
#ifdef WORDS_BIGENDIAN
Genomecomp_T high, low, flags;
#endif
@@ -372,7 +377,7 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
}
altnt = 'N';
} else {
- altnt = check_acgt(snptype[1],snps_iit,divno,divstring,intervals[i]->origindex,intervals[i]->interval);
+ altnt = check_acgt(snptype[1],snps_iit,divstring,intervals[i]->origindex,intervals[i]->interval);
}
} else if (refnt == snptype[1]) {
if (altstring[stringi] != '\0' && altstring[stringi] != snptype[0]) {
@@ -391,7 +396,7 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
}
altnt = 'N';
} else {
- altnt = check_acgt(snptype[0],snps_iit,divno,divstring,intervals[i]->origindex,intervals[i]->interval);
+ altnt = check_acgt(snptype[0],snps_iit,divstring,intervals[i]->origindex,intervals[i]->interval);
}
} else {
nerrors++;
@@ -564,7 +569,13 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
/* writing offsets */
for (p = Uintlist_next(oligomers); p != NULL; p = Uintlist_next(p)) {
oligo = Uintlist_head(p);
- offsets[oligo + 1U] += 1;
+ /* offsets[oligo + 1U] += 1; */
+ bmer = oligo/BLOCKSIZE;
+ if (Bitpack64_access_filledp(oligo,(int) packsizes[bmer],bitpacks[bmer]) == true) {
+ bitpacks[bmer] = Bitpack64_realloc_one((int) packsizes[bmer],bitpacks[bmer]);
+ packsizes[bmer] += 2;
+ }
+ Bitpack64_incr_bitpack(oligo,(int) packsizes[bmer],bitpacks[bmer]);
debug1(nt = shortoligo_nt(oligo,index1part);
printf("Storing %s at %llu (%s:%u)\n",nt,(unsigned long long) position,divstring,chrpos+1U);
FREE(nt));
@@ -575,7 +586,8 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
if (coord_values_8p == true) {
for (p = Uintlist_next(oligomers); p != NULL; p = Uintlist_next(p)) {
oligo = Uintlist_head(p);
- positions8[offsets[oligo]++] = position;
+ offset = Bitpack64_read_one(oligo,snponly_offsetsmeta,snponly_offsetsstrm) + Bitpack64_incr(oligo,countermeta,counterstrm);
+ positions8[offset] = position;
debug1(nt = shortoligo_nt(oligo,index1part);
printf("Storing %s at %llu (%s:%u)\n",nt,(unsigned long long) position,divstring,chrpos+1U);
FREE(nt));
@@ -584,7 +596,8 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
} else {
for (p = Uintlist_next(oligomers); p != NULL; p = Uintlist_next(p)) {
oligo = Uintlist_head(p);
- positions4[offsets[oligo]++] = (UINT4) position;
+ offset = Bitpack64_read_one(oligo,snponly_offsetsmeta,snponly_offsetsstrm) + Bitpack64_incr(oligo,countermeta,counterstrm);
+ positions4[offset] = (UINT4) position;
debug1(nt = shortoligo_nt(oligo,index1part);
printf("Storing %s at %llu (%s:%u)\n",nt,(unsigned long long) position,divstring,chrpos+1U);
FREE(nt));
@@ -604,27 +617,62 @@ process_snp_block (int *nwarnings, Positionsptr_T *offsets, UINT4 *positions4, U
}
-static Positionsptr_T *
-compute_offsets (IIT_T snps_iit, Univ_IIT_T chromosome_iit, Genome_T genome, Genomecomp_T *snp_blocks,
- Oligospace_T oligospace, int index1part) {
- Positionsptr_T *offsets;
+/* Copied from bitpack64-write.c */
+static UINT4
+compute_ascending (UINT4 *ascending, UINT4 *counts) {
+ int i;
+
+ ascending[0] = 0;
+ for (i = 1; i <= 64; i++) {
+ ascending[i] = ascending[i-1] + counts[i-1];
+ }
+
+ return ascending[64];
+}
+
+
+static void
+write_offsets (char *snponly_offsetsmetafile, char *snponly_offsetsstrmfile,
+ char *snp_offsetsmetafile, char *snp_offsetsstrmfile, IIT_T snps_iit,
+ UINT4 *ref_offsetsmeta, UINT4 *ref_offsetsstrm,
+ Univ_IIT_T chromosome_iit, Genome_T genome,
+ Genomecomp_T *snp_blocks, Oligospace_T oligospace, int index1part) {
+ char *packsizes;
+ UINT4 **bitpacks;
Labeled_interval_T *intervals;
int origindex;
Interval_T interval, copy;
int nintervals, nintervals_alias, nerrors, divno, i, j;
- Oligospace_T oligoi;
+ Oligospace_T bmerspace, bmer, oligoi;
char *divstring;
Chrnum_T chrnum;
Univcoord_T chroffset;
Chrpos_T chrlength;
int nwarnings = 0;
- offsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
+ FILE *ptrs_fp, *comp_fp;
+ UINT4 *ptrs, nregisters;
+ UINT4 totalcount;
+ UINT4 ptri;
+ UINT4 ptr, end;
+
+ /* Buffer is used to avoid frequent writes to the file */
+ UINT4 *buffer;
+ int buffer_size = BUFFER_SIZE;
+ int buffer_i;
+
+ UINT4 diffs[BLOCKSIZE], ascending[BLOCKSIZE+1], counts[BLOCKSIZE], offsets[BLOCKSIZE+1];
+ int packsize;
+
+
+ bmerspace = oligospace/BLOCKSIZE;
+ packsizes = (char *) CALLOC(bmerspace,sizeof(char));
+ bitpacks = (UINT4 **) CALLOC(bmerspace,sizeof(UINT4 *));
for (divno = 1; divno < snps_iit->ndivs; divno++) {
divstring = IIT_divstring(snps_iit,divno);
- fprintf(stderr,"Processing offsets for chromosome %s...",divstring);
+ fprintf(stderr,"Processing snp offsets for chromosome %s...",divstring);
if ((chrnum = Univ_IIT_find_one(chromosome_iit,divstring)) <= 0) {
fprintf(stderr,"not found in chromosome iit\n");
} else {
@@ -668,10 +716,11 @@ compute_offsets (IIT_T snps_iit, Univ_IIT_T chromosome_iit, Genome_T genome, Gen
while (j < nintervals_alias && Interval_low(intervals[j]->interval) < Interval_low(intervals[j-1]->interval) + index1part) {
j++;
}
- nerrors += process_snp_block(&nwarnings,offsets,/*positions4*/NULL,/*positions8*/NULL,
- &(intervals[i]),/*nintervals*/j-i,
+ nerrors += process_snp_block(&nwarnings,packsizes,bitpacks,
+ /*snponly_offsetsmeta*/NULL,/*snponly_offsetsstrm*/NULL,/*countermeta*/NULL,/*counterstrm*/NULL,
+ /*positions4*/NULL,/*positions8*/NULL,&(intervals[i]),/*nintervals*/j-i,
chroffset,genome,snp_blocks,
- divno,divstring,/*intervali*/i,snps_iit,chromosome_iit,index1part,
+ divstring,snps_iit,index1part,
/*coord_values_8p (irrelevant)*/false);
i = j;
}
@@ -688,24 +737,112 @@ compute_offsets (IIT_T snps_iit, Univ_IIT_T chromosome_iit, Genome_T genome, Gen
}
}
- /* Do not add extra for sentinel */
+ Bitpack64_write_differential_bitpacks(snponly_offsetsmetafile,snponly_offsetsstrmfile,packsizes,bitpacks,oligospace);
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
- offsets[oligoi] = offsets[oligoi] + offsets[oligoi-1];
- debug(if (offsets[oligoi] != offsets[oligoi-1]) {
- printf("Offset for %lX: %u\n",oligoi,offsets[oligoi]);
- });
+
+ /* Code derived from Bitpack64_write_differential_bitpacks */
+ fprintf(stderr,"Computing combined ref+snp offsets");
+ if ((comp_fp = FOPEN_WRITE_BINARY(snp_offsetsstrmfile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",snp_offsetsstrmfile);
+ exit(9);
}
- return offsets;
+ ptrs = (UINT4 *) CALLOC(((oligospace + BLOCKSIZE)/BLOCKSIZE + 1) * DIFFERENTIAL_METAINFO_SIZE,sizeof(UINT4));
+ ptri = 0;
+ buffer = (UINT4 *) CALLOC(buffer_size,sizeof(UINT4));
+ buffer_i = 0;
+ nregisters = 0;
+
+ totalcount = 0;
+ for (oligoi = 0, bmer = 0; oligoi + BLOCKSIZE <= oligospace; oligoi += BLOCKSIZE, bmer++) {
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+ ptrs[ptri++] = totalcount;
+ Bitpack64_extract_bitpack(counts,packsizes[bmer],bitpacks[bmer]);
+ Bitpack64_block_offsets(offsets,oligoi,ref_offsetsmeta,ref_offsetsstrm);
+ for (i = 0; i < 64; i++) {
+ if ((oligoi + i) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ counts[i] += (offsets[i+1] - offsets[i]);
+ }
+ totalcount += compute_ascending(ascending,counts);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending); /* Note: This packsize may differ from packsizes[bmer] */
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+
+ nregisters += packsize / 2;
+ }
+ fprintf(stderr,"done\n");
+
+ /* For nucleotides, expect a single final block where oligoi == oligospace */
+ if (oligoi <= oligospace) {
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+ ptrs[ptri++] = totalcount;
+
+ if (oligoi == oligospace) {
+ /* Don't have a bitpack at [bmerspace] */
+ Bitpack64_extract_bitpack(counts,/*packsize*/0,/*bitpack*/NULL);
+ } else {
+ Bitpack64_extract_bitpack(counts,packsizes[bmer],bitpacks[bmer]);
+ }
+
+ /* For differential, want <=. For direct, want < */
+ for (i = 0; i <= (int) (oligospace - oligoi); i++) {
+ ptr = Bitpack64_read_two(&end,oligoi,ref_offsetsmeta,ref_offsetsstrm);
+ counts[i] += (end - ptr);
+ }
+ for ( ; i < BLOCKSIZE; i++) {
+ /* Copy last value for rest of block */
+ counts[i] = 0;
+ }
+
+ /* Pack block of < 64 diffs */
+ totalcount += compute_ascending(ascending,counts);
+ packsize = Bitpack64_compute_q4_diffs_bidir(diffs,ascending);
+ buffer_i = Bitpack64_write_columnar(comp_fp,buffer,buffer_size,buffer_i,diffs,packsize);
+
+ nregisters += packsize / 2;
+ }
+
+ /* Write the final pointers, which will point after the end of the file */
+ ptrs[ptri++] = nregisters; /* In 128-bit registers */
+ ptrs[ptri++] = totalcount;
+
+ if ((ptrs_fp = FOPEN_WRITE_BINARY(snp_offsetsmetafile)) == NULL) {
+ fprintf(stderr,"Can't write to file %s\n",snp_offsetsmetafile);
+ exit(9);
+ } else {
+ FWRITE_UINTS(ptrs,ptri,ptrs_fp);
+ FREE(ptrs);
+ fclose(ptrs_fp);
+ }
+
+ /* Empty buffer */
+ if (buffer_i > 0) {
+ FWRITE_UINTS(buffer,buffer_i,comp_fp);
+ buffer_i = 0;
+ }
+ FREE(buffer);
+ fclose(comp_fp);
+
+
+ /* Clean up */
+ FREE(ptrs);
+ for (bmer = 0; bmer < bmerspace; bmer++) {
+ FREE(bitpacks[bmer]);
+ }
+ FREE(bitpacks);
+ FREE(packsizes);
+
+ return;
}
static void *
-compute_positions (Positionsptr_T *offsets, IIT_T snps_iit, Univ_IIT_T chromosome_iit,
+compute_positions (UINT4 *snponly_offsetsmeta, UINT4 *snponly_offsetsstrm, IIT_T snps_iit, Univ_IIT_T chromosome_iit,
Genome_T genome, Oligospace_T oligospace, bool coord_values_8p) {
UINT4 *positions4 = NULL;
UINT8 *positions8 = NULL;
+ UINT4 offsets[BLOCKSIZE+1];
Labeled_interval_T *intervals;
int origindex;
@@ -716,12 +853,13 @@ compute_positions (Positionsptr_T *offsets, IIT_T snps_iit, Univ_IIT_T chromosom
Chrnum_T chrnum;
Univcoord_T chroffset;
Chrpos_T chrlength;
- Positionsptr_T *pointers, totalcounts, block_start, block_end, npositions;
+ Positionsptr_T totalcounts, npositions;
+ UINT4 *countermeta, *counterstrm;
int nwarnings = 0;
- totalcounts = offsets[oligospace];
+ totalcounts = Bitpack64_read_one(oligospace,snponly_offsetsmeta,snponly_offsetsstrm);
if (totalcounts == 0) {
- fprintf(stderr,"Something is wrong with the offsets. Total counts is zero.\n");
+ fprintf(stderr,"Something is wrong with the SNP-only offsets. Total counts is zero.\n");
fprintf(stderr,"Do the chromosomes in the IIT file match those in the genome?\n");
fprintf(stderr,"Here are known chromosomes in the genome: ");
Univ_IIT_dump_labels(stderr,chromosome_iit);
@@ -750,11 +888,8 @@ compute_positions (Positionsptr_T *offsets, IIT_T snps_iit, Univ_IIT_T chromosom
}
}
- /* Copy offsets */
- pointers = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
- for (i = 0; i <= oligospace; i++) {
- pointers[i] = offsets[i];
- }
+ /* Prepare counter */
+ countermeta = Indexdb_bitpack_counter(&counterstrm,snponly_offsetsmeta,snponly_offsetsstrm,index1part);
for (divno = 1; divno < snps_iit->ndivs; divno++) {
divstring = IIT_divstring(snps_iit,divno);
@@ -801,11 +936,11 @@ compute_positions (Positionsptr_T *offsets, IIT_T snps_iit, Univ_IIT_T chromosom
while (j < nintervals_alias && Interval_low(intervals[j]->interval) < Interval_low(intervals[j-1]->interval) + index1part) {
j++;
}
- process_snp_block(&nwarnings,/*offsets*/pointers,positions4,positions8,
- &(intervals[i]),/*nintervals*/j-i,
+ process_snp_block(&nwarnings,/*packsizes*/NULL,/*bitpacks*/NULL,
+ snponly_offsetsmeta,snponly_offsetsstrm,countermeta,counterstrm,
+ positions4,positions8,&(intervals[i]),/*nintervals*/j-i,
chroffset,genome,/*snp_blocks*/NULL,
- divno,divstring,/*intervali*/i,snps_iit,chromosome_iit,index1part,
- coord_values_8p);
+ divstring,snps_iit,index1part,coord_values_8p);
i = j;
}
@@ -821,26 +956,39 @@ compute_positions (Positionsptr_T *offsets, IIT_T snps_iit, Univ_IIT_T chromosom
}
}
- FREE(pointers);
+ FREE(counterstrm);
+ FREE(countermeta);
/* Sort positions in each block */
+ fprintf(stderr,"Sorting snp positions");
if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 1) {
- qsort(&(positions8[block_start]),npositions,sizeof(UINT8),UINT8_compare);
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(offsets,oligoi,snponly_offsetsmeta,snponly_offsetsstrm);
+ for (i = 0; i < 64; i++) {
+ if ((oligoi + i) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ if ((npositions = offsets[i+1] - offsets[i]) > 1) {
+ qsort(&(positions8[offsets[i]]),npositions,sizeof(UINT8),UINT8_compare);
+ }
}
}
+ fprintf(stderr,"done\n");
return positions8;
+
} else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
- block_start = offsets[oligoi];
- block_end = offsets[oligoi+1];
- if ((npositions = block_end - block_start) > 1) {
- qsort(&(positions4[block_start]),npositions,sizeof(UINT4),UINT4_compare);
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(offsets,oligoi,snponly_offsetsmeta,snponly_offsetsstrm);
+ for (i = 0; i < 64; i++) {
+ if ((oligoi + i) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ if ((npositions = offsets[i+1] - offsets[i]) > 1) {
+ qsort(&(positions4[offsets[i]]),npositions,sizeof(UINT4),UINT4_compare);
+ }
}
}
+ fprintf(stderr,"done\n");
return positions4;
}
}
@@ -849,7 +997,7 @@ compute_positions (Positionsptr_T *offsets, IIT_T snps_iit, Univ_IIT_T chromosom
static void
merge_positions8 (FILE *positions_high_fp, FILE *positions_low_fp,
UINT8 *start1, UINT8 *end1, UINT8 *start2, UINT8 *end2,
- Storedoligomer_T oligo, int index1part) {
+ Oligospace_T oligo, int index1part) {
unsigned char position8_high;
UINT4 position8_low;
UINT8 *ptr1 = start1, *ptr2 = start2;
@@ -913,33 +1061,47 @@ merge_positions8 (FILE *positions_high_fp, FILE *positions_low_fp,
#endif
}
- while (ptr1 < end1) {
#ifdef WORDS_BIGENDIAN
+ while (ptr1 < end1) {
position1 = Bigendian_convert_uint8(*ptr1);
position8_high = position1 >> POSITIONS8_HIGH_SHIFT;
position8_low = position1 & POSITIONS8_LOW_MASK;
+
+ FWRITE_CHAR(position8_high,positions_high_fp);
+ FWRITE_UINT(position8_low,positions_low_fp);
+ ptr1++;
+ }
+
#else
+ while (ptr1 < end1) {
position8_high = *ptr1 >> POSITIONS8_HIGH_SHIFT;
position8_low = *ptr1 & POSITIONS8_LOW_MASK;
-#endif
FWRITE_CHAR(position8_high,positions_high_fp);
FWRITE_UINT(position8_low,positions_low_fp);
ptr1++;
}
+#endif
- while (ptr2 < end2) {
#ifdef WORDS_BIGENDIAN
+ while (ptr2 < end2) {
position2 = Bigendian_convert_uint8(*ptr2);
position8_high = position2 >> POSITIONS8_HIGH_SHIFT;
position8_low = position2 & POSITIONS8_LOW_MASK;
+
+ FWRITE_CHAR(position8_high,positions_high_fp);
+ FWRITE_UINT(position8_low,positions_low_fp);
+ ptr2++;
+ }
#else
+ while (ptr2 < end2) {
position8_high = *ptr2 >> POSITIONS8_HIGH_SHIFT;
position8_low = *ptr2 & POSITIONS8_LOW_MASK;
-#endif
+
FWRITE_CHAR(position8_high,positions_high_fp);
FWRITE_UINT(position8_low,positions_low_fp);
ptr2++;
}
+#endif
return;
}
@@ -947,7 +1109,7 @@ merge_positions8 (FILE *positions_high_fp, FILE *positions_low_fp,
static void
merge_positions4 (FILE *positions_fp, UINT4 *start1, UINT4 *end1,
- UINT4 *start2, UINT4 *end2, Storedoligomer_T oligo, int index1part) {
+ UINT4 *start2, UINT4 *end2, Oligospace_T oligo, int index1part) {
UINT4 *ptr1 = start1, *ptr2 = start2;
char *nt;
#ifdef WORDS_BIGENDIAN
@@ -998,25 +1160,29 @@ merge_positions4 (FILE *positions_fp, UINT4 *start1, UINT4 *end1,
#endif
}
- while (ptr1 < end1) {
#ifdef WORDS_BIGENDIAN
+ while (ptr1 < end1) {
position1 = Bigendian_convert_uint(*ptr1);
FWRITE_UINT(position1,positions_fp);
-#else
- FWRITE_UINT(*ptr1,positions_fp);
-#endif
ptr1++;
}
+#else
+ if (ptr1 < end1) {
+ FWRITE_UINTS(ptr1,end1-ptr1,positions_fp);
+ }
+#endif
- while (ptr2 < end2) {
#ifdef WORDS_BIGENDIAN
+ while (ptr2 < end2) {
position2 = Bigendian_convert_uint(*ptr2);
FWRITE_UINT(position2,positions_fp);
-#else
- FWRITE_UINT(*ptr2,positions_fp);
-#endif
ptr2++;
}
+#else
+ if (ptr2 < end2) {
+ FWRITE_UINTS(ptr2,end2-ptr2,positions_fp);
+ }
+#endif
return;
}
@@ -1033,13 +1199,13 @@ main (int argc, char *argv[]) {
Univ_IIT_T chromosome_iit;
IIT_T snps_iit;
Genome_T genome;
- Positionsptr_T *offsets, *snp_offsets, *ref_offsets;
+ UINT4 *ref_offsetsmeta, *ref_offsetsstrm, *snponly_offsetsmeta, *snponly_offsetsstrm;
+
size_t totalcounts, i;
#ifdef EXTRA_ALLOCATION
Positionsptr_T npositions;
#endif
- int shmid;
unsigned char *ref_positions8_high;
UINT4 *ref_positions8_low;
UINT8 *snp_positions8, *ref_positions8;
@@ -1047,19 +1213,20 @@ main (int argc, char *argv[]) {
Univcoord_T nblocks;
Genomecomp_T *snp_blocks;
Oligospace_T oligospace, oligoi;
+ int ii;
#ifndef HAVE_MMAP
double seconds;
#endif
bool coord_values_8p;
Filenames_T filenames;
- char *filename, *filename1, *filename2;
+ char *filename, *snp_offsetsmetafile, *snp_offsetsstrmfile, *snponly_offsetsmetafile, *snponly_offsetsstrmfile;
FILE *genome_fp, *genomebits_fp, *positions_high_fp, *positions_low_fp;
- int ref_positions_high_fd, ref_positions_low_fd;
- size_t ref_positions_high_len, ref_positions_low_len;
-#ifdef WORDS_BIGENDIAN
- Positionsptr_T offset1, offset2;
-#endif
+ int ref_offsetsmeta_fd, ref_offsetsstrm_fd, ref_positions_high_fd, ref_positions_low_fd,
+ snponly_offsetsmeta_fd, snponly_offsetsstrm_fd;
+ size_t ref_offsetsmeta_len, ref_offsetsstrm_len, ref_positions_high_len, ref_positions_low_len,
+ snponly_offsetsmeta_len, snponly_offsetsstrm_len;
+ UINT4 ref_offsets[BLOCKSIZE+1], snponly_offsets[BLOCKSIZE+1];
int opt;
extern int optind;
@@ -1118,8 +1285,7 @@ main (int argc, char *argv[]) {
} else {
fprintf(stderr,"Reading SNPs IIT file %s...",argv[1]);
if ((snps_iit = IIT_read(argv[1],/*name*/NULL,/*readonlyp*/true,
- /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false,
- /*labels_read_p*/true)) == NULL) {
+ /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false)) == NULL) {
fprintf(stderr,"SNP IIT file %s is not valid\n",argv[1]);
exit(9);
}
@@ -1138,8 +1304,7 @@ main (int argc, char *argv[]) {
exit(9);
} else {
if ((snps_iit = IIT_read(filename,/*name*/NULL,/*readonlyp*/true,
- /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false,
- /*labels_read_p*/true)) == NULL) {
+ /*divread*/READ_ALL,/*divstring*/NULL,/*add_iit_p*/false)) == NULL) {
fprintf(stderr,"SNP IIT file %s is not valid\n",filename);
exit(9);
}
@@ -1171,7 +1336,7 @@ main (int argc, char *argv[]) {
genome = Genome_new(sourcedir,fileroot,/*snps_root*/NULL,/*genometype*/GENOME_OLIGOS,
/*uncompressedp*/false,/*access*/USE_MMAP_ONLY,/*sharedp*/false);
- /* Copy genome */
+ /* Copy reference genome as basis for snp genome */
nblocks = Genome_totallength(genome)/32U;
snp_blocks = (Genomecomp_T *) CALLOC(nblocks*3,sizeof(Genomecomp_T));
fprintf(stderr,"Allocating %llu*3*%d bytes for compressed genome\n",
@@ -1190,16 +1355,42 @@ main (int argc, char *argv[]) {
show_warnings_p = false;
}
-
+ oligospace = power(4,index1part);
filenames = Indexdb_get_filenames(&compression_type,&index1part,&index1interval,
sourcedir,fileroot,IDX_FILESUFFIX,/*snps_root*/NULL,
required_index1part,required_interval,
/*offsets_only_p*/false);
- /* Compute offsets and write genomecomp */
- oligospace = power(4,index1part);
- snp_offsets = compute_offsets(snps_iit,chromosome_iit,genome,snp_blocks,oligospace,index1part);
- fprintf(stderr,"last offset = %u\n",snp_offsets[oligospace]);
+ /* Write offsets and compute snp_blocks */
+#ifdef HAVE_MMAP
+ ref_offsetsmeta = (UINT4 *) Access_mmap(&ref_offsetsmeta_fd,&ref_offsetsmeta_len,filenames->pointers_filename,/*randomp*/false);
+ ref_offsetsstrm = (UINT4 *) Access_mmap(&ref_offsetsstrm_fd,&ref_offsetsstrm_len,filenames->offsets_filename,/*randomp*/false);
+#else
+ ref_offsetsmeta = (UINT4 *) Access_allocate_private(&ref_offsetsmeta_len,&seconds,filenames->pointers_filename,sizeof(UINT4));
+ ref_offsetsstrm = (UINT4 *) Access_allocate_private(&ref_offsetsstrm_len,&seconds,filenames->offsets_filename,sizeof(UINT4));
+#endif
+
+ /* Write snponly and SNP offsets */
+ snp_offsetsmetafile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(filenames->pointers_basename_ptr)+
+ strlen(".")+strlen(snps_root)+1,sizeof(char));
+ sprintf(snp_offsetsmetafile,"%s/%s.%s",destdir,filenames->pointers_basename_ptr,snps_root);
+ snp_offsetsstrmfile = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(filenames->offsets_basename_ptr)+
+ strlen(".")+strlen(snps_root)+1,sizeof(char));
+ sprintf(snp_offsetsstrmfile,"%s/%s.%s",destdir,filenames->offsets_basename_ptr,snps_root);
+
+ snponly_offsetsmetafile = (char *) CALLOC(strlen(snp_offsetsmetafile) + strlen(".only") + 1,sizeof(char));
+ sprintf(snponly_offsetsmetafile,"%s.only",snp_offsetsmetafile);
+ snponly_offsetsstrmfile = (char *) CALLOC(strlen(snp_offsetsstrmfile) + strlen(".only") + 1,sizeof(char));
+ sprintf(snponly_offsetsstrmfile,"%s.only",snp_offsetsstrmfile);
+
+ write_offsets(snponly_offsetsmetafile,snponly_offsetsstrmfile,snp_offsetsmetafile,snp_offsetsstrmfile,
+ snps_iit,ref_offsetsmeta,ref_offsetsstrm,chromosome_iit,genome,snp_blocks,oligospace,index1part);
+
+ FREE(snp_offsetsmetafile);
+ FREE(snp_offsetsstrmfile);
+
+
+ /* Write genomecomp */
filename = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(fileroot)+
strlen(".genomecomp.")+strlen(snps_root)+1,sizeof(char));
sprintf(filename,"%s/%s.genomecomp.%s",destdir,fileroot,snps_root);
@@ -1207,7 +1398,7 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Can't open file %s for writing genome\n",filename);
exit(9);
}
- fprintf(stderr,"Writing filename %s...",filename);
+ fprintf(stderr,"Writing genome file %s...",filename);
FWRITE_UINTS(snp_blocks,nblocks*3,genome_fp);
fclose(genome_fp);
FREE(snp_blocks);
@@ -1228,114 +1419,45 @@ main (int argc, char *argv[]) {
fprintf(stderr,"Can't open file %s for writing genome\n",filename);
exit(9);
}
- fprintf(stderr,"Writing filename %s...",filename);
+ fprintf(stderr,"Writing genome file %s...",filename);
Compress_unshuffle_bits128(/*out*/genomebits_fp,/*in*/genome_fp);
fclose(genomebits_fp);
fclose(genome_fp);
FREE(filename);
+ fprintf(stderr,"done\n");
- /* Compute positions */
- show_warnings_p = false; /* Already shown in compute_offsets */
- if (coord_values_8p == true) {
- snp_positions8 = compute_positions(snp_offsets,snps_iit,chromosome_iit,genome,oligospace,/*coord_values_8p*/true);
- } else {
- snp_positions4 = compute_positions(snp_offsets,snps_iit,chromosome_iit,genome,oligospace,/*coord_values_8p*/false);
- }
-
+ /* Compute snponly positions and keep in memory */
+ show_warnings_p = false; /* Already shown in write_offsets */
- /* Read reference offsets and update */
-#ifdef EXTRA_ALLOCATION
- if (compression_type == BITPACK64_COMPRESSION) {
- ref_offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part);
- } else {
- abort();
- }
- offsets = (Positionsptr_T *) CALLOC(oligospace+1,sizeof(Positionsptr_T));
- offsets[0] = 0U;
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
-#ifdef WORDS_BIGENDIAN
- npositions = (Bigendian_convert_uint(ref_offsets[oligoi]) - Bigendian_convert_uint(ref_offsets[oligoi-1])) +
- (snp_offsets[oligoi] - snp_offsets[oligoi-1]);
-#else
- npositions = (ref_offsets[oligoi] - ref_offsets[oligoi-1]) + (snp_offsets[oligoi] - snp_offsets[oligoi-1]);
-#endif
- offsets[oligoi] = offsets[oligoi-1] + npositions;
- }
-
-#else
- /* This version saves on one allocation of oligospace * sizeof(Positionsptr_T) */
- if (compression_type == BITPACK64_COMPRESSION) {
- offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part);
- } else {
- abort();
- }
- for (oligoi = oligospace; oligoi >= 1; oligoi--) {
-#ifdef WORDS_BIGENDIAN
- offsets[oligoi] = Bigendian_convert_uint(offsets[oligoi]) - Bigendian_convert_uint(offsets[oligoi-1]);
+#ifdef HAVE_MMAP
+ snponly_offsetsmeta = (UINT4 *) Access_mmap(&snponly_offsetsmeta_fd,&snponly_offsetsmeta_len,snponly_offsetsmetafile,/*randomp*/false);
+ snponly_offsetsstrm = (UINT4 *) Access_mmap(&snponly_offsetsstrm_fd,&snponly_offsetsstrm_len,snponly_offsetsstrmfile,/*randomp*/false);
#else
- offsets[oligoi] = offsets[oligoi] - offsets[oligoi-1];
-#endif
- }
-
- for (oligoi = 1; oligoi <= oligospace; oligoi++) {
- offsets[oligoi] = offsets[oligoi-1] + offsets[oligoi] + (snp_offsets[oligoi] - snp_offsets[oligoi-1]);
- }
+ snponly_offsetsmeta = (UINT4 *) Access_allocate_private(&snponly_offsetsmeta_len,&seconds,snponly_offsetsmetafile,sizeof(UINT4));
+ snponly_offsetsstrm = (UINT4 *) Access_allocate_private(&snponly_offsetsstrm_len,&seconds,snponly_offsetsstrmfile,sizeof(UINT4));
#endif
-
-
- /* Write offsets */
- if (filenames->pointers_basename_ptr == NULL) {
- filename1 = (char *) NULL;
+ if (coord_values_8p == true) {
+ snp_positions8 = compute_positions(snponly_offsetsmeta,snponly_offsetsstrm,snps_iit,chromosome_iit,genome,oligospace,/*coord_values_8p*/true);
} else {
- filename1 = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(filenames->pointers_basename_ptr)+
- strlen(".")+strlen(snps_root)+1,sizeof(char));
- sprintf(filename1,"%s/%s.%s",destdir,filenames->pointers_basename_ptr,snps_root);
+ snp_positions4 = compute_positions(snponly_offsetsmeta,snponly_offsetsstrm,snps_iit,chromosome_iit,genome,oligospace,/*coord_values_8p*/false);
}
- filename2 = (char *) CALLOC(strlen(destdir)+strlen("/")+strlen(filenames->offsets_basename_ptr)+
- strlen(".")+strlen(snps_root)+1,sizeof(char));
- sprintf(filename2,"%s/%s.%s",destdir,filenames->offsets_basename_ptr,snps_root);
-
-
- fprintf(stderr,"Writing %llu offsets with %llu total positions\n",
- (unsigned long long) oligospace+1,(unsigned long long) offsets[oligospace]);
- if (compression_type == BITPACK64_COMPRESSION) {
- Bitpack64_write_differential(/*ptrsfile*/filename1,/*compfile*/filename2,offsets,oligospace);
- } else {
- abort();
- }
- FREE(filename2);
- if (filename1 != NULL) {
- FREE(filename1);
- }
- FREE(offsets);
-
/* Read reference positions and merge */
-#if 0
- if ((positions_low_fp = FOPEN_READ_BINARY(filenames->positions_low_filename)) == NULL) {
- fprintf(stderr,"Can't open file %s\n",filenames->positions_low_filename);
- exit(9);
- } else {
- fclose(positions_low_fp);
- }
-#endif
-
if (coord_values_8p == true) {
#ifdef HAVE_MMAP
ref_positions8_high = (unsigned char *) Access_mmap(&ref_positions_high_fd,&ref_positions_high_len,
- filenames->positions_high_filename,sizeof(unsigned char),/*randomp*/false);
+ filenames->positions_high_filename,/*randomp*/false);
ref_positions8_low = (UINT4 *) Access_mmap(&ref_positions_low_fd,&ref_positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->positions_low_filename,/*randomp*/false);
#else
- ref_positions8_high = (unsigned char *) Access_allocate(&shmid,&ref_positions_high_len,&seconds,
- filenames->positions_high_filename,sizeof(unsigned char),
- /*sharedp*/false);
- ref_positions8_low = (UINT4 *) Access_allocate(&shmid,&ref_positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),/*sharedp*/false);
+ ref_positions8_high = (unsigned char *) Access_allocate_private(&ref_positions_high_len,&seconds,
+ filenames->positions_high_filename,sizeof(unsigned char));
+ ref_positions8_low = (UINT4 *) Access_allocate_private(&ref_positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
#endif
- /* Unpack */
+ /* Unpack 8-byte positions into memory */
totalcounts = ref_positions_high_len/sizeof(unsigned char);
if (totalcounts > 4294967295) {
fprintf(stderr,"Program not yet designed to handle huge genomes\n");
@@ -1351,17 +1473,19 @@ main (int argc, char *argv[]) {
close(ref_positions_high_fd);
close(ref_positions_low_fd);
#else
- FREE(ref_positions8_high);
- FREE(ref_positions8_low);
+ FREE(ref_positions8_high); /* Not using shared */
+ FREE(ref_positions8_low); /* Not using shared */
+ /* Access_deallocate(ref_positions8_high,ref_positions_high_shmid,ref_positions_high_key); */
+ /* Access_deallocate(ref_positions8_low,ref_positions_low_shmid,ref_positions_low_key); */
#endif
} else {
#ifdef HAVE_MMAP
ref_positions4 = (UINT4 *) Access_mmap(&ref_positions_low_fd,&ref_positions_low_len,
- filenames->positions_low_filename,sizeof(UINT4),/*randomp*/false);
+ filenames->positions_low_filename,/*randomp*/false);
#else
- ref_positions4 = (UINT4 *) Access_allocate(&shmid,&ref_positions_low_len,&seconds,
- filenames->positions_low_filename,sizeof(UINT4),/*sharedp*/false);
+ ref_positions4 = (UINT4 *) Access_allocate_private(&ref_positions_low_len,&seconds,
+ filenames->positions_low_filename,sizeof(UINT4));
#endif
}
@@ -1387,45 +1511,35 @@ main (int argc, char *argv[]) {
FREE(filename);
- fprintf(stderr,"Merging snp positions with reference positions\n");
-#ifndef EXTRA_ALLOCATION
- if (compression_type == BITPACK64_COMPRESSION) {
- ref_offsets = Indexdb_offsets_from_bitpack(filenames->pointers_filename,filenames->offsets_filename,index1part);
- } else {
- abort();
- }
-#endif
-
+ fprintf(stderr,"Merging snp positions with reference positions");
if (coord_values_8p == true) {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
-#ifdef WORDS_BIGENDIAN
- offset1 = Bigendian_convert_uint(ref_offsets[oligoi]);
- offset2 = Bigendian_convert_uint(ref_offsets[oligoi+1]);
- merge_positions8(positions_high_fp,positions_low_fp,
- &(snp_positions8[snp_offsets[oligoi]]),&(snp_positions8[snp_offsets[oligoi+1]]),
- &(ref_positions8[offset1]),&(ref_positions8[offset2]),oligoi,index1part);
-#else
- merge_positions8(positions_high_fp,positions_low_fp,
- &(snp_positions8[snp_offsets[oligoi]]),&(snp_positions8[snp_offsets[oligoi+1]]),
- &(ref_positions8[ref_offsets[oligoi]]),&(ref_positions8[ref_offsets[oligoi+1]]),oligoi,index1part);
-#endif
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(snponly_offsets,oligoi,snponly_offsetsmeta,snponly_offsetsstrm);
+ Bitpack64_block_offsets(ref_offsets,oligoi,ref_offsetsmeta,ref_offsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ merge_positions8(positions_high_fp,positions_low_fp,
+ &(snp_positions8[snponly_offsets[ii]]),&(snp_positions8[snponly_offsets[ii+1]]),
+ &(ref_positions8[ref_offsets[ii]]),&(ref_positions8[ref_offsets[ii+1]]),oligoi + ii,index1part);
+ }
}
} else {
- for (oligoi = 0; oligoi < oligospace; oligoi++) {
-#ifdef WORDS_BIGENDIAN
- offset1 = Bigendian_convert_uint(ref_offsets[oligoi]);
- offset2 = Bigendian_convert_uint(ref_offsets[oligoi+1]);
- merge_positions4(positions_low_fp,&(snp_positions4[snp_offsets[oligoi]]),&(snp_positions4[snp_offsets[oligoi+1]]),
- &(ref_positions4[offset1]),&(ref_positions4[offset2]),oligoi,index1part);
-#else
- merge_positions4(positions_low_fp,&(snp_positions4[snp_offsets[oligoi]]),&(snp_positions4[snp_offsets[oligoi+1]]),
- &(ref_positions4[ref_offsets[oligoi]]),&(ref_positions4[ref_offsets[oligoi+1]]),oligoi,index1part);
-#endif
+ for (oligoi = 0; oligoi < oligospace; oligoi += BLOCKSIZE) {
+ Bitpack64_block_offsets(snponly_offsets,oligoi,snponly_offsetsmeta,snponly_offsetsstrm);
+ Bitpack64_block_offsets(ref_offsets,oligoi,ref_offsetsmeta,ref_offsetsstrm);
+ for (ii = 0; ii < BLOCKSIZE; ii++) {
+ if ((oligoi + ii) % MONITOR_INTERVAL == 0) {
+ fprintf(stderr,".");
+ }
+ merge_positions4(positions_low_fp,&(snp_positions4[snponly_offsets[ii]]),&(snp_positions4[snponly_offsets[ii+1]]),
+ &(ref_positions4[ref_offsets[ii]]),&(ref_positions4[ref_offsets[ii+1]]),oligoi + ii,index1part);
+ }
}
}
+ fprintf(stderr,"done\n");
-
- FREE(ref_offsets);
fclose(positions_low_fp);
if (coord_values_8p == true) {
fclose(positions_high_fp);
@@ -1441,17 +1555,41 @@ main (int argc, char *argv[]) {
munmap((void *) ref_positions4,ref_positions_low_len);
close(ref_positions_low_fd);
#else
- FREE(ref_positions4);
+ FREE(ref_positions4); /* Not using shared */
+ /* Access_deallocate(ref_positions4,ref_positions_low_shmid,ref_positions_low_key); */
#endif
}
+#ifdef HAVE_MMAP
+ munmap((void *) ref_offsetsmeta,ref_offsetsmeta_len);
+ munmap((void *) ref_offsetsstrm,ref_offsetsstrm_len);
+ close(ref_offsetsmeta_fd);
+ close(ref_offsetsstrm_fd);
+#else
+ FREE(ref_offsetsmeta);
+ FREE(ref_offsetsstrm);
+#endif
if (coord_values_8p == true) {
FREE(snp_positions8);
} else {
FREE(snp_positions4);
}
- FREE(snp_offsets);
+
+#ifdef HAVE_MMAP
+ munmap((void *) snponly_offsetsmeta,snponly_offsetsmeta_len);
+ munmap((void *) snponly_offsetsstrm,snponly_offsetsstrm_len);
+ close(snponly_offsetsmeta_fd);
+ close(snponly_offsetsstrm_fd);
+#else
+ FREE(snponly_offsetsmeta);
+ FREE(snponly_offsetsstrm);
+#endif
+ remove(snponly_offsetsmetafile);
+ remove(snponly_offsetsstrmfile);
+ FREE(snponly_offsetsmetafile);
+ FREE(snponly_offsetsstrmfile);
+
Genome_free(&genome);
Univ_IIT_free(&chromosome_iit);
diff --git a/src/spanningelt.c b/src/spanningelt.c
index 3bbda53..9d16a5a 100644
--- a/src/spanningelt.c
+++ b/src/spanningelt.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: spanningelt.c 146624 2014-09-02 21:32:50Z twu $";
+static char rcsid[] = "$Id: spanningelt.c 184022 2016-02-10 01:52:03Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -203,7 +203,7 @@ Spanningelt_print_set (List_T spanningset) {
static void
Spanningelt_compute (int *candidates_score, Spanningelt_T new,
- Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+ Oligospace_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
@@ -415,7 +415,7 @@ Spanningelt_compute (int *candidates_score, Spanningelt_T new,
static void
make_spanningset_aux (int *minscore, int *nelts, Spanningelt_T *array,
- Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+ Oligospace_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
@@ -520,7 +520,7 @@ make_spanningset_aux (int *minscore, int *nelts, Spanningelt_T *array,
void
Spanningelt_set (int *minscore, int *nelts, Spanningelt_T *array,
- Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+ Oligospace_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
diff --git a/src/spanningelt.h b/src/spanningelt.h
index 9590152..f400e14 100644
--- a/src/spanningelt.h
+++ b/src/spanningelt.h
@@ -1,4 +1,4 @@
-/* $Id: spanningelt.h 146624 2014-09-02 21:32:50Z twu $ */
+/* $Id: spanningelt.h 180341 2015-12-07 18:29:40Z twu $ */
#ifndef SPANNINGELT_INCLUDED
#define SPANNINGELT_INCLUDED
@@ -85,7 +85,7 @@ Spanningelt_print_set (List_T spanningset);
extern void
Spanningelt_set (int *minscore, int *nelts, Spanningelt_T *array,
- Storedoligomer_T *stage1_oligos, bool **stage1_retrievedp,
+ Oligospace_T *stage1_oligos, bool **stage1_retrievedp,
#ifdef LARGE_GENOMES
unsigned char ***stage1_positions_high, UINT4 ***stage1_positions_low,
#else
diff --git a/src/splice.c b/src/splice.c
index 04f9695..4752c84 100644
--- a/src/splice.c
+++ b/src/splice.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splice.c 173900 2015-09-12 00:46:34Z twu $";
+static char rcsid[] = "$Id: splice.c 186965 2016-04-04 20:29:04Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -101,16 +101,12 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
int *segmentj_antidonor_knowni, int *segmenti_antiacceptor_knowni,
int segmenti_donor_nknown, int segmentj_acceptor_nknown,
int segmentj_antidonor_nknown, int segmenti_antiacceptor_nknown,
- int splicing_penalty, int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
int best_splice_pos = -1, splice_pos_start, splice_pos_end, splice_pos, i, j;
int best_nmismatches, nmismatches;
- int best_segmenti_nmismatches, best_segmentj_nmismatches, segmenti_nmismatches, segmentj_nmismatches;
- Univcoord_T best_donor_splicecoord, best_acceptor_splicecoord;
- int best_donor_knowni, best_acceptor_knowni;
- double best_prob, best_donor_prob, best_acceptor_prob, probi, probj;
- /* bool sufficient1p, sufficient2p; */
+ int segmenti_nmismatches, segmentj_nmismatches;
+ double best_prob, probi, probj;
int donori_nsites, acceptorj_nsites, antiacceptori_nsites, antidonorj_nsites;
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
@@ -136,6 +132,12 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
splice_pos_start = querystart;
splice_pos_end = queryend;
+ if (splice_pos_start < min_shortend) {
+ splice_pos_start = min_shortend;
+ }
+ if (splice_pos_end > querylength - min_shortend) {
+ splice_pos_end = querylength - min_shortend;
+ }
if (plusp == true) {
/* Originally from plus strand. No complement. */
@@ -197,10 +199,15 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/querystart,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - querystart)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (queryend - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ debug1(printf("nmismatches %d + %d <= best_nmismatches %d\n",segmenti_nmismatches,segmentj_nmismatches,best_nmismatches));
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -311,10 +318,15 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/querystart,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - querystart)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (queryend - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ debug1(printf("nmismatches %d + %d <= best_nmismatches %d\n",segmenti_nmismatches,segmentj_nmismatches,best_nmismatches));
if (antiacceptori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -366,12 +378,15 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
if (*best_prob_i > 0.95 && *best_prob_j > 0.70) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
+ debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
return best_splice_pos;
} else if (*best_prob_i > 0.70 && *best_prob_j > 0.95) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
+ debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
return best_splice_pos;
} else if (*best_prob_i > 0.80 && *best_prob_j > 0.85) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
+ debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
return best_splice_pos;
} else {
debug1(printf("Not returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
@@ -396,16 +411,12 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
int *segmentj_antidonor_knowni, int *segmenti_antiacceptor_knowni,
int segmenti_donor_nknown, int segmentj_acceptor_nknown,
int segmentj_antidonor_nknown, int segmenti_antiacceptor_nknown,
- int splicing_penalty, int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
int best_splice_pos = -1, splice_pos_start, splice_pos_end, splice_pos, i, j;
int best_nmismatches, nmismatches;
- int best_segmenti_nmismatches, best_segmentj_nmismatches, segmenti_nmismatches, segmentj_nmismatches;
- Univcoord_T best_donor_splicecoord, best_acceptor_splicecoord;
- int best_donor_knowni, best_acceptor_knowni;
- double best_prob, best_donor_prob, best_acceptor_prob, probi, probj;
- /* bool sufficient1p, sufficient2p; */
+ int segmenti_nmismatches, segmentj_nmismatches;
+ double best_prob, probi, probj;
int donori_nsites, acceptorj_nsites, antiacceptori_nsites, antidonorj_nsites;
int *donori_positions, *acceptorj_positions, *antiacceptori_positions, *antidonorj_positions;
@@ -430,6 +441,12 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
splice_pos_start = querystart;
splice_pos_end = queryend;
+ if (splice_pos_start < min_shortend) {
+ splice_pos_start = min_shortend;
+ }
+ if (splice_pos_end > querylength - min_shortend) {
+ splice_pos_end = querylength - min_shortend;
+ }
if (plusp == false) {
/* minus */
@@ -492,10 +509,14 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/querystart,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - querystart)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (queryend - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -605,10 +626,14 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/querystart,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - querystart)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (queryend - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (antiacceptori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -660,12 +685,15 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
if (*best_prob_i > 0.95 && *best_prob_j > 0.70) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
+ debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
return best_splice_pos;
} else if (*best_prob_i > 0.70 && *best_prob_j > 0.95) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
+ debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
return best_splice_pos;
} else if (*best_prob_i > 0.80 && *best_prob_j > 0.85) {
debug1(printf("Returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
+ debug1(printf("nmismatches %d and %d\n",*best_nmismatches_i,*best_nmismatches_j));
return best_splice_pos;
} else {
debug1(printf("Not returning %d with probi %f and probj %f\n",best_splice_pos,*best_prob_i,*best_prob_j));
@@ -826,10 +854,14 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - 0)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (querylength - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -933,10 +965,14 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - 0)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (querylength - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (antiacceptori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -991,13 +1027,13 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
donor = Substring_new_donor(best_donor_splicecoord,best_donor_knowni,
best_splice_pos,best_segmenti_nmismatches,
best_donor_prob,/*left*/segmenti_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmenti_chrnum,segmenti_chroffset,segmenti_chrhigh,segmenti_chrlength);
acceptor = Substring_new_acceptor(best_acceptor_splicecoord,best_acceptor_knowni,
best_splice_pos,best_segmentj_nmismatches,
best_acceptor_prob,/*left*/segmentj_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmentj_chrnum,segmentj_chroffset,segmentj_chrhigh,segmentj_chrlength);
if (donor == NULL || acceptor == NULL) {
@@ -1017,7 +1053,7 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
return List_push(hits,(void *) Stage3end_new_splice(&(*found_score),best_segmenti_nmismatches,best_segmentj_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1037,7 +1073,7 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
(void *) Stage3end_new_splice(&(*found_score),best_segmenti_nmismatches,best_segmentj_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1059,13 +1095,13 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
donor = Substring_new_donor(best_donor_splicecoord,best_donor_knowni,
best_splice_pos,best_segmentj_nmismatches,
best_donor_prob,/*left*/segmentj_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmentj_chrnum,segmentj_chroffset,segmentj_chrhigh,segmentj_chrlength);
acceptor = Substring_new_acceptor(best_acceptor_splicecoord,best_acceptor_knowni,
best_splice_pos,best_segmenti_nmismatches,
best_acceptor_prob,/*left*/segmenti_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmenti_chrnum,segmenti_chroffset,segmenti_chrhigh,segmenti_chrlength);
if (donor == NULL || acceptor == NULL) {
@@ -1084,7 +1120,7 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
return List_push(hits,(void *) Stage3end_new_splice(&(*found_score),best_segmentj_nmismatches,best_segmenti_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1104,7 +1140,7 @@ Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lo
(void *) Stage3end_new_splice(&(*found_score),best_segmentj_nmismatches,best_segmenti_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1274,10 +1310,14 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - 0)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (querylength - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -1381,10 +1421,14 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/splice_pos,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
- if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
+ plusp,genestrand);
+ if (segmenti_nmismatches > (splice_pos - 0)/10) {
+ /* Skip, because too many mismatches in segmenti */
+ } else if (segmentj_nmismatches > (querylength - splice_pos)/10) {
+ /* Skip, because too many mismatches in segmentj */
+ } else if ((nmismatches = segmenti_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (antiacceptori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
} else {
@@ -1439,13 +1483,13 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
donor = Substring_new_donor(best_donor_splicecoord,best_donor_knowni,
best_splice_pos,best_segmenti_nmismatches,
best_donor_prob,/*left*/segmenti_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmenti_chrnum,segmenti_chroffset,segmenti_chrhigh,segmenti_chrlength);
acceptor = Substring_new_acceptor(best_acceptor_splicecoord,best_acceptor_knowni,
best_splice_pos,best_segmentj_nmismatches,
best_acceptor_prob,/*left*/segmentj_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmentj_chrnum,segmentj_chroffset,segmentj_chrhigh,segmentj_chrlength);
if (donor == NULL || acceptor == NULL) {
@@ -1465,7 +1509,7 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
return List_push(hits,(void *) Stage3end_new_splice(&(*found_score),best_segmenti_nmismatches,best_segmentj_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1485,7 +1529,7 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
(void *) Stage3end_new_splice(&(*found_score),best_segmenti_nmismatches,best_segmentj_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1507,13 +1551,13 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
donor = Substring_new_donor(best_donor_splicecoord,best_donor_knowni,
best_splice_pos,best_segmentj_nmismatches,
best_donor_prob,/*left*/segmentj_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmentj_chrnum,segmentj_chroffset,segmentj_chrhigh,segmentj_chrlength);
acceptor = Substring_new_acceptor(best_acceptor_splicecoord,best_acceptor_knowni,
best_splice_pos,best_segmenti_nmismatches,
best_acceptor_prob,/*left*/segmenti_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmenti_chrnum,segmenti_chroffset,segmenti_chrhigh,segmenti_chrlength);
if (donor == NULL || acceptor == NULL) {
@@ -1532,7 +1576,7 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
return List_push(hits,(void *) Stage3end_new_splice(&(*found_score),best_segmentj_nmismatches,best_segmenti_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1552,7 +1596,7 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
(void *) Stage3end_new_splice(&(*found_score),best_segmentj_nmismatches,best_segmenti_nmismatches,
donor,acceptor,best_donor_prob,best_acceptor_prob,
/*distance*/segmentj_left - segmenti_left,
- /*shortdistancep*/true,splicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,splicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -1575,6 +1619,7 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
}
+#if 0
List_T
Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
@@ -1594,7 +1639,7 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
int *segmentj_antidonor_knowni, int *segmentm_antiacceptor_knowni, int *segmentm_antidonor_knowni, int *segmenti_antiacceptor_knowni,
int segmenti_donor_nknown, int segmentm_acceptor_nknown, int segmentm_donor_nknown, int segmentj_acceptor_nknown,
int segmentj_antidonor_nknown, int segmentm_antiacceptor_nknown, int segmentm_antidonor_nknown, int segmenti_antiacceptor_nknown,
- int splicing_penalty, int max_mismatches_allowed, bool plusp, int genestrand, bool first_read_p,
+ int splicing_penalty, int max_mismatches_allowed, bool plusp, int genestrand,
bool subs_or_indels_p, bool sarrayp) {
Substring_T donor, shortexon, acceptor;
int best_splice_pos_1, best_splice_pos_2, splice_pos_start, splice_pos_end, splice_pos_1, splice_pos_2;
@@ -1767,11 +1812,11 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/splice_pos_1,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentm_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentm_left,/*pos5*/splice_pos_1,/*pos3*/splice_pos_2,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos_2,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
if ((nmismatches = segmenti_nmismatches + segmentm_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (donori_knowni[i] >= 0) {
probi = 1.0; /* Needs to be 1.0 for output */
@@ -1962,11 +2007,11 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
j++;
} else {
segmenti_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/splice_pos_1,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentm_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentm_left,/*pos5*/splice_pos_1,/*pos3*/splice_pos_2,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
segmentj_nmismatches = Genome_count_mismatches_substring(query_compress,/*left*/segmentj_left,/*pos5*/splice_pos_2,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
if ((nmismatches = segmenti_nmismatches + segmentm_nmismatches + segmentj_nmismatches) <= best_nmismatches) {
if (antiacceptori_knowni[i] >= 0) {
@@ -2047,7 +2092,7 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
donor = Substring_new_donor(best_donor1_splicecoord,best_donor1_knowni,
best_splice_pos_1,best_segmenti_nmismatches,
best_donor1_prob,/*left*/segmenti_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmenti_chrnum,segmenti_chroffset,segmenti_chrhigh,segmenti_chrlength);
shortexon = Substring_new_shortexon(best_acceptor1_splicecoord,best_acceptor1_knowni,
@@ -2055,14 +2100,14 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
/*acceptor_pos*/best_splice_pos_1,/*donor_pos*/best_splice_pos_2,best_segmentm_nmismatches,
/*acceptor_prob*/best_acceptor1_prob,/*donor_prob*/best_donor2_prob,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/false,/*donor_ambp*/false,
segmentm_chrnum,segmentm_chroffset,segmentm_chrhigh,segmentm_chrlength);
acceptor = Substring_new_acceptor(best_acceptor2_splicecoord,best_acceptor2_knowni,
best_splice_pos_2,best_segmentj_nmismatches,
best_acceptor2_prob,/*left*/segmentj_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmentj_chrnum,segmentj_chroffset,segmentj_chrhigh,segmentj_chrlength);
if (donor == NULL || shortexon == NULL || acceptor == NULL) {
@@ -2085,13 +2130,12 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
best_donor1_prob,/*shortexonA_prob*/best_acceptor1_prob,
/*shortexonD_prob*/best_donor2_prob,best_acceptor2_prob,
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,sarrayp));
+ splicing_penalty,querylength,sensedir,sarrayp));
} else if (subs_or_indels_p == true) {
/* Don't alter hits */
if (donor != NULL) Substring_free(&donor);
@@ -2107,13 +2151,12 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
best_donor1_prob,/*shortexonA_prob*/best_acceptor1_prob,
/*shortexonD_prob*/best_donor2_prob,best_acceptor2_prob,
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,sarrayp));
+ splicing_penalty,querylength,sensedir,sarrayp));
} else {
if (donor != NULL) Substring_free(&donor);
if (shortexon != NULL) Substring_free(&shortexon);
@@ -2128,7 +2171,7 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
donor = Substring_new_donor(best_donor2_splicecoord,best_donor2_knowni,
best_splice_pos_2,best_segmentj_nmismatches,
best_donor2_prob,/*left*/segmentj_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmentj_chrnum,segmentj_chroffset,segmentj_chrhigh,segmentj_chrlength);
shortexon = Substring_new_shortexon(best_acceptor2_splicecoord,best_acceptor2_knowni,
@@ -2136,13 +2179,13 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
/*acceptor_pos*/best_splice_pos_2,/*donor_pos*/best_splice_pos_1,best_segmentm_nmismatches,
/*acceptor_prob*/best_acceptor2_prob,/*donor_prob*/best_donor1_prob,
/*left*/segmentm_left,query_compress,querylength,
- plusp,genestrand,first_read_p,sensedir,/*acceptor_ambp*/false,/*donor_ambp*/false,
+ plusp,genestrand,sensedir,/*acceptor_ambp*/false,/*donor_ambp*/false,
segmentm_chrnum,segmentm_chroffset,segmentm_chrhigh,segmentm_chrlength);
acceptor = Substring_new_acceptor(best_acceptor1_splicecoord,best_acceptor1_knowni,
best_splice_pos_1,best_segmenti_nmismatches,
best_acceptor1_prob,/*left*/segmenti_left,query_compress,
- querylength,plusp,genestrand,first_read_p,sensedir,
+ querylength,plusp,genestrand,sensedir,
segmenti_chrnum,segmenti_chroffset,segmenti_chrhigh,segmenti_chrlength);
if (donor == NULL || shortexon == NULL || acceptor == NULL) {
@@ -2165,13 +2208,12 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
best_donor2_prob,/*shortexonA_prob*/best_acceptor2_prob,
/*shortexonD_prob*/best_donor1_prob,best_acceptor1_prob,
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,sarrayp));
+ splicing_penalty,querylength,sensedir,sarrayp));
} else if (subs_or_indels_p == true) {
/* Don't alter hits */
if (donor != NULL) Substring_free(&donor);
@@ -2187,13 +2229,12 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
best_donor2_prob,/*shortexonA_prob*/best_acceptor2_prob,
/*shortexonD_prob*/best_donor1_prob,best_acceptor1_prob,
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,sarrayp));
+ splicing_penalty,querylength,sensedir,sarrayp));
} else {
if (donor != NULL) Substring_free(&donor);
if (shortexon != NULL) Substring_free(&shortexon);
@@ -2206,6 +2247,7 @@ Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
return hits;
}
+#endif
static int
@@ -2264,7 +2306,7 @@ group_by_segmenti_aux (int *found_score, List_T winners, List_T *ambiguous,
Intlist_T amb_knowni, amb_nmismatches;
Doublelist_T amb_probs;
int donor_length, acceptor_length;
- bool plusp;
+
i = 0;
while (i < n) {
@@ -2280,7 +2322,6 @@ group_by_segmenti_aux (int *found_score, List_T winners, List_T *ambiguous,
winners = List_push(winners,(void *) hit);
} else {
- plusp = Stage3end_plusp(hit);
best_nmismatches = querylength;
best_prob = 0.0;
for (k = i; k < j; k++) {
@@ -2412,7 +2453,6 @@ group_by_segmenti_aux (int *found_score, List_T winners, List_T *ambiguous,
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,donor_prob,/*acceptor_prob*/prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -2481,7 +2521,6 @@ group_by_segmenti_aux (int *found_score, List_T winners, List_T *ambiguous,
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*donor_prob*/prob,acceptor_prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -2587,7 +2626,6 @@ group_by_segmentj_aux (int *found_score, List_T winners, List_T *ambiguous,
double best_prob, prob, donor_prob, acceptor_prob;
List_T accepted_hits, rejected_hits, donor_hits, acceptor_hits, p;
int donor_length, acceptor_length;
- bool plusp;
int sensedir;
#ifdef LARGE_GENOMES
@@ -2612,7 +2650,6 @@ group_by_segmentj_aux (int *found_score, List_T winners, List_T *ambiguous,
winners = List_push(winners,(void *) hit);
} else {
- plusp = Stage3end_plusp(hit);
best_nmismatches = querylength;
best_prob = 0.0;
for (k = i; k < j; k++) {
@@ -2747,7 +2784,6 @@ group_by_segmentj_aux (int *found_score, List_T winners, List_T *ambiguous,
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,donor_prob,/*acceptor_prob*/prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -2816,7 +2852,6 @@ group_by_segmentj_aux (int *found_score, List_T winners, List_T *ambiguous,
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*donor_prob*/prob,acceptor_prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
diff --git a/src/splice.h b/src/splice.h
index 3f017e5..b7a1a7b 100644
--- a/src/splice.h
+++ b/src/splice.h
@@ -1,4 +1,4 @@
-/* $Id: splice.h 166641 2015-05-29 21:13:04Z twu $ */
+/* $Id: splice.h 184446 2016-02-17 21:19:48Z twu $ */
#ifndef SPLICE_INCLUDED
#define SPLICE_INCLUDED
#include "bool.h"
@@ -25,8 +25,7 @@ Splice_resolve_sense (int *best_knowni_i, int *best_knowni_j,
int *segmentj_antidonor_knowni, int *segmenti_antiacceptor_knowni,
int segmenti_donor_nknown, int segmentj_acceptor_nknown,
int segmentj_antidonor_nknown, int segmenti_antiacceptor_nknown,
- int splicing_penalty, int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p);
+ int max_mismatches_allowed, bool plusp, int genestrand);
extern int
Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
@@ -43,8 +42,7 @@ Splice_resolve_antisense (int *best_knowni_i, int *best_knowni_j,
int *segmentj_antidonor_knowni, int *segmenti_antiacceptor_knowni,
int segmenti_donor_nknown, int segmentj_acceptor_nknown,
int segmentj_antidonor_nknown, int segmenti_antiacceptor_nknown,
- int splicing_penalty, int max_mismatches_allowed,
- bool plusp, int genestrand, bool first_read_p);
+ int max_mismatches_allowed, bool plusp, int genestrand);
extern List_T
Splice_solve_single_sense (int *found_score, int *nhits, List_T hits, List_T *lowprob,
@@ -89,28 +87,6 @@ Splice_solve_single_antisense (int *found_score, int *nhits, List_T hits, List_T
bool subs_or_indels_p, bool sarrayp);
extern List_T
-Splice_solve_double (int *found_score, int *nhits, List_T hits, List_T *lowprob,
-
- bool *segmenti_usedp, bool *segmentm_usedp, bool *segmentj_usedp,
- Univcoord_T segmenti_left, Univcoord_T segmentm_left, Univcoord_T segmentj_left,
- Chrnum_T segmenti_chrnum, Univcoord_T segmenti_chroffset,
- Univcoord_T segmenti_chrhigh, Chrpos_T segmenti_chrlength,
- Chrnum_T segmentm_chrnum, Univcoord_T segmentm_chroffset,
- Univcoord_T segmentm_chrhigh, Chrpos_T segmentm_chrlength,
- Chrnum_T segmentj_chrnum, Univcoord_T segmentj_chroffset,
- Univcoord_T segmentj_chrhigh, Chrpos_T segmentj_chrlength,
-
- int querylength, Compress_T query_compress,
- int *segmenti_donor_knownpos, int *segmentm_acceptor_knownpos, int *segmentm_donor_knownpos, int *segmentj_acceptor_knownpos,
- int *segmentj_antidonor_knownpos, int *segmentm_antiacceptor_knownpos, int *segmentm_antidonor_knownpos, int *segmenti_antiacceptor_knownpos,
- int *segmenti_donor_knowni, int *segmentm_acceptor_knowni, int *segmentm_donor_knowni, int *segmentj_acceptor_knowni,
- int *segmentj_antidonor_knowni, int *segmentm_antiacceptor_knowni, int *segmentm_antidonor_knowni, int *segmenti_antiacceptor_knowni,
- int segmenti_donor_nknown, int segmentm_acceptor_nknown, int segmentm_donor_nknown, int segmentj_acceptor_nknown,
- int segmentj_antidonor_nknown, int segmentm_antiacceptor_nknown, int segmentm_antidonor_nknown, int segmenti_antiacceptor_nknown,
- int splicing_penalty, int max_mismatches_allowed, bool plusp, int genestrand, bool first_read_p,
- bool subs_or_indels_p, bool sarrayp);
-
-extern List_T
Splice_group_by_segmenti (int *found_score, List_T localsplicing, List_T *ambiguous,
int querylength, bool first_read_p, bool sarrayp);
diff --git a/src/splicetrie.c b/src/splicetrie.c
index 36a0fdd..d06520b 100644
--- a/src/splicetrie.c
+++ b/src/splicetrie.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splicetrie.c 145990 2014-08-25 21:47:32Z twu $";
+static char rcsid[] = "$Id: splicetrie.c 184475 2016-02-18 00:13:10Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -336,10 +336,10 @@ solve_end5_aux (Univcoord_T **coordsptr, Univcoord_T *coords,
}
if ((pairs = Dynprog_end5_splicejunction(&(*dynprogindex),&score,&miss_score,&nmatches0,&nmismatches0,
&nopens0,&nindels0,dynprog,revsequence1,revsequenceuc1,
- /*revsequence2*/&(splicejunction[length2-1]),/*revsequenceuc2*/&(splicejunction[length2-1]),
+ /*revsequence2*/&(splicejunction[length2-1]),
/*revsequencealt2*/&(splicejunction_alt[length2-1]),
length1,length2,revoffset1,spliceoffset2_anchor,spliceoffset2_far,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,contlength)) != NULL) {
/* miss_score = perfect_score - score; */
@@ -432,10 +432,10 @@ solve_end5_aux (Univcoord_T **coordsptr, Univcoord_T *coords,
}
if ((pairs = Dynprog_end5_splicejunction(&(*dynprogindex),&score,&miss_score,&nmatches0,&nmismatches0,
&nopens0,&nindels0,dynprog,revsequence1,revsequenceuc1,
- /*revsequence2*/&(splicejunction[length2-1]),/*revsequenceuc2*/&(splicejunction[length2-1]),
+ /*revsequence2*/&(splicejunction[length2-1]),
/*revsequencealt2*/&(splicejunction_alt[length2-1]),
length1,length2,revoffset1,spliceoffset2_anchor,spliceoffset2_far,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,contlength)) != NULL) {
/* miss_score = perfect_score - score; */
@@ -614,10 +614,9 @@ solve_end3_aux (Univcoord_T **coordsptr, Univcoord_T *coords,
}
if ((pairs = Dynprog_end3_splicejunction(&(*dynprogindex),&score,&miss_score,&nmatches0,&nmismatches0,
&nopens0,&nindels0,dynprog,sequence1,sequenceuc1,
- /*sequence2*/splicejunction,/*sequenceuc2*/splicejunction,
- /*sequencealt2*/splicejunction_alt,
+ /*sequence2*/splicejunction,/*sequencealt2*/splicejunction_alt,
length1,length2,offset1,spliceoffset2_anchor,spliceoffset2_far,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,contlength)) != NULL) {
/* miss_score = perfect_score - score; */
@@ -708,10 +707,9 @@ solve_end3_aux (Univcoord_T **coordsptr, Univcoord_T *coords,
}
if ((pairs = Dynprog_end3_splicejunction(&(*dynprogindex),&score,&miss_score,&nmatches0,&nmismatches0,
&nopens0,&nindels0,dynprog,sequence1,sequenceuc1,
- /*sequence2*/splicejunction,/*sequenceuc2*/splicejunction,
- /*sequencealt2*/splicejunction_alt,
+ /*sequence2*/splicejunction,/*sequencealt2*/splicejunction_alt,
length1,length2,offset1,spliceoffset2_anchor,spliceoffset2_far,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,contlength)) != NULL) {
/* miss_score = perfect_score - score; */
@@ -1455,7 +1453,7 @@ search_left (int *best_nmismatches, Intlist_T *nmismatches_list, Intlist_T splic
/* Can happen in search for short middle exon */
segment_left = splicesites[leaf] - pos3;
nmismatches =
- Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand,first_read_p);
+ Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand);
}
debug2(printf("Found leaf %u at %u, but still have characters to check against Genome: %.*s => %d mismatches\n",
@@ -1527,7 +1525,7 @@ search_left (int *best_nmismatches, Intlist_T *nmismatches_list, Intlist_T splic
/* Can happen in search for short middle exon */
segment_left = splicesites[leaf] - pos3;
nmismatches =
- Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand,first_read_p);
+ Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand);
}
debug2(printf("Found leaf %u at %u => %d mismatches\n",leaf,position,nmismatches));
@@ -1666,7 +1664,7 @@ search_right (int *best_nmismatches, Intlist_T *nmismatches_list, Intlist_T spli
/* Can happen in search for short middle exon */
segment_left = splicesites[leaf] - pos5;
nmismatches =
- Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand,first_read_p);
+ Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand);
}
debug2(printf("Found leaf %u at %u => %d mismatches\n",leaf,position,nmismatches));
@@ -1737,7 +1735,7 @@ search_right (int *best_nmismatches, Intlist_T *nmismatches_list, Intlist_T spli
/* Can happen in search for short middle exon */
segment_left = splicesites[leaf] - pos5;
nmismatches =
- Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand,first_read_p);
+ Genome_count_mismatches_substring(query_compress,segment_left,pos5,pos3,plusp,genestrand);
}
debug2(printf("Found leaf %u at %u => %d mismatches\n",leaf,position,nmismatches));
@@ -1892,7 +1890,7 @@ Splicetrie_find_left (int *best_nmismatches, Intlist_T *nmismatches_list, int i,
}
nmismatches_int =
- Genome_count_mismatches_substring(query_compress,origleft,pos3,spliceregion,plusp,genestrand,first_read_p);
+ Genome_count_mismatches_substring(query_compress,origleft,pos3,spliceregion,plusp,genestrand);
debug2(printf(" internal at %u => %d nmismatches/%d\n",
origleft,nmismatches_int,SPLICE_REGION));
if (nmismatches_int > SPLICE_REGION_MISMATCHES) {
@@ -2091,7 +2089,7 @@ Splicetrie_find_right (int *best_nmismatches, Intlist_T *nmismatches_list, int i
}
nmismatches_int =
- Genome_count_mismatches_substring(query_compress,origleft,spliceregion,pos5,plusp,genestrand,first_read_p);
+ Genome_count_mismatches_substring(query_compress,origleft,spliceregion,pos5,plusp,genestrand);
debug2(printf(" internal at %u => %d nmismatches/%d\n",
origleft,nmismatches_int,SPLICE_REGION));
if (nmismatches_int > SPLICE_REGION_MISMATCHES) {
diff --git a/src/splicetrie_build.c b/src/splicetrie_build.c
index 2908e80..d764328 100644
--- a/src/splicetrie_build.c
+++ b/src/splicetrie_build.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: splicetrie_build.c 135656 2014-05-09 01:47:27Z twu $";
+static char rcsid[] = "$Id: splicetrie_build.c 184476 2016-02-18 00:13:26Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -56,12 +56,6 @@ Splicetype_string (Splicetype_T splicetype) {
}
-#define RIGHT_A 0x00
-#define RIGHT_C 0x01
-#define RIGHT_G 0x02
-#define RIGHT_T 0x03
-
-
/* 87654321 */
#define LOW_TWO_BITS 0x00000003
@@ -129,7 +123,7 @@ Splicetrie_dump (Trieoffset_T *triestart, Univcoord_T *splicesites,
if (single_leaf_p(leaf = triestart[0])) {
position = splicesites[leaf];
- printf("%d %u",(int) leaf,position);
+ printf("%d %llu",(int) leaf,(unsigned long long) position);
if (splicetype == DONOR || splicetype == ANTIACCEPTOR) {
splicefrag_nt_rightward(gbuffer,splicefrags_ref[leaf]);
printf(" %s (rightward)\n",gbuffer);
@@ -143,7 +137,7 @@ Splicetrie_dump (Trieoffset_T *triestart, Univcoord_T *splicesites,
for (i = 1; i <= nleaves; i++) {
leaf = triestart[i];
position = splicesites[leaf];
- printf("%d %u",(int) leaf,position);
+ printf("%d %llu",(int) leaf,(unsigned long long) position);
if (splicetype == DONOR || splicetype == ANTIACCEPTOR) {
splicefrag_nt_rightward(gbuffer,splicefrags_ref[leaf]);
printf(" %s (rightward)\n",gbuffer);
@@ -182,11 +176,11 @@ Splicetrie_dump (Trieoffset_T *triestart, Univcoord_T *splicesites,
/* 87654321 */
-#define LEFT_A 0x00000000
-#define LEFT_C 0x40000000
-#define LEFT_G 0x80000000
-#define LEFT_T 0xC0000000
-#define HIGH2 0xC0000000
+#define UINT4_LEFT_A 0x00000000
+#define UINT4_LEFT_C 0x40000000
+#define UINT4_LEFT_G 0x80000000
+#define UINT4_LEFT_T 0xC0000000
+#define UINT4_HIGH2 0xC0000000
/* Puts leftmost character into lowest bits */
@@ -204,9 +198,9 @@ compress16 (bool *saw_n_p, char *buffer) {
low >>= 2;
switch (c) {
case 'A': break;
- case 'C': low |= LEFT_C; break;
- case 'G': low |= LEFT_G; break;
- case 'T': low |= LEFT_T; break;
+ case 'C': low |= UINT4_LEFT_C; break;
+ case 'G': low |= UINT4_LEFT_G; break;
+ case 'T': low |= UINT4_LEFT_T; break;
default: *saw_n_p = true; break;
}
}
@@ -345,8 +339,8 @@ allelic_combinations (Genomecomp_T refstring, Genomecomp_T altstring, Genomecomp
for (i = 0; i < 16; i++) {
newcombinations = NULL;
- refc = (refstring & HIGH2) >> 30;
- altc = (altstring & HIGH2) >> 30;
+ refc = (refstring & UINT4_HIGH2) >> 30;
+ altc = (altstring & UINT4_HIGH2) >> 30;
refstring <<= 2;
altstring <<= 2;
if (refc != altc) {
@@ -403,7 +397,8 @@ Splicetrie_retrieve_via_splicesites (bool *distances_observed_p,
Interval_T *intervals, interval;
struct Interval_T *interval_structs;
char gbuffer_ref[17], gbuffer_alt[17], *chr;
- char *restofheader, *annot;
+ char *restofheader;
+ /* char *annot; */
bool firstp = true, saw_n_p, allocp, alloc_header_p;
int ntoolong = 0;
@@ -425,7 +420,7 @@ Splicetrie_retrieve_via_splicesites (bool *distances_observed_p,
0U,chrlength-1U,/*sortp*/false);
if (nsplicesites1 > 0) {
if (firstp == true) {
- annot = IIT_annotation(&restofheader,splicing_iit,splicesites1[0],&alloc_header_p);
+ /* annot = */ IIT_annotation(&restofheader,splicing_iit,splicesites1[0],&alloc_header_p);
if (restofheader[0] == '\0') {
fprintf(stderr,"splice distances absent...");
*distances_observed_p = false;
@@ -546,7 +541,7 @@ Splicetrie_retrieve_via_splicesites (bool *distances_observed_p,
/* No, want to have essentially zero distance */
/* Interval_store_length(intervals[i],shortsplicedist); */
} else {
- annot = IIT_annotation(&restofheader,splicing_iit,splicesites1[i],&alloc_header_p);
+ /* annot = */ IIT_annotation(&restofheader,splicing_iit,splicesites1[i],&alloc_header_p);
if (sscanf(restofheader,"%d",&distance) != 1) {
fprintf(stderr,"splicesites file missing distance in entry %s...exiting\n",
IIT_label(splicing_iit,splicesites1[i],&allocp));
@@ -1236,6 +1231,7 @@ Splicetrie_retrieve_via_introns (
}
+#if 0
static bool
get_exons (Uintlist_T *donors, Uintlist_T *acceptors, char *annot) {
Chrpos_T exonstart, exonend;
@@ -1274,8 +1270,7 @@ get_exons (Uintlist_T *donors, Uintlist_T *acceptors, char *annot) {
return true;
}
}
-
-
+#endif
/************************************************************************/
@@ -1386,7 +1381,7 @@ Trie_new (Splicestring_T *sites, int nsites, int charpos) {
static int
Trie_output_size (int size, Splicestring_T *sites, int nsites, int charpos) {
int i, k;
- unsigned int posa, posc, posg, post;
+ /* unsigned int posa, posc, posg, post; */
int na, nc, ng, nt;
if (nsites == 0) {
diff --git a/src/stage1.c b/src/stage1.c
index 51d75b1..abd678d 100644
--- a/src/stage1.c
+++ b/src/stage1.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage1.c 173039 2015-08-31 19:12:10Z twu $";
+static char rcsid[] = "$Id: stage1.c 184461 2016-02-18 00:07:47Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -178,17 +178,15 @@ static Width_T index1part_aa;
static int leftreadshift;
static Chrpos_T maxextension;
static Chrpos_T maxtotallen_bound;
-static int min_extra_end;
static int circular_typeint;
void
Stage1_setup (Width_T index1part_aa_in, Chrpos_T maxextension_in, Chrpos_T maxtotallen_bound_in,
- int min_extra_end_in, int circular_typeint_in) {
+ int circular_typeint_in) {
index1part_aa = index1part_aa_in;
leftreadshift = 32 - 2*index1part_aa_in; /* chars are shifted into left of a 32 bit word */
maxextension = maxextension_in;
maxtotallen_bound = maxtotallen_bound_in;
- min_extra_end = min_extra_end_in;
circular_typeint = circular_typeint_in;
return;
}
@@ -198,19 +196,22 @@ static Width_T index1part;
static int leftreadshift;
static Chrpos_T maxextension;
static Chrpos_T maxtotallen_bound;
-static int min_extra_end;
-static Storedoligomer_T oligobase_mask;
+static Oligospace_T oligobase_mask;
static int circular_typeint;
void
Stage1_setup (Width_T index1part_in, Chrpos_T maxextension_in, Chrpos_T maxtotallen_bound_in,
- int min_extra_end_in, int circular_typeint_in) {
+ int circular_typeint_in) {
index1part = index1part_in;
- leftreadshift = 32 - 2*index1part_in; /* chars are shifted into left of a 32 bit word */
- oligobase_mask = ~(~0UL << 2*index1part_in);
+#ifdef HAVE_64_BIT
+ leftreadshift = 64 - 2*index1part_in; /* chars are shifted into left of a 64-bit word */
+ oligobase_mask = ~(~0ULL << 2*index1part_in);
+#else
+ leftreadshift = 32 - 2*index1part_in; /* chars are shifted into left of a 32-bit word */
+ oligobase_mask = ~(~0U << 2*index1part_in);
+#endif
maxextension = maxextension_in;
maxtotallen_bound = maxtotallen_bound_in;
- min_extra_end = min_extra_end_in;
circular_typeint = circular_typeint_in;
return;
}
@@ -245,10 +246,10 @@ struct T {
int queryend; /* Changes during computation */
#ifdef PMAP
- Storedoligomer_T *oligos;
+ Oligospace_T *oligos;
#else
- Storedoligomer_T *forward_oligos;
- Storedoligomer_T *revcomp_oligos;
+ Oligospace_T *forward_oligos;
+ Oligospace_T *revcomp_oligos;
#endif
};
@@ -350,10 +351,10 @@ Stage1_new (Sequence_T queryuc, int maxtotallen, int maxentries) {
new->validp = (bool *) NULL;
#ifdef PMAP
- new->oligos = (Storedoligomer_T *) NULL;
+ new->oligos = (Oligospace_T *) NULL;
#else
- new->forward_oligos = (Storedoligomer_T *) NULL;
- new->revcomp_oligos = (Storedoligomer_T *) NULL;
+ new->forward_oligos = (Oligospace_T *) NULL;
+ new->revcomp_oligos = (Oligospace_T *) NULL;
#endif
return new;
@@ -481,18 +482,18 @@ connectable_p (Match_T match5, Match_T match3, int maxtotallen) {
/* This procedure is called a lot. Replacing calls to Match_npairings and so on with direct calls to Match_T object */
/* Updates a list of Stage1_T objects */
static List_T
-pair_up (bool *foundpairp, List_T gregionlist, Width_T matchsize, Width_T oligosize,
+pair_up (bool *foundpairp, List_T gregionlist, Width_T matchsize,
List_T newmatches5, List_T newmatches3, List_T matches5, List_T matches3,
int genestrand, Univ_IIT_T chromosome_iit, int querylength,
int maxtotallen, int trimstart, int trimend, int trimlength) {
List_T p, q, s, new_gregions = NULL;
Match_T match5, match3;
- Width_T matchinterval;
+ /* Width_T matchinterval; */
#ifdef DEBUG
Gregion_T gregion;
#endif
- matchinterval = matchsize - oligosize;
+ /* matchinterval = matchsize - oligosize; */
/* Do N vs N */
for (q = newmatches5; q != NULL; q = q->rest) {
@@ -600,16 +601,16 @@ pair_up (bool *foundpairp, List_T gregionlist, Width_T matchsize, Width_T oligos
#if 0
static bool
-repetitivep (Storedoligomer_T oligo, int oligosize) {
+repetitivep (Oligospace_T oligo, int oligosize) {
int i;
- oligos = (Storedoligomer_T *) CALLOC(this->querylength,sizeof(Storedoligomer_T));
+ oligos = (Oligospace_T *) CALLOC(this->querylength,sizeof(Oligospace_T));
for (querypos = 0; querypos <= this->querylength - this->oligobase; querypos++) {
if (this->validp[querypos] == true) {
oligos[k++] = this->forward_oligos[querypos];
}
}
- qsort(oligos,k,sizeof(Storedoligomer_T),Storedoligomer_compare);
+ qsort(oligos,k,sizeof(Oligospace_T),Oligospace_compare);
for (i = 0, j = 1; j < k; i++, j++) {
if (oligos[j] == oligos[i]) {
@@ -1179,14 +1180,14 @@ find_5prime_matches (int *nnew, List_T matches5, T this, Width_T matchsize,
Width_T merstart; /* Note: negative values must be allowed */
int nnewplus = 0, nnewminus = 0;
bool overflowp;
- Width_T matchinterval, matchinterval_nt;
+ Width_T matchinterval;
#ifdef PMAP
matchinterval = matchsize - index1part_aa;
- matchinterval_nt = matchinterval*3;
+ /*matchinterval_nt = matchinterval*3; */
#else
matchinterval = matchsize - index1part;
- matchinterval_nt = matchinterval;
+ /* matchinterval_nt = matchinterval; */
#endif
if ((merstart = querystart - matchinterval) < 0) {
@@ -1237,14 +1238,14 @@ find_3prime_matches (int *nnew, List_T matches3, T this, Width_T matchsize,
Width_T merstart;
int nnewplus = 0, nnewminus = 0;
bool overflowp;
- Width_T matchinterval, matchinterval_nt;
+ Width_T matchinterval;
#ifdef PMAP
matchinterval = matchsize - index1part_aa;
- matchinterval_nt = matchinterval*3;
+ /* matchinterval_nt = matchinterval*3; */
#else
matchinterval = matchsize - index1part;
- matchinterval_nt = matchinterval;
+ /* matchinterval_nt = matchinterval; */
#endif
if (queryend + matchsize > querylength) {
@@ -1431,7 +1432,7 @@ stutter (List_T gregionlist, T this, Width_T matchsize,
debug(printf("*** Ending stutter ***\n"));
- gregionlist = pair_up(&foundpairp,gregionlist,matchsize,this->oligosize,newmatches5,newmatches3,
+ gregionlist = pair_up(&foundpairp,gregionlist,matchsize,newmatches5,newmatches3,
this->matches5,this->matches3,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
this->trimstart,this->trimend,this->trimlength);
@@ -1492,7 +1493,7 @@ fill_in_5 (List_T gregionlist, T this, Width_T matchsize, List_T dangling3,
fillindist5 = Block_querypos(this->block5) - start5;
if (nnew > 0) {
- gregionlist = pair_up(&foundpairp,gregionlist,matchsize,this->oligosize,
+ gregionlist = pair_up(&foundpairp,gregionlist,matchsize,
newmatches5,/*newmatches3*/(List_T) NULL,
(List_T) NULL,dangling3,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
@@ -1502,7 +1503,7 @@ fill_in_5 (List_T gregionlist, T this, Width_T matchsize, List_T dangling3,
}
/* Mark newmatches5 as being pairedp if they match non-dangling matches3 */
- gregionlist = pair_up(&foundpairp,gregionlist,matchsize,this->oligosize,
+ gregionlist = pair_up(&foundpairp,gregionlist,matchsize,
newmatches5,/*newmatches3*/(List_T) NULL,
(List_T) NULL,this->matches3,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
@@ -1564,7 +1565,7 @@ fill_in_3 (List_T gregionlist, T this, Width_T matchsize, List_T dangling5,
fillindist3 = start3 - Block_querypos(this->block3);
if (nnew > 0) {
- gregionlist = pair_up(&foundpairp,gregionlist,matchsize,this->oligosize,
+ gregionlist = pair_up(&foundpairp,gregionlist,matchsize,
/*newmatches5*/(List_T) NULL,newmatches3,
dangling5,(List_T) NULL,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
@@ -1574,7 +1575,7 @@ fill_in_3 (List_T gregionlist, T this, Width_T matchsize, List_T dangling5,
}
/* Mark newmatches3 as being pairedp if they match non-dangling matches5 */
- gregionlist = pair_up(&foundpairp,gregionlist,matchsize,this->oligosize,
+ gregionlist = pair_up(&foundpairp,gregionlist,matchsize,
/*newmatches5*/(List_T) NULL,newmatches3,
this->matches5,(List_T) NULL,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
@@ -1920,7 +1921,7 @@ static List_T
find_first_pair (bool *foundpairp, List_T gregionlist, T this, Width_T matchsize,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int genestrand,
Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end,
- Matchpool_T matchpool, int maxattempts) {
+ Matchpool_T matchpool) {
List_T newmatches5 = NULL, newmatches3 = NULL;
bool donep = false;
int nnew;
@@ -1976,7 +1977,7 @@ find_first_pair (bool *foundpairp, List_T gregionlist, T this, Width_T matchsize
if (nnew > 0) {
n5hits += 1.0/(double) (1 + nnew);
debug(printf(" n5hits: %.1f, n3hits: %.1f\n",n5hits,n3hits));
- gregionlist = pair_up(&(*foundpairp),gregionlist,matchsize,this->oligosize,
+ gregionlist = pair_up(&(*foundpairp),gregionlist,matchsize,
newmatches5,/*newmatches3*/NULL,
this->matches5,this->matches3,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
@@ -2024,7 +2025,7 @@ find_first_pair (bool *foundpairp, List_T gregionlist, T this, Width_T matchsize
if (nnew > 0) {
n3hits += 1.0/(double) (1 + nnew);
debug(printf(" n5hits: %.1f, n3hits: %.1f\n",n5hits,n3hits));
- gregionlist = pair_up(&(*foundpairp),gregionlist,matchsize,this->oligosize,
+ gregionlist = pair_up(&(*foundpairp),gregionlist,matchsize,
/*newmatches5*/NULL,newmatches3,
this->matches5,this->matches3,genestrand,chromosome_iit,
this->querylength,this->maxtotallen,
@@ -2115,22 +2116,22 @@ read_oligos (T this, Sequence_T queryuc) {
int querypos;
Oligostate_T last_state = INIT;
#ifdef PMAP
- unsigned int aaindex = 0U;
+ Oligospace_T aaindex = 0U;
#else
- Storedoligomer_T forward = 0U, revcomp = 0U;
+ Oligospace_T forward = 0U, revcomp = 0U;
#endif
this->validp = (bool *) CALLOC(this->querylength,sizeof(bool));
#ifdef PMAP
- this->oligos = (Storedoligomer_T *) CALLOC(this->querylength,sizeof(Storedoligomer_T));
+ this->oligos = (Oligospace_T *) CALLOC(this->querylength,sizeof(Oligospace_T));
reader = Reader_new(Sequence_fullpointer(queryuc),/*querystart*/0,/*queryend*/this->querylength);
/* Prevents us from processing invalid query 12-mers */
for (querypos = 0; querypos <= this->querylength - index1part_aa; querypos++) {
this->validp[querypos] = false;
}
#else
- this->forward_oligos = (Storedoligomer_T *) CALLOC(this->querylength,sizeof(Storedoligomer_T));
- this->revcomp_oligos = (Storedoligomer_T *) CALLOC(this->querylength,sizeof(Storedoligomer_T));
+ this->forward_oligos = (Oligospace_T *) CALLOC(this->querylength,sizeof(Oligospace_T));
+ this->revcomp_oligos = (Oligospace_T *) CALLOC(this->querylength,sizeof(Oligospace_T));
reader = Reader_new(Sequence_fullpointer(queryuc),/*querystart*/0,/*queryend*/this->querylength);
debug(printf("oligobase is %d, oligobase_mask is %08X\n",index1part,oligobase_mask));
/* Prevents us from processing invalid query 12-mers */
@@ -2171,7 +2172,7 @@ read_oligos (T this, Sequence_T queryuc) {
struct Rep_T {
- Storedoligomer_T oligo;
+ Oligospace_T oligo;
int querypos;
};
@@ -2394,6 +2395,33 @@ sample_oligos_sizelimit (T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, i
static void
+sample_oligos_nolimit (T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int querylength, int oligobase) {
+ int querypos;
+
+ for (querypos = 0; querypos < querylength - oligobase; querypos++) {
+ /* FORMULA */
+ if (this->validp[querypos] == true && this->processedp[querypos] == false) {
+ this->plus_positions[querypos] =
+ Indexdb_read_with_diagterm(&(this->plus_npositions[querypos]),indexdb_fwd,this->forward_oligos[querypos],
+ /*diagterm*/querylength-querypos);
+
+ this->minus_positions[querypos] =
+ Indexdb_read_with_diagterm(&(this->minus_npositions[querypos]),indexdb_rev,this->revcomp_oligos[querypos],
+ /*diagterm*/querypos + index1part);
+
+ debug(printf("Sampling at querypos %d, plus_npositions = %d, minus_npositions = %d\n",
+ querypos,this->plus_npositions[querypos],this->minus_npositions[querypos]));
+ this->processedp[querypos] = true;
+ }
+ }
+
+ return;
+}
+#endif
+
+
+#if 0
+static void
sample_oligos_findlimit (T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int querylength, int oligobase) {
int querypos;
@@ -2440,31 +2468,6 @@ sample_oligos_findlimit (T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, i
return;
}
-
-
-static void
-sample_oligos_nolimit (T this, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int querylength, int oligobase) {
- int querypos;
-
- for (querypos = 0; querypos < querylength - oligobase; querypos++) {
- /* FORMULA */
- if (this->validp[querypos] == true && this->processedp[querypos] == false) {
- this->plus_positions[querypos] =
- Indexdb_read_with_diagterm(&(this->plus_npositions[querypos]),indexdb_fwd,this->forward_oligos[querypos],
- /*diagterm*/querylength-querypos);
-
- this->minus_positions[querypos] =
- Indexdb_read_with_diagterm(&(this->minus_npositions[querypos]),indexdb_rev,this->revcomp_oligos[querypos],
- /*diagterm*/querypos + index1part);
-
- debug(printf("Sampling at querypos %d, plus_npositions = %d, minus_npositions = %d\n",
- querypos,this->plus_npositions[querypos],this->minus_npositions[querypos]));
- this->processedp[querypos] = true;
- }
- }
-
- return;
-}
#endif
@@ -2533,8 +2536,7 @@ struct Segment_T {
/* Reduces diagonals to handle small indels */
static void
-collapse_diagonals (Univcoord_T **diagonals, int *ndiagonals,
- Storedoligomer_T *oligos, int oligobase, int querylength) {
+collapse_diagonals (Univcoord_T **diagonals, int *ndiagonals, int oligobase, int querylength) {
Batch_T batch, *heap, sentinel;
struct Batch_T sentinel_struct, *batchpool;
int maxsegments, heapsize = 0, i;
@@ -2682,8 +2684,7 @@ collapse_diagonals (Univcoord_T **diagonals, int *ndiagonals,
static struct Segment_T *
find_segments (int *nsegments, Univcoord_T **diagonals, int *ndiagonals,
- Storedoligomer_T *oligos, int oligobase, int querylength,
- int threshold_score, bool plusp) {
+ int oligobase, int querylength, int threshold_score) {
struct Segment_T *segments, *ptr;
Batch_T batch, *heap, sentinel;
struct Batch_T sentinel_struct, *batchpool;
@@ -3328,7 +3329,7 @@ find_good_paths (List_T gregionlist, int nexons, int *prev, int *scores,
if (plusp == true) {
querystart = segments[besti].querypos5;
queryend = segments[bestj].querypos3;
- if (segments[besti].diagonal + querystart > querylength) {
+ if (segments[besti].diagonal + querystart > (Univcoord_T) querylength) {
genomicstart = segments[besti].diagonal + querystart - querylength;
genomicend = segments[bestj].diagonal + queryend - querylength;
debug9(printf("Pushing gregion for %d plus: %d..%d: %u..%u, score=%d\n",
@@ -3348,7 +3349,7 @@ find_good_paths (List_T gregionlist, int nexons, int *prev, int *scores,
} else if (plusp == false) {
querystart = segments[bestj].querypos5;
queryend = segments[besti].querypos3;
- if (segments[besti].diagonal > queryend) {
+ if (segments[besti].diagonal > (Univcoord_T) queryend) {
genomicstart = segments[besti].diagonal - queryend;
genomicend = segments[bestj].diagonal - querystart;
debug9(printf("Pushing gregion for %d minus: %d..%d: %u..%u, score=%d\n",
@@ -3392,7 +3393,6 @@ scan_ends (bool *shortseqp, bool second_pass_p, List_T oldlist, T this,
List_T dangling5, dangling3;
bool foundpairp = false, loopp = true;
Width_T matchsize;
- int maxattempts = MAX_ATTEMPTS_UNIT;
debug(printf("Starting scan_ends\n"));
@@ -3425,7 +3425,7 @@ scan_ends (bool *shortseqp, bool second_pass_p, List_T oldlist, T this,
while (loopp && matchsize >= this->oligosize && foundpairp == false) {
newlist = find_first_pair(&foundpairp,newlist,this,matchsize,
indexdb_fwd,indexdb_rev,genestrand,chromosome_iit,
- chrsubset_start,chrsubset_end,matchpool,maxattempts);
+ chrsubset_start,chrsubset_end,matchpool);
if (matchsize == this->oligosize) {
loopp = false;
} else if (foundpairp == false) {
@@ -3438,7 +3438,6 @@ scan_ends (bool *shortseqp, bool second_pass_p, List_T oldlist, T this,
matchsize = this->oligosize;
}
#endif
- maxattempts += MAX_ATTEMPTS_UNIT;
stutterhits *= 2;
}
if (iteratep == false) {
@@ -3542,7 +3541,7 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
List_T gregionlist = NULL, p, q;
T this = NULL;
int trimlength, trimstart, trimend, maxentries, i;
- Width_T matchsize;
+ /* Width_T matchsize; */
Chrpos_T maxtotallen;
Univcoord_T extension5, extension3;
Gregion_T gregion;
@@ -3597,9 +3596,9 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
/* Scan ends (find first pair and stutter) */
#ifdef PMAP
- matchsize = index1part_aa + index1part_aa;
+ /* matchsize = index1part_aa + index1part_aa; */
#else
- matchsize = 24 /* Was index1part + index1part. matchsize now set in scan_ends */;
+ /* matchsize = 24 */ /* Was index1part + index1part. matchsize now set in scan_ends */;
#endif
maxentries = MAXENTRIES;
@@ -3658,30 +3657,30 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
debug(printf("Starting sample_oligos\n"));
#ifdef PMAP
sample_oligos(this,indexdb_fwd,indexdb_rev,this->querylength,/*oligobase*/index1part_aa);
- collapse_diagonals(this->plus_positions,this->plus_npositions,this->oligos,
+ collapse_diagonals(this->plus_positions,this->plus_npositions,
/*oligobase*/index1part_aa,this->querylength);
plus_segments = find_segments(&plus_nsegments,this->plus_positions,this->plus_npositions,
- this->oligos,/*oligobase*/index1part_aa,this->querylength,
- /*threshold_score*/27,/*plusp*/true);
- collapse_diagonals(this->minus_positions,this->minus_npositions,this->oligos,
+ /*oligobase*/index1part_aa,this->querylength,
+ /*threshold_score*/27);
+ collapse_diagonals(this->minus_positions,this->minus_npositions,
/*oligobase*/index1part_aa,this->querylength);
minus_segments = find_segments(&minus_nsegments,this->minus_positions,this->minus_npositions,
- this->oligos,/*oligobase*/index1part_aa,this->querylength,
- /*threshold_score*/27,/*plusp*/false);
+ /*oligobase*/index1part_aa,this->querylength,
+ /*threshold_score*/27);
#else
sample_oligos_sizelimit(this,indexdb_fwd,indexdb_rev,this->querylength,/*oligobase*/index1part,
indexdb_size_threshold);
- collapse_diagonals(this->plus_positions,this->plus_npositions,this->forward_oligos,
+ collapse_diagonals(this->plus_positions,this->plus_npositions,
/*oligobase*/index1part,this->querylength);
plus_segments = find_segments(&plus_nsegments,this->plus_positions,this->plus_npositions,
- this->forward_oligos,/*oligobase*/index1part,this->querylength,
- /*threshold_score*/18,/*plusp*/true);
+ /*oligobase*/index1part,this->querylength,
+ /*threshold_score*/18);
- collapse_diagonals(this->minus_positions,this->minus_npositions,this->revcomp_oligos,
+ collapse_diagonals(this->minus_positions,this->minus_npositions,
/*oligobase*/index1part,this->querylength);
minus_segments = find_segments(&minus_nsegments,this->minus_positions,this->minus_npositions,
- this->revcomp_oligos,/*oligobase*/index1part,this->querylength,
- /*threshold_score*/18,/*plusp*/false);
+ /*oligobase*/index1part,this->querylength,
+ /*threshold_score*/18);
#endif
maxexons = 3;
@@ -3731,7 +3730,7 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
if (Gregion_extendedp(gregion) == false) {
/* Need to extend, otherwise we won't align NM_003360 */
find_extensions(&extension5,&extension3,this,gregion,this->maxtotallen,/*continuousp*/false);
- Gregion_extend(gregion,extension5,extension3,this->querylength,min_extra_end);
+ Gregion_extend(gregion,extension5,extension3,this->querylength);
}
}
debug(printf("Finished with extensions\n"));
@@ -3836,15 +3835,13 @@ Stage1_compute (bool *lowidentityp, Sequence_T queryuc, Indexdb_T indexdb_fwd, I
List_T
Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
- int indexdb_size_threshold, Univ_IIT_T chromosome_iit,
- Univcoord_T chrsubset_start, Univcoord_T chrsubset_end,
+ Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end,
Matchpool_T matchpool, int stutterhits, Diagnostic_T diagnostic, Stopwatch_T stopwatch,
int nbest) {
List_T gregionlist = NULL, p, q;
T this_fwd = NULL, this_rev = NULL;
Sequence_T queryrc;
int trimlength, trimstart, trimend, maxentries, i;
- Width_T matchsize;
Chrpos_T maxtotallen;
Univcoord_T extension5, extension3;
Gregion_T gregion;
@@ -3883,9 +3880,9 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
/* FWD */
#ifdef PMAP
- matchsize = index1part_aa + index1part_aa;
+ /* matchsize = index1part_aa + index1part_aa; */
#else
- matchsize = 24 /* Was index1part + index1part. matchsize now set in scan_ends */;
+ /* matchsize = 24 */ /* Was index1part + index1part. matchsize now set in scan_ends */;
#endif
maxentries = MAXENTRIES;
@@ -4013,31 +4010,31 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
#ifdef PMAP
debug(printf("Starting sample_oligos, fwd\n"));
sample_oligos_nolimit(this_fwd,indexdb_fwd,indexdb_fwd,this_fwd->querylength,/*oligobase*/index1part_aa);
- collapse_diagonals(this_fwd->plus_positions,this_fwd->plus_npositions,this_fwd->oligos,
+ collapse_diagonals(this_fwd->plus_positions,this_fwd->plus_npositions,
/*oligobase*/index1part_aa,this_fwd->querylength);
plus_segments_fwd = find_segments(&plus_nsegments_fwd,this_fwd->plus_positions,this_fwd->plus_npositions,
- this_fwd->oligos,/*oligobase*/index1part_aa,this_fwd->querylength,
- /*threshold_score*/18,/*plusp*/true);
+ /*oligobase*/index1part_aa,this_fwd->querylength,
+ /*threshold_score*/18);
- collapse_diagonals(this_fwd->minus_positions,this_fwd->minus_npositions,this_fwd->oligos,
+ collapse_diagonals(this_fwd->minus_positions,this_fwd->minus_npositions,
/*oligobase*/index1part_aa,this_fwd->querylength);
minus_segments_fwd = find_segments(&minus_nsegments_fwd,this_fwd->minus_positions,this_fwd->minus_npositions,
- this_fwd->oligos,/*oligobase*/index1part_aa,this_fwd->querylength,
- /*threshold_score*/18,/*plusp*/false);
+ /*oligobase*/index1part_aa,this_fwd->querylength,
+ /*threshold_score*/18);
#else
debug(printf("Starting sample_oligos, fwd\n"));
sample_oligos_nolimit(this_fwd,indexdb_fwd,indexdb_fwd,this_fwd->querylength,/*oligobase*/index1part);
- collapse_diagonals(this_fwd->plus_positions,this_fwd->plus_npositions,this_fwd->forward_oligos,
+ collapse_diagonals(this_fwd->plus_positions,this_fwd->plus_npositions,
/*oligobase*/index1part,this_fwd->querylength);
plus_segments_fwd = find_segments(&plus_nsegments_fwd,this_fwd->plus_positions,this_fwd->plus_npositions,
- this_fwd->forward_oligos,/*oligobase*/index1part,this_fwd->querylength,
- /*threshold_score*/18,/*plusp*/true);
+ /*oligobase*/index1part,this_fwd->querylength,
+ /*threshold_score*/18);
- collapse_diagonals(this_fwd->minus_positions,this_fwd->minus_npositions,this_fwd->revcomp_oligos,
+ collapse_diagonals(this_fwd->minus_positions,this_fwd->minus_npositions,
/*oligobase*/index1part,this_fwd->querylength);
minus_segments_fwd = find_segments(&minus_nsegments_fwd,this_fwd->minus_positions,this_fwd->minus_npositions,
- this_fwd->revcomp_oligos,/*oligobase*/index1part,this_fwd->querylength,
- /*threshold_score*/18,/*plusp*/false);
+ /*oligobase*/index1part,this_fwd->querylength,
+ /*threshold_score*/18);
#endif
maxexons = 3;
@@ -4056,31 +4053,31 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
#ifdef PMAP
debug(printf("Starting sample_oligos, rev\n"));
sample_oligos_nolimit(this_rev,indexdb_rev,indexdb_rev,this_rev->querylength,/*oligobase*/index1part_aa);
- collapse_diagonals(this_rev->plus_positions,this_rev->plus_npositions,this_rev->oligos,
+ collapse_diagonals(this_rev->plus_positions,this_rev->plus_npositions,
/*oligobase*/index1part_aa,this_rev->querylength);
plus_segments_rev = find_segments(&plus_nsegments_rev,this_rev->plus_positions,this_rev->plus_npositions,
- this_rev->oligos,/*oligobase*/index1part_aa,this_rev->querylength,
- /*threshold_score*/18,/*plusp*/true);
+ /*oligobase*/index1part_aa,this_rev->querylength,
+ /*threshold_score*/18);
- collapse_diagonals(this_rev->minus_positions,this_rev->minus_npositions,this_rev->oligos,
+ collapse_diagonals(this_rev->minus_positions,this_rev->minus_npositions,
/*oligobase*/index1part_aa,this_rev->querylength);
minus_segments_rev = find_segments(&minus_nsegments_rev,this_rev->minus_positions,this_rev->minus_npositions,
- this_rev->oligos,/*oligobase*/index1part_aa,this_rev->querylength,
- /*threshold_score*/18,/*plusp*/false);
+ /*oligobase*/index1part_aa,this_rev->querylength,
+ /*threshold_score*/18);
#else
debug(printf("Starting sample_oligos, rev\n"));
sample_oligos_nolimit(this_rev,indexdb_rev,indexdb_rev,this_rev->querylength,/*oligobase*/index1part);
- collapse_diagonals(this_rev->plus_positions,this_rev->plus_npositions,this_rev->forward_oligos,
+ collapse_diagonals(this_rev->plus_positions,this_rev->plus_npositions,
/*oligobase*/index1part,this_rev->querylength);
plus_segments_rev = find_segments(&plus_nsegments_rev,this_rev->plus_positions,this_rev->plus_npositions,
- this_rev->forward_oligos,/*oligobase*/index1part,this_rev->querylength,
- /*threshold_score*/18,/*plusp*/true);
+ /*oligobase*/index1part,this_rev->querylength,
+ /*threshold_score*/18);
- collapse_diagonals(this_rev->minus_positions,this_rev->minus_npositions,this_rev->revcomp_oligos,
+ collapse_diagonals(this_rev->minus_positions,this_rev->minus_npositions,
/*oligobase*/index1part,this_rev->querylength);
minus_segments_rev = find_segments(&minus_nsegments_rev,this_rev->minus_positions,this_rev->minus_npositions,
- this_rev->revcomp_oligos,/*oligobase*/index1part,this_rev->querylength,
- /*threshold_score*/18,/*plusp*/false);
+ /*oligobase*/index1part,this_rev->querylength,
+ /*threshold_score*/18);
#endif
maxexons = 3;
@@ -4168,10 +4165,10 @@ Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
/* Need to extend, otherwise we won't align NM_003360 */
if (Gregion_genestrand(gregion) > 0) {
find_extensions(&extension5,&extension3,this_fwd,gregion,this_fwd->maxtotallen,/*continuousp*/false);
- Gregion_extend(gregion,extension5,extension3,this_fwd->querylength,min_extra_end);
+ Gregion_extend(gregion,extension5,extension3,this_fwd->querylength);
} else {
find_extensions(&extension5,&extension3,this_rev,gregion,this_rev->maxtotallen,/*continuousp*/false);
- Gregion_extend(gregion,extension5,extension3,this_rev->querylength,min_extra_end);
+ Gregion_extend(gregion,extension5,extension3,this_rev->querylength);
}
}
}
diff --git a/src/stage1.h b/src/stage1.h
index 96f0a2c..b7cfdad 100644
--- a/src/stage1.h
+++ b/src/stage1.h
@@ -1,4 +1,4 @@
-/* $Id: stage1.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: stage1.h 184461 2016-02-18 00:07:47Z twu $ */
#ifndef STAGE1_INCLUDED
#define STAGE1_INCLUDED
@@ -21,11 +21,11 @@ typedef struct T *T;
#ifdef PMAP
extern void
Stage1_setup (int index1part_aa_in, Chrpos_T maxextension_in, Chrpos_T maxtotallen_bound_in,
- int min_extra_end_in, int circular_typeint_in);
+ int circular_typeint_in);
#else
extern void
Stage1_setup (int index1part_in, Chrpos_T maxextension_in, Chrpos_T maxtotallen_bound_in,
- int min_extra_end_in, int circular_typeint_in);
+ int circular_typeint_in);
#endif
@@ -40,8 +40,7 @@ Stage1_compute (bool *samplingp, Sequence_T queryuc,
extern List_T
Stage1_compute_nonstranded (bool *lowidentityp, Sequence_T queryuc,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
- int indexdb_size_threshold, Univ_IIT_T chromosome_iit,
- Univcoord_T chrsubset_start, Univcoord_T chrsubset_end,
+ Univ_IIT_T chromosome_iit, Univcoord_T chrsubset_start, Univcoord_T chrsubset_end,
Matchpool_T matchpool, int stutterhits, Diagnostic_T diagnostic, Stopwatch_T stopwatch,
int nbest);
#undef T
diff --git a/src/stage1hr.c b/src/stage1hr.c
index c5dfbeb..bb016fd 100644
--- a/src/stage1hr.c
+++ b/src/stage1hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage1hr.c 186090 2016-03-17 22:21:17Z twu $";
+static char rcsid[] = "$Id: stage1hr.c 186091 2016-03-17 22:23:16Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -110,8 +110,9 @@ static int maxpaths_search;
static Chrpos_T overall_max_distance;
/* Other distances */
-static Chrpos_T max_middle_insertions;
-static Chrpos_T max_middle_deletions;
+static int min_indel_end_matches;
+static int max_middle_insertions_default; /* If negative, then compute querylength - 2*min_indel_end_matches */
+static int max_middle_deletions;
static Chrpos_T shortsplicedist;
static Chrpos_T shortsplicedist_known;
static Chrpos_T shortsplicedist_novelend;
@@ -119,7 +120,6 @@ static Chrpos_T shortsplicedist_novelend;
/* Penalties */
static int subopt_levels;
-static int reject_trimlength;
static bool novelsplicingp;
static bool knownsplicingp;
@@ -158,8 +158,6 @@ static int max_gmap_pairsearch;
static int max_gmap_segments; /* Not used */
static int max_gmap_improvement;
-static int minendexon = 9;
-
#define A_CHAR 0x0
#define C_CHAR 0x1
@@ -201,7 +199,7 @@ static int nchromosomes;
static Genome_T genome;
static int leftreadshift;
-static unsigned int oligobase_mask; /* same as kmer_mask */
+static Oligospace_T oligobase_mask; /* same as kmer_mask */
static int one_miss_querylength;
static int end_miss_one; /* Used for computing max_terminal_length */
@@ -820,10 +818,10 @@ struct T {
#endif
bool *omitted;
- Storedoligomer_T *forward_oligos_allocated;
- Storedoligomer_T *forward_oligos; /* points to above[index1interval-1] */
- Storedoligomer_T *revcomp_oligos_allocated;
- Storedoligomer_T *revcomp_oligos; /* points to above[index1interval-1] */
+ Oligospace_T *forward_oligos_allocated;
+ Oligospace_T *forward_oligos; /* points to above[index1interval-1] */
+ Oligospace_T *revcomp_oligos_allocated;
+ Oligospace_T *revcomp_oligos; /* points to above[index1interval-1] */
struct Segment_T *plus_segments;
struct Segment_T *minus_segments;
@@ -1059,11 +1057,11 @@ check_dinucleotides (char *sequence, int querylength) {
static int
read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
- int query_lastpos, int genestrand, bool first_read_p) {
+ int query_lastpos, int genestrand) {
Reader_T reader;
int querypos, noligos = 0;
Oligostate_T last_state = INIT;
- Storedoligomer_T forward = 0U, revcomp = 0U;
+ Oligospace_T forward = 0, revcomp = 0;
/* This estimate may be too high */
/* this->maxfloor = 1 + querylength/oligobase * 2; */
@@ -1100,7 +1098,8 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
}
/* Note: leftshifting is done here, rather than in Oligo_lookup */
- debug(printf("oligobase_mask: %08X\n",oligobase_mask));
+ /* Format is 010llX because 19-mer is maximum k-mer size, which would require 10 chars */
+ debug(printf("oligobase_mask: %010llX\n",oligobase_mask));
#if 0
*any_omitted_p = false;
*all_omitted_p = true;
@@ -1130,7 +1129,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = forward & oligobase_mask;
this->revcomp_oligos[querypos] = (revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1161,7 +1160,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = Cmet_reduce_ga(forward) & oligobase_mask;
this->revcomp_oligos[querypos] = Cmet_reduce_ct(revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1191,7 +1190,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = Cmet_reduce_ct(forward) & oligobase_mask;
this->revcomp_oligos[querypos] = Cmet_reduce_ga(revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1223,7 +1222,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = Atoi_reduce_tc(forward) & oligobase_mask;
this->revcomp_oligos[querypos] = Atoi_reduce_ag(revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1252,7 +1251,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = Atoi_reduce_ag(forward) & oligobase_mask;
this->revcomp_oligos[querypos] = Atoi_reduce_tc(revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1284,7 +1283,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = Atoi_reduce_ag(forward) & oligobase_mask;
this->revcomp_oligos[querypos] = Atoi_reduce_tc(revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1313,7 +1312,7 @@ read_oligos (bool *allvalidp, T this, char *queryuc_ptr, int querylength,
this->forward_oligos[querypos] = Atoi_reduce_tc(forward) & oligobase_mask;
this->revcomp_oligos[querypos] = Atoi_reduce_ag(revcomp >> leftreadshift) & oligobase_mask;
- debug(printf("At querypos %d, read oligo = %06X\n",querypos,this->forward_oligos[querypos]));
+ debug(printf("At querypos %d, read oligo = %010llX\n",querypos,this->forward_oligos[querypos]));
noligos++;
}
}
@@ -1600,9 +1599,9 @@ Stage1_new (int querylength) {
#endif
new->omitted = (bool *) CALLOC(querylength,sizeof(bool));
- new->forward_oligos_allocated = (Storedoligomer_T *) CALLOC(querylength+overhang,sizeof(Storedoligomer_T));
+ new->forward_oligos_allocated = (Oligospace_T *) CALLOC(querylength+overhang,sizeof(Oligospace_T));
new->forward_oligos = &(new->forward_oligos_allocated[overhang]);
- new->revcomp_oligos_allocated = (Storedoligomer_T *) CALLOC(querylength+overhang,sizeof(Storedoligomer_T));
+ new->revcomp_oligos_allocated = (Oligospace_T *) CALLOC(querylength+overhang,sizeof(Oligospace_T));
new->revcomp_oligos = &(new->revcomp_oligos_allocated[overhang]);
new->plus_segments = (struct Segment_T *) NULL;
@@ -1831,14 +1830,14 @@ static List_T
report_perfect_segment (int *found_score, int *nhits, List_T hits, Univcoord_T left,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Chrpos_T chrlength, int querylength, Compress_T query_compress,
- int nmisses_allowed, bool plusp, int genestrand, bool first_read_p) {
+ int nmisses_allowed, bool plusp, int genestrand) {
Stage3end_T hit;
int nmismatches;
if (snpp == true) {
if ((hit = Stage3end_new_substitution(&(*found_score),/*nmismatches*/0,
left,/*genomiclength*/querylength,query_compress,
- plusp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ plusp,genestrand,chrnum,chroffset,chrhigh,chrlength,
/*sarrayp*/false)) == NULL) {
return hits;
} else {
@@ -1850,7 +1849,7 @@ report_perfect_segment (int *found_score, int *nhits, List_T hits, Univcoord_T l
/* Count actual number of mismatches. May not be a perfect segment. */
nmismatches = Genome_count_mismatches_limit(query_compress,left,/*pos5*/0,/*pos3*/querylength,
/*max_mismatches_allowed*/nmisses_allowed,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug(printf("Got %d mismatches\n",nmismatches));
if (nmismatches > nmisses_allowed) {
return hits;
@@ -1858,7 +1857,7 @@ report_perfect_segment (int *found_score, int *nhits, List_T hits, Univcoord_T l
/* Don't use Stage3end_new_exact, because need to mark mismatches */
if ((hit = Stage3end_new_substitution(&(*found_score),nmismatches,
left,/*genomiclength*/querylength,
- query_compress,plusp,genestrand,first_read_p,
+ query_compress,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,
/*sarrayp*/false)) == NULL) {
return hits;
@@ -1871,7 +1870,7 @@ report_perfect_segment (int *found_score, int *nhits, List_T hits, Univcoord_T l
} else {
/* mode == STANDARD && spansize == index1part */
if ((hit = Stage3end_new_exact(&(*found_score),left,/*genomiclength*/querylength,
- query_compress,plusp,genestrand,first_read_p,
+ query_compress,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,/*sarrayp*/false)) == NULL) {
return hits;
} else {
@@ -1899,7 +1898,7 @@ report_perfect_segment_dibase (int *found_score, int *nhits, List_T hits, Univco
/* Need to fill buffer with nucleotide genome anyway */
if ((hit = Stage3end_new_substitution(&(*found_score),/*nmismatches*/0,
left,/*genomiclength*/querylength,
- query_compress,plusp,genestrand,first_read_p,
+ query_compress,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,
/*sarrayp*/false)) == NULL) {
return hits;
@@ -2044,7 +2043,7 @@ static List_T
identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroffset, Univcoord_T *chrhigh,
Chrpos_T *chrlength, int *nhits, List_T hits, Univcoord_T goal, struct List_T *prev, int *nempty,
int *global_miss_querypos5, int *global_miss_querypos3,
- int querylength, Compress_T query_compress, bool plusp, int genestrand, bool first_read_p,
+ int querylength, Compress_T query_compress, bool plusp, int genestrand,
int nmisses_allowed, int nmisses_seen, int miss_querypos5, int miss_querypos3) {
List_T spanningset;
Stage3end_T hit;
@@ -2446,7 +2445,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
return hits;
} else {
return report_perfect_segment(&(*found_score),&(*nhits),hits,left,*chrnum,*chroffset,*chrhigh,*chrlength,
- querylength,query_compress,nmisses_allowed,plusp,genestrand,first_read_p);
+ querylength,query_compress,nmisses_allowed,plusp,genestrand);
}
} else {
if (goal < (unsigned int) querylength) {
@@ -2469,11 +2468,11 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
if (snpp || mode != STANDARD || spansize != index1part) {
debug7(printf(" Testing in entire query\n"));
nmismatches = Genome_count_mismatches_substring(query_compress,left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
} else {
debug7(printf(" Testing in query bounds %d..%d\n",miss_querypos5,miss_querypos3));
nmismatches = Genome_count_mismatches_substring(query_compress,left,/*pos5*/miss_querypos5,/*pos3*/miss_querypos3,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
}
debug7(printf("nmismatches = %d (vs %d misses allowed)\n",nmismatches,nmisses_allowed));
@@ -2486,7 +2485,7 @@ identify_multimiss_iter (int *found_score, Chrnum_T *chrnum, Univcoord_T *chroff
debug(printf("Reporting hit with %d mismatches\n",nmismatches));
if ((hit = Stage3end_new_substitution(&(*found_score),nmismatches,
left,/*genomiclength*/querylength,
- query_compress,plusp,genestrand,first_read_p,
+ query_compress,plusp,genestrand,
*chrnum,*chroffset,*chrhigh,*chrlength,
/*sarrayp*/false)) == NULL) {
return hits;
@@ -2523,7 +2522,7 @@ most_specific_oligomer_1 (int *best_plus_querypos, int *best_minus_querypos, T t
#endif
this->plus_npositions[querypos] = Indexdb_count_no_subst(plus_indexdb,this->forward_oligos[querypos]);
this->minus_npositions[querypos] = Indexdb_count_no_subst(minus_indexdb,this->revcomp_oligos[querypos]);
- debug(printf("Counting at querypos %d, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos %d, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
querypos,this->plus_npositions[querypos],this->forward_oligos[querypos],
this->minus_npositions[querypos],this->revcomp_oligos[querypos]));
@@ -2572,7 +2571,7 @@ most_specific_oligomer_2 (int *best_plus_querypos, int *best_minus_querypos, T t
#endif
this->plus_npositions[-1] = Indexdb_count_left_subst_1(plus_indexdb,this->forward_oligos[0]);
this->minus_npositions[-1] = Indexdb_count_right_subst_1(minus_indexdb,this->revcomp_oligos[0]);
- debug(printf("Counting at querypos 0, neg 1, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos 0, neg 1, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
this->plus_npositions[-1],this->forward_oligos[0],this->minus_npositions[-1],this->revcomp_oligos[0]));
best_plus_count[1] = this->plus_npositions[-1];
best_minus_count[1] = this->minus_npositions[-1];
@@ -2587,7 +2586,7 @@ most_specific_oligomer_2 (int *best_plus_querypos, int *best_minus_querypos, T t
mod = querypos % 2;
this->plus_npositions[querypos] = Indexdb_count_no_subst(plus_indexdb,this->forward_oligos[querypos]);
this->minus_npositions[querypos] = Indexdb_count_no_subst(minus_indexdb,this->revcomp_oligos[querypos]);
- debug(printf("Counting at querypos %d, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos %d, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
querypos,this->plus_npositions[querypos],this->forward_oligos[querypos],
this->minus_npositions[querypos],this->revcomp_oligos[querypos]));
@@ -2616,7 +2615,7 @@ most_specific_oligomer_2 (int *best_plus_querypos, int *best_minus_querypos, T t
mod = (querypos+1) % 2;
this->plus_npositions[querypos+1] = Indexdb_count_right_subst_1(plus_indexdb,this->forward_oligos[querypos]);
this->minus_npositions[querypos+1] = Indexdb_count_left_subst_1(minus_indexdb,this->revcomp_oligos[querypos]);
- debug(printf("Counting at querypos %d, pos 1, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos %d, pos 1, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
querypos,this->plus_npositions[querypos+1],this->forward_oligos[querypos],
this->minus_npositions[querypos+1],this->revcomp_oligos[querypos]));
@@ -2671,14 +2670,14 @@ most_specific_oligomer_3 (int *best_plus_querypos, int *best_minus_querypos, T t
#endif
this->plus_npositions[-2] = Indexdb_count_left_subst_2(plus_indexdb,this->forward_oligos[0]);
this->minus_npositions[-2] = Indexdb_count_right_subst_2(minus_indexdb,this->revcomp_oligos[0]);
- debug(printf("Counting at querypos 0, neg 2, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos 0, neg 2, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
this->plus_npositions[-2],this->forward_oligos[0],this->minus_npositions[-2],this->revcomp_oligos[0]));
best_plus_count[1] = this->plus_npositions[-2];
best_minus_count[1] = this->minus_npositions[-2];
this->plus_npositions[-1] = Indexdb_count_left_subst_1(plus_indexdb,this->forward_oligos[0]);
this->minus_npositions[-1] = Indexdb_count_right_subst_1(minus_indexdb,this->revcomp_oligos[0]);
- debug(printf("Counting at querypos 0, neg 1, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos 0, neg 1, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
this->plus_npositions[-1],this->forward_oligos[0],this->minus_npositions[-1],this->revcomp_oligos[0]));
best_plus_count[2] = this->plus_npositions[-1];
best_minus_count[2] = this->minus_npositions[-1];
@@ -2693,7 +2692,7 @@ most_specific_oligomer_3 (int *best_plus_querypos, int *best_minus_querypos, T t
mod = querypos % 3;
this->plus_npositions[querypos] = Indexdb_count_no_subst(plus_indexdb,this->forward_oligos[querypos]);
this->minus_npositions[querypos] = Indexdb_count_no_subst(minus_indexdb,this->revcomp_oligos[querypos]);
- debug(printf("Counting at querypos %d, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos %d, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
querypos,this->plus_npositions[querypos],this->forward_oligos[querypos],
this->minus_npositions[querypos],this->revcomp_oligos[querypos]));
@@ -2724,7 +2723,7 @@ most_specific_oligomer_3 (int *best_plus_querypos, int *best_minus_querypos, T t
mod = (querypos+1) % 3;
this->plus_npositions[querypos+1] = Indexdb_count_right_subst_1(plus_indexdb,this->forward_oligos[querypos]);
this->minus_npositions[querypos+1] = Indexdb_count_left_subst_1(minus_indexdb,this->revcomp_oligos[querypos]);
- debug(printf("Counting at querypos %d, pos 1, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos %d, pos 1, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
querypos,this->plus_npositions[querypos+1],this->forward_oligos[querypos],
this->minus_npositions[querypos+1],this->revcomp_oligos[querypos]));
@@ -2743,7 +2742,7 @@ most_specific_oligomer_3 (int *best_plus_querypos, int *best_minus_querypos, T t
mod = (querypos+2) % 3;
this->plus_npositions[querypos+2] = Indexdb_count_right_subst_2(plus_indexdb,this->forward_oligos[querypos]);
this->minus_npositions[querypos+2] = Indexdb_count_left_subst_2(minus_indexdb,this->revcomp_oligos[querypos]);
- debug(printf("Counting at querypos %d, pos 2, plus_npositions = %d (oligo %06X), minus_npositions = %d (oligo %06X)\n",
+ debug(printf("Counting at querypos %d, pos 2, plus_npositions = %d (oligo %010llX), minus_npositions = %d (oligo %010llX)\n",
querypos,this->plus_npositions[querypos+2],this->forward_oligos[querypos],
this->minus_npositions[querypos+2],this->revcomp_oligos[querypos]));
@@ -2768,7 +2767,7 @@ most_specific_oligomer_3 (int *best_plus_querypos, int *best_minus_querypos, T t
static List_T
-find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand, bool first_read_p,
+find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand,
int querylength, int query_lastpos, Indexdb_T plus_indexdb, Indexdb_T minus_indexdb,
Compress_T query_compress_fwd, Compress_T query_compress_rev) {
Spanningelt_T *array;
@@ -2877,7 +2876,7 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/0,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
@@ -2911,7 +2910,7 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/0,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
@@ -2994,7 +2993,7 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/0,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
@@ -3028,7 +3027,7 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/0,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/0,
/*nmisses_seen*/0,global_miss_querypos5,global_miss_querypos3);
}
@@ -3041,7 +3040,7 @@ find_spanning_exact_matches (int *found_score, int *nhits, List_T hits, T this,
static List_T
-find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand, bool first_read_p,
+find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand,
int querylength, Compress_T query_compress_fwd, Compress_T query_compress_rev) {
Spanningelt_T *array;
List_T prev;
@@ -3097,7 +3096,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
++diagonals0;
--ndiagonals0;
@@ -3107,7 +3106,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal1,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
++diagonals1;
--ndiagonals1;
@@ -3118,7 +3117,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/nempty,global_miss_querypos5,global_miss_querypos3);
++diagonals0;
--ndiagonals0;
@@ -3132,7 +3131,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
}
@@ -3141,7 +3140,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals1++,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/true,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
}
@@ -3188,7 +3187,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
++diagonals0;
--ndiagonals0;
@@ -3198,7 +3197,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal1,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
++diagonals1;
--ndiagonals1;
@@ -3209,7 +3208,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal0,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/nempty,global_miss_querypos5,global_miss_querypos3);
++diagonals0;
--ndiagonals0;
@@ -3223,7 +3222,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals0++,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss1_querypos5,miss1_querypos3);
}
@@ -3232,7 +3231,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,*diagonals1++,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,/*nmisses_allowed*/1,
+ /*plusp*/false,genestrand,/*nmisses_allowed*/1,
/*nmisses_seen*/1+nempty,miss0_querypos5,miss0_querypos3);
}
@@ -3244,7 +3243,7 @@ find_spanning_onemiss_matches (int *found_score, int *nhits, List_T hits, T this
static List_T
-find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand, bool first_read_p,
+find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T this, int genestrand,
int nrequired, int querylength, Compress_T query_compress_fwd, Compress_T query_compress_rev,
int nmisses_allowed) {
Univcoord_T *diagonals, diagonal;
@@ -3379,7 +3378,7 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,nmisses_allowed,
+ /*plusp*/true,genestrand,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
}
diagonal = batch->diagonal;
@@ -3425,7 +3424,7 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_fwd,
- /*plusp*/true,genestrand,first_read_p,nmisses_allowed,
+ /*plusp*/true,genestrand,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
}
@@ -3542,7 +3541,7 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,nmisses_allowed,
+ /*plusp*/false,genestrand,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
}
diagonal = batch->diagonal;
@@ -3588,7 +3587,7 @@ find_spanning_multimiss_matches (int *found_score, int *nhits, List_T hits, T th
hits = identify_multimiss_iter(&(*found_score),&chrnum,&chroffset,&chrhigh,&chrlength,&(*nhits),hits,diagonal,
prev,&nempty,&global_miss_querypos5,&global_miss_querypos3,
querylength,/*query_compress*/query_compress_rev,
- /*plusp*/false,genestrand,first_read_p,nmisses_allowed,
+ /*plusp*/false,genestrand,nmisses_allowed,
/*nmisses_seen*/nunion-count+nempty,global_miss_querypos5,global_miss_querypos3);
}
@@ -3656,7 +3655,7 @@ trim_ends_unknowns_only (int *trim5, int *trim3, char *sequence1, char *sequence
static List_T
find_complete_mm (int *found_score, int *nhits, List_T hits, List_T anchor_segments,
int querylength, Compress_T query_compress,
- int max_mismatches_allowed, bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
Stage3end_T hit;
int nmismatches;
Univcoord_T left;
@@ -3669,11 +3668,11 @@ find_complete_mm (int *found_score, int *nhits, List_T hits, List_T anchor_segme
if (segmenti->floor <= max_mismatches_allowed) {
left = segmenti->diagonal - querylength;
nmismatches = Genome_count_mismatches_limit(query_compress,left,/*pos5*/0,/*pos3*/querylength,
- max_mismatches_allowed,plusp,genestrand,first_read_p);
+ max_mismatches_allowed,plusp,genestrand);
if (nmismatches <= max_mismatches_allowed) {
if ((hit = Stage3end_new_substitution(&(*found_score),nmismatches,
left,/*genomiclength*/querylength,
- query_compress,plusp,genestrand,first_read_p,segmenti->chrnum,
+ query_compress,plusp,genestrand,segmenti->chrnum,
segmenti->chroffset,segmenti->chrhigh,segmenti->chrlength,
/*sarrayp*/false)) != NULL) {
segmenti->usedp = true;
@@ -3698,7 +3697,7 @@ identify_all_segments (int *nsegments, List_T *anchor_segments, Segment_T **spli
Univcoord_T **positions,
#endif
int *npositions, bool *omitted, int querylength, int query_lastpos, Floors_T floors,
- int max_mismatches_allowed, bool plusp) {
+ bool plusp) {
List_T all_segments = NULL;
struct Segment_T *segments = NULL;
Segment_T *array;
@@ -4675,7 +4674,7 @@ static void
pair_up_anchor_segments (List_T plus_anchor_segments_5, List_T minus_anchor_segments_5,
List_T plus_anchor_segments_3, List_T minus_anchor_segments_3,
Chrpos_T pairmax) {
- Univcoord_T insert_start;
+ /* Univcoord_T insert_start; */
Segment_T segment5, segment3;
List_T q, pstart, pend, p;
@@ -4686,7 +4685,7 @@ pair_up_anchor_segments (List_T plus_anchor_segments_5, List_T minus_anchor_segm
for (q = plus_anchor_segments_5; q != NULL && pstart != NULL; q = List_next(q)) {
segment5 = (Segment_T) List_head(q);
assert(segment5->diagonal != (Univcoord_T) -1);
- insert_start = segment5->diagonal;
+ /* insert_start = segment5->diagonal; */
while (pstart != NULL && ((Segment_T) pstart->first)->diagonal < segment5->diagonal) {
pstart = List_next(pstart);
@@ -4712,7 +4711,7 @@ pair_up_anchor_segments (List_T plus_anchor_segments_5, List_T minus_anchor_segm
for (q = minus_anchor_segments_3; q != NULL && pstart != NULL; q = List_next(q)) {
segment3 = (Segment_T) List_head(q);
assert(segment3->diagonal != (Univcoord_T) -1);
- insert_start = segment3->diagonal;
+ /* insert_start = segment3->diagonal; */
while (pstart != NULL && ((Segment_T) pstart->first)->diagonal < segment3->diagonal) {
pstart = List_next(pstart);
@@ -4789,11 +4788,18 @@ find_middle_indels (int *found_score, int *nhits, List_T hits,
#endif
Floors_T floors, int querylength, int query_lastpos,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
- int max_mismatches_allowed, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, int genestrand) {
Segment_T segmenti, segmentj, segmentj_end, *ptr;
int indels, floor, pos, prev, middle;
int *floors_from_neg3, *floors_to_pos3;
bool foundp;
+ int max_middle_insertions;
+
+ if (max_middle_insertions_default >= 0) {
+ max_middle_insertions = max_middle_insertions_default;
+ } else {
+ max_middle_insertions = querylength - 2*min_indel_end_matches;
+ }
debug(printf("*** find_middle_indels with querylength %d and max_mismatches_allowed %d ***\n",
querylength,max_mismatches_allowed));
@@ -4860,7 +4866,7 @@ find_middle_indels (int *found_score, int *nhits, List_T hits,
segmenti->chrnum,segmenti->chroffset,segmenti->chrhigh,segmenti->chrlength,
indels,/*query_compress*/query_compress_fwd,
querylength,max_mismatches_allowed,
- /*plusp*/true,genestrand,first_read_p,/*sarrayp*/false);
+ /*plusp*/true,genestrand,/*sarrayp*/false);
} else {
debug2(printf("too many mismatches, because floor %d+middle+%d=%d > %d\n",
floors->scorefrom[-index1interval][segmentj->querypos5],
@@ -4924,7 +4930,7 @@ find_middle_indels (int *found_score, int *nhits, List_T hits,
segmenti->chrnum,segmenti->chroffset,segmenti->chrhigh,segmenti->chrlength,
indels,/*query_compress*/query_compress_fwd,querylength,
max_mismatches_allowed,
- /*plusp*/true,genestrand,first_read_p,/*sarrayp*/false);
+ /*plusp*/true,genestrand,/*sarrayp*/false);
} else {
debug2(printf("too many mismatches, because floor = %d+middle+%d=%d > %d\n",
floors->scorefrom[-index1interval][segmenti->querypos5],
@@ -5000,7 +5006,7 @@ find_middle_indels (int *found_score, int *nhits, List_T hits,
segmenti->chrnum,segmenti->chroffset,segmenti->chrhigh,segmenti->chrlength,
indels,/*query_compress*/query_compress_rev,querylength,
max_mismatches_allowed,
- /*plusp*/false,genestrand,first_read_p,/*sarrayp*/false);
+ /*plusp*/false,genestrand,/*sarrayp*/false);
} else {
debug2(printf("too many mismatches, because floor = %d+middle+%d=%d > %d\n",
floors->scorefrom[-index1interval][segmentj->querypos5],
@@ -5065,7 +5071,7 @@ find_middle_indels (int *found_score, int *nhits, List_T hits,
segmenti->chrnum,segmenti->chroffset,segmenti->chrhigh,segmenti->chrlength,
indels,/*query_compress*/query_compress_rev,
querylength,max_mismatches_allowed,
- /*plusp*/false,genestrand,first_read_p,/*sarrayp*/false);
+ /*plusp*/false,genestrand,/*sarrayp*/false);
} else {
debug2(printf("too many mismatches, because floor %d+middle+%d=%d > %d\n",
floors->scorefrom[-index1interval][segmenti->querypos5],
@@ -5099,7 +5105,7 @@ compute_end_indels_right (int *indels, int *nmismatches_longcont, int *nmismatch
int *mismatch_positions_long, int nmismatches_avail_long,
int breakpoint, int querylength, Univcoord_T left, Compress_T query_compress,
int min_indel_end_matches, int max_end_insertions, int max_end_deletions,
- int max_mismatches_short, bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_short, bool plusp, int genestrand) {
#ifdef DEBUG2E
int i;
#endif
@@ -5141,7 +5147,7 @@ compute_end_indels_right (int *indels, int *nmismatches_longcont, int *nmismatch
nmismatches_avail_shift = Genome_mismatches_right(mismatch_positions_shift,
max_mismatches_short,query_compress,
left-(-sep),/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2e(
printf("A. Trying deletion of %d. ",-sep);
printf("%d mismatches on right at:",nmismatches_avail_shift);
@@ -5343,7 +5349,7 @@ compute_end_indels_right (int *indels, int *nmismatches_longcont, int *nmismatch
nmismatches_avail_shift = Genome_mismatches_right(mismatch_positions_shift,
max_mismatches_short,query_compress,
left-(+sep),/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2e(
printf("B. Trying insertion of %d. ",+sep);
@@ -5546,12 +5552,12 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
int *mismatch_positions_long, int nmismatches_avail_long,
int breakpoint, int querylength, Univcoord_T left, Compress_T query_compress,
int min_indel_end_matches, int max_end_insertions, int max_end_deletions,
- int max_mismatches_short, bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_short, bool plusp, int genestrand) {
#ifdef DEBUG2E
int i;
#endif
int length1;
- int sep, start;
+ int sep;
int nmismatches_avail_shift, nmatches;
int sum, best_sum = querylength;
int conti, shifti;
@@ -5590,7 +5596,7 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
nmismatches_avail_shift = Genome_mismatches_left(mismatch_positions_shift,
max_mismatches_short,query_compress,
left+(+sep),/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2e(
printf("D. Trying insertion of %d. ",+sep);
printf("%d mismatches on left at:",nmismatches_avail_shift);
@@ -5673,7 +5679,7 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
#else
shifti = nmismatches_avail_shift - 1;
conti = 0;
- while (conti < nmismatches_avail_long && mismatch_positions_long[conti] > mismatch_positions_shift[shifti]) {
+ while (conti < nmismatches_avail_long && mismatch_positions_long[conti] > mismatch_positions_shift[shifti]) { /* ? >= */
conti++;
}
indel_pos_cont = mismatch_positions_long[conti] - sep + 1;
@@ -5775,6 +5781,8 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
if (max_end_deletions > 0) {
+#if 0
+ /* start is never used */
if (left < (unsigned int) max_end_deletions) {
debug2e(printf("left %llu < max_end_deletions %d, so start = left\n",
(unsigned long long) left,max_end_deletions));
@@ -5782,13 +5790,14 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
} else {
start = 1;
}
+#endif
for (sep = max_end_deletions; sep >= 1; sep--) {
/* *indels = -sep; */
nmismatches_avail_shift = Genome_mismatches_left(mismatch_positions_shift,
max_mismatches_short,query_compress,
left+(-sep),/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2e(
printf("C. Trying deletion of %d. ",-sep);
printf("%d mismatches on left at:",nmismatches_avail_shift);
@@ -5871,7 +5880,7 @@ compute_end_indels_left (int *indels, int *nmismatches_longcont, int *nmismatche
#else
shifti = nmismatches_avail_shift - 1;
conti = 0;
- while (conti < nmismatches_avail_long && mismatch_positions_long[conti] > mismatch_positions_shift[shifti]) {
+ while (conti < nmismatches_avail_long && mismatch_positions_long[conti] > mismatch_positions_shift[shifti]) { /* ? >= */
conti++;
}
indel_pos_cont = mismatch_positions_long[conti] + 1;
@@ -5990,7 +5999,7 @@ solve_end_indel_low (int *found_score, int *nhits, List_T hits, Segment_T ptr,
#endif
int querylength, Compress_T query_compress,
int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
- int indel_penalty_end, int max_mismatches, bool plusp, int genestrand, bool first_read_p) {
+ int indel_penalty_end, int max_mismatches, bool plusp, int genestrand) {
#ifdef DEBUG2E
char *gbuffer;
#endif
@@ -6031,7 +6040,7 @@ solve_end_indel_low (int *found_score, int *nhits, List_T hits, Segment_T ptr,
/* No need to check chromosome bounds */
nmismatches = Genome_mismatches_right(mismatch_positions,max_mismatches,
query_compress,left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2e(
printf("full read: %d (max %d) mismatches from right:",nmismatches,max_mismatches);
@@ -6077,7 +6086,7 @@ solve_end_indel_low (int *found_score, int *nhits, List_T hits, Segment_T ptr,
breakpoint,querylength,left,query_compress,
min_indel_end_matches,max_end_insertions,max_end_deletions,
/*max_mismatches_allowed*/max_mismatches-nmismatches_long+1,
- plusp,genestrand,first_read_p)) >= 0) {
+ plusp,genestrand)) >= 0) {
debug2e(printf("Got indel_pos %d.\n",indel_pos));
/* formulas for query_indel_pos have been checked on examples */
@@ -6098,10 +6107,10 @@ solve_end_indel_low (int *found_score, int *nhits, List_T hits, Segment_T ptr,
/* end2_indel_p = true; */
}
+ /* genomiclength = querylength-indels; */
if ((hit = Stage3end_new_insertion(&(*found_score),indels,query_indel_pos,
- nmismatches1,nmismatches2,
- left+indels,/*genomiclength*/querylength-indels,
- query_compress,querylength,plusp,genestrand,first_read_p,
+ nmismatches1,nmismatches2,left+indels,
+ query_compress,querylength,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,indel_penalty_end,
/*sarrayp*/false)) != NULL) {
ptr->usedp = true;
@@ -6126,10 +6135,10 @@ solve_end_indel_low (int *found_score, int *nhits, List_T hits, Segment_T ptr,
/* end2_indel_p = true; */
}
+ /*genomiclength = querylength-indels; */
if ((hit = Stage3end_new_deletion(&(*found_score),-indels,query_indel_pos,
- nmismatches1,nmismatches2,
- left+indels,/*genomiclength*/querylength-indels,
- query_compress,querylength,plusp,genestrand,first_read_p,
+ nmismatches1,nmismatches2,left+indels,
+ query_compress,querylength,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,indel_penalty_end,
/*sarrayp*/false)) != NULL) {
ptr->usedp = true;
@@ -6156,7 +6165,7 @@ solve_end_indel_high (int *found_score, int *nhits, List_T hits, Segment_T ptr,
#endif
int querylength, Compress_T query_compress,
int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
- int indel_penalty_end, int max_mismatches, bool plusp, int genestrand, bool first_read_p) {
+ int indel_penalty_end, int max_mismatches, bool plusp, int genestrand) {
#ifdef DEBUG2E
char *gbuffer;
#endif
@@ -6198,7 +6207,7 @@ solve_end_indel_high (int *found_score, int *nhits, List_T hits, Segment_T ptr,
/* Previously checked from 0 to lastbound */
nmismatches = Genome_mismatches_left(mismatch_positions,max_mismatches,
query_compress,left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug2e(
printf("full read: %d (max %d) mismatches from left:",nmismatches,max_mismatches);
@@ -6243,7 +6252,7 @@ solve_end_indel_high (int *found_score, int *nhits, List_T hits, Segment_T ptr,
breakpoint,querylength,left,query_compress,
min_indel_end_matches,max_end_insertions,max_end_deletions,
/*max_mismatches_allowed*/max_mismatches-nmismatches_long+1,
- plusp,genestrand,first_read_p)) >= 0) {
+ plusp,genestrand)) >= 0) {
debug2e(printf("Got indel_pos %d\n",indel_pos));
/* formulas for query_indel_pos have been checked on examples */
@@ -6264,10 +6273,10 @@ solve_end_indel_high (int *found_score, int *nhits, List_T hits, Segment_T ptr,
/* end2_indel_p = false; */
}
+ /* genomiclength = querylength-indels; */
if ((hit = Stage3end_new_insertion(&(*found_score),indels,query_indel_pos,
- nmismatches1,nmismatches2,
- left,/*genomiclength*/querylength-indels,
- query_compress,querylength,plusp,genestrand,first_read_p,
+ nmismatches1,nmismatches2,left,
+ query_compress,querylength,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,indel_penalty_end,
/*sarrayp*/false)) != NULL) {
ptr->usedp = true;
@@ -6292,10 +6301,10 @@ solve_end_indel_high (int *found_score, int *nhits, List_T hits, Segment_T ptr,
/* end2_indel_p = false; */
}
+ /*genomiclength = querylength-indels; */
if ((hit = Stage3end_new_deletion(&(*found_score),-indels,query_indel_pos,
- nmismatches1,nmismatches2,
- left,/*genomiclength*/querylength-indels,
- query_compress,querylength,plusp,genestrand,first_read_p,
+ nmismatches1,nmismatches2,left,
+ query_compress,querylength,plusp,genestrand,
chrnum,chroffset,chrhigh,chrlength,indel_penalty_end,
/*sarrayp*/false)) != NULL) {
ptr->usedp = true;
@@ -6324,7 +6333,7 @@ find_end_indels (int *found_score, int *nhits, List_T hits,
int querylength, int firstbound, int lastbound,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
- int indel_penalty_end, int max_mismatches_allowed, int genestrand, bool first_read_p) {
+ int indel_penalty_end, int max_mismatches_allowed, int genestrand) {
Segment_T ptr;
List_T p;
@@ -6345,7 +6354,7 @@ find_end_indels (int *found_score, int *nhits, List_T hits,
#endif
querylength,/*query_compress*/query_compress_fwd,
max_end_insertions,max_end_deletions,min_indel_end_matches,
- indel_penalty_end,max_mismatches_allowed,/*plusp*/true,genestrand,first_read_p);
+ indel_penalty_end,max_mismatches_allowed,/*plusp*/true,genestrand);
}
if (ptr->floor_xlast <= max_mismatches_allowed) {
@@ -6358,7 +6367,7 @@ find_end_indels (int *found_score, int *nhits, List_T hits,
#endif
querylength,/*query_compress*/query_compress_fwd,
max_end_insertions,max_end_deletions,min_indel_end_matches,
- indel_penalty_end,max_mismatches_allowed,/*plusp*/true,genestrand,first_read_p);
+ indel_penalty_end,max_mismatches_allowed,/*plusp*/true,genestrand);
}
}
}
@@ -6377,7 +6386,7 @@ find_end_indels (int *found_score, int *nhits, List_T hits,
#endif
querylength,/*query_compress*/query_compress_rev,
max_end_insertions,max_end_deletions,min_indel_end_matches,
- indel_penalty_end,max_mismatches_allowed,/*plusp*/false,genestrand,first_read_p);
+ indel_penalty_end,max_mismatches_allowed,/*plusp*/false,genestrand);
}
if (ptr->floor_xlast <= max_mismatches_allowed) {
@@ -6390,7 +6399,7 @@ find_end_indels (int *found_score, int *nhits, List_T hits,
#endif
querylength,/*query_compress*/query_compress_rev,
max_end_insertions,max_end_deletions,min_indel_end_matches,
- indel_penalty_end,max_mismatches_allowed,/*plusp*/false,genestrand,first_read_p);
+ indel_penalty_end,max_mismatches_allowed,/*plusp*/false,genestrand);
}
}
}
@@ -6682,7 +6691,7 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
if (segmenti->leftmost < 0) {
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
segmenti->leftmost = (nmismatches_left == 0) ? 0 : mismatch_positions_left[nmismatches_left-1];
debug4s(printf("%d mismatches on left at:",nmismatches_left);
for (i = 0; i <= nmismatches_left; i++) {
@@ -6695,7 +6704,7 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
if (segmentj->rightmost < 0) {
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,/*left*/segmentj_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
segmentj->rightmost = (nmismatches_right == 0) ? 0 : mismatch_positions_right[nmismatches_right-1];
debug4s(printf("%d mismatches on right at:",nmismatches_right);
for (i = 0; i <= nmismatches_right; i++) {
@@ -6901,7 +6910,6 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,donor_prob,/*acceptor_prob*/prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donor*/NULL,amb_nmismatches,
@@ -6973,7 +6981,6 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*donor_prob*/prob,acceptor_prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -7140,7 +7147,6 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,donor_prob,/*acceptor_prob*/prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donort*/NULL,amb_nmismatches,
@@ -7212,7 +7218,6 @@ find_singlesplices_plus (int *found_score, List_T hits, List_T *ambiguous, List_
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*donor_prob*/prob,acceptor_prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -7408,7 +7413,7 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
if (segmenti->leftmost < 0) {
nmismatches_left = Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,
query_compress,/*left*/segmenti_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
segmenti->leftmost = (nmismatches_left == 0) ? 0 : mismatch_positions_left[nmismatches_left-1];
debug4s(printf("%d mismatches on left at:",nmismatches_left);
for (i = 0; i <= nmismatches_left; i++) {
@@ -7421,7 +7426,7 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
if (segmentj->rightmost < 0) {
nmismatches_right = Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,
query_compress,/*left*/segmentj_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
segmentj->rightmost = (nmismatches_right == 0) ? 0 : mismatch_positions_right[nmismatches_right-1];
debug4s(printf("%d mismatches on right at:",nmismatches_right);
for (i = 0; i <= nmismatches_right; i++) {
@@ -7626,7 +7631,6 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,donor_prob,/*acceptor_prob*/prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donort*/NULL,amb_nmismatches,
@@ -7698,7 +7702,6 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*donor_prob*/prob,acceptor_prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -7865,7 +7868,6 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
/*nmismatches_donor*/Substring_nmismatches_whole(donor),nmismatches_acceptor,
donor,/*acceptor*/NULL,donor_prob,/*acceptor_prob*/prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(acceptor),/*amb_prob*/prob,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,amb_knowni,
/*amb_nmismatches_donort*/NULL,amb_nmismatches,
@@ -7936,7 +7938,6 @@ find_singlesplices_minus (int *found_score, List_T hits, List_T *ambiguous, List
nmismatches_donor,/*nmismatches_acceptor*/Substring_nmismatches_whole(acceptor),
/*donor*/NULL,acceptor,/*donor_prob*/prob,acceptor_prob,/*distance*/0U,
/*shortdistancep*/false,/*penalty*/0,querylength,
- /*amb_length*/Substring_match_length_orig(donor),/*amb_prob*/prob,
ambcoords,/*ambcoords_acceptor*/NULL,
amb_knowni,/*amb_knowni_acceptor*/NULL,
amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
@@ -8010,6 +8011,7 @@ lookup_splicesites (Doublelist_T *probs_list, Intlist_T splicesites_i, Univcoord
#endif
+#if 0
static int
substringD_match_length_cmp (const void *a, const void *b) {
Stage3end_T x = * (Stage3end_T *) a;
@@ -8034,7 +8036,9 @@ substringD_match_length_cmp (const void *a, const void *b) {
}
}
}
+#endif
+#if 0
static int
substringA_match_length_cmp (const void *a, const void *b) {
Stage3end_T x = * (Stage3end_T *) a;
@@ -8059,9 +8063,10 @@ substringA_match_length_cmp (const void *a, const void *b) {
}
}
}
+#endif
-
+#if 0
static List_T
find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Segment_T *spliceable, int nspliceable, struct Segment_T *segments,
@@ -8325,8 +8330,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
segmenti->leftmost,segmentj->rightmost));
} else if (Genome_count_mismatches_limit(query_compress,segmentm_left,
/*pos5*/segmenti->leftmost,/*pos3*/segmentj->rightmost,
- max_mismatches_allowed,
- plusp,genestrand,first_read_p) <= max_mismatches_allowed) {
+ max_mismatches_allowed,plusp,genestrand) <= max_mismatches_allowed) {
debug4d(printf("Double splice is possible\n"));
segmentj_left = segmentj->diagonal - querylength;
@@ -8366,7 +8370,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
segmentj_antidonor_knowni,segmentm_antiacceptor_knowni,segmentm_antidonor_knowni,segmenti_antiacceptor_knowni,
segmenti_donor_nknown,segmentm_acceptor_nknown,segmentm_donor_nknown,segmentj_acceptor_nknown,
segmentj_antidonor_nknown,segmentm_antiacceptor_nknown,segmentm_antidonor_nknown,segmenti_antiacceptor_nknown,
- splicing_penalty,max_mismatches_allowed,plusp,genestrand,first_read_p,
+ splicing_penalty,max_mismatches_allowed,plusp,genestrand,
subs_or_indels_p,/*sarrayp*/false);
}
}
@@ -8528,39 +8532,36 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*donor_prob*/Doublelist_max(donor_amb_probs),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),/*acceptor_prob*/Doublelist_max(acceptor_amb_probs),
/*amb_length_donor*/donor_length,/*amb_length_acceptor*/acceptor_length,
- /*amb_prob_donor*/Doublelist_max(donor_amb_probs),/*amb_prob_acceptor*/Doublelist_max(acceptor_amb_probs),
donor_ambcoords,acceptor_ambcoords,
donor_amb_knowni,acceptor_amb_knowni,
donor_amb_nmismatches,acceptor_amb_nmismatches,
donor_amb_probs,acceptor_amb_probs,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/true,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
} else if (Intlist_length(donor_amb_nmismatches) > 1) {
hits = List_push(hits,(void *) Stage3end_new_shortexon(&(*found_score),/*donor*/NULL,acceptor,shortexon,
/*donor_prob*/Doublelist_max(donor_amb_probs),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),/*acceptor_prob*/Substring_chimera_prob(acceptor),
/*amb_length_donor*/donor_length,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/Doublelist_max(donor_amb_probs),/*amb_length_acceptor*/0.0,
donor_ambcoords,/*acceptor_ambcoords*/NULL,
donor_amb_knowni,/*amb_knowni_acceptor*/NULL,
donor_amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
donor_amb_probs,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/true,/*copy_shortexon_p*/true,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
} else if (Intlist_length(acceptor_amb_nmismatches) > 1) {
hits = List_push(hits,(void *) Stage3end_new_shortexon(&(*found_score),donor,/*acceptor*/NULL,shortexon,
/*donor_prob*/Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),/*acceptor_prob*/Doublelist_max(acceptor_amb_probs),
/*amb_length_donor*/0,/*amb_length_acceptor*/acceptor_length,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/Doublelist_max(acceptor_amb_probs),
/*ambcoords_donor*/NULL,acceptor_ambcoords,
/*amb_knowni_donor*/NULL,acceptor_amb_knowni,
/*amb_nmismatches_donor*/NULL,acceptor_amb_nmismatches,
/*amb_probs_donor*/NULL,acceptor_amb_probs,
/*copy_donor_p*/true,/*copy_acceptor_p*/false,/*copy_shortexon_p*/true,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
} else {
/* A singleton, apparently due to many duplicates. Is this possible? */
@@ -8568,13 +8569,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*donor_prob*/Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),/*acceptor_prob*/Substring_chimera_prob(acceptor),
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/true,/*copy_acceptor_p*/true,/*copy_shortexon_p*/true,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
}
@@ -8643,13 +8643,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*donor_prob*/Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),/*acceptor_prob*/Doublelist_max(acceptor_amb_probs),
/*amb_length_donor*/0,/*amb_length_acceptor*/Substring_match_length_orig(acceptor),
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/Doublelist_max(acceptor_amb_probs),
/*ambcoords_donor*/NULL,acceptor_ambcoords,
/*amb_knowni_donor*/NULL,acceptor_amb_knowni,
/*amb_nmismatches_donor*/NULL,acceptor_amb_nmismatches,
/*amb_probs_donor*/NULL,acceptor_amb_probs,
/*copy_donor_p*/true,/*copy_acceptor_p*/false,/*copy_shortexon_p*/true,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&acceptor_amb_probs);
Intlist_free(&acceptor_amb_nmismatches);
Intlist_free(&acceptor_amb_knowni);
@@ -8709,13 +8708,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*donor_prob*/Doublelist_max(donor_amb_probs),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),/*acceptor_prob*/Substring_chimera_prob(acceptor),
/*amb_length_donor*/Substring_match_length_orig(donor),/*amb_length_acceptor*/0,
- /*amb_prob_donor*/Doublelist_max(donor_amb_probs),/*amb_prob_acceptor*/0.0,
donor_ambcoords,/*acceptor_ambcoords*/NULL,
donor_amb_knowni,/*amb_knowni_acceptor*/NULL,
donor_amb_nmismatches,/*amb_nmismatches_acceptor*/NULL,
donor_amb_probs,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/true,/*copy_shortexon_p*/true,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&donor_amb_probs);
Intlist_free(&donor_amb_nmismatches);
Intlist_free(&donor_amb_knowni);
@@ -8760,7 +8758,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
debug4k(printf(" Doing Splicetrie_find_right from rightpos %d (plus)\n",rightpos));
if ((nmismatches_shortexon_middle =
Genome_count_mismatches_substring(query_compress,segmentm_left,/*pos5*/leftpos,/*pos3*/rightpos,
- plusp,genestrand,first_read_p)) <= max_mismatches_allowed - nmismatches_shortexon_left &&
+ plusp,genestrand)) <= max_mismatches_allowed - nmismatches_shortexon_left &&
(splicesites_i_right =
Splicetrie_find_right(&nmismatches_shortexon_right,&nmismatches_list_right,j2,
/*origleft*/segmentm_left,/*pos5*/rightpos,/*pos3*/querylength,segmentm->chrhigh,
@@ -8782,7 +8780,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
nmismatches_shortexon_middle,
/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/true,/*donor_ambp*/true,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
if (shortexon != NULL) {
@@ -8796,13 +8794,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Doublelist_max(probs_donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Doublelist_max(probs_acceptor),
amb_length_donor,amb_length_acceptor,
- /*amb_prob_donor*/2.0,/*amb_prob_acceptor*/2.0,
ambcoords_donor,ambcoords_acceptor,
/*amb_knowni_donor*/splicesites_i_left,/*amb_knowni_acceptor*/splicesites_i_right,
/*amb_nmismatches_donor*/nmismatches_list_left,/*amb_nmismatches_acceptor*/nmismatches_list_right,
/*amb_probs_donor*/probs_donor,/*amb_nmismatches_acceptor*/probs_acceptor,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&probs_donor);
Doublelist_free(&probs_acceptor);
#ifdef LARGE_GENOMES
@@ -8826,7 +8823,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
nmismatches_shortexon_middle,
/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/true,/*donor_ambp*/false,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
@@ -8834,7 +8831,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[best_right_j],/*acceptor_knowni*/best_right_j,
/*splice_pos*/rightpos,nmismatches_shortexon_right,
/*prob*/2.0,/*left*/splicesites[best_right_j]-rightpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
if (shortexon == NULL || acceptor == NULL) {
@@ -8850,13 +8847,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Doublelist_max(probs_donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Substring_chimera_prob(acceptor),
amb_length_donor,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/2.0,/*amb_length_acceptor*/0,
ambcoords_donor,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/splicesites_i_left,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/nmismatches_list_left,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/probs_donor,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&probs_donor);
#ifdef LARGE_GENOMES
Uint8list_free(&ambcoords_donor);
@@ -8873,7 +8869,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
donor = Substring_new_donor(/*donor_coord*/splicesites[best_left_j],/*donor_knowni*/best_left_j,
/*splice_pos*/leftpos,nmismatches_shortexon_left,
/*prob*/2.0,/*left*/splicesites[best_left_j]-leftpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
debug4k(printf("shortexon with acceptor at %d (%llu) ... amb_donor %d (%llu)\n",
@@ -8884,7 +8880,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
nmismatches_shortexon_middle,
/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/false,/*donor_ambp*/true,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
@@ -8899,13 +8895,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Doublelist_max(probs_acceptor),
/*amb_length_donor*/0,amb_length_acceptor,
- /*amb_prob_donor*/0.0,/*amb_length_acceptor*/2.0,
/*ambcoords_donor*/NULL,ambcoords_acceptor,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/splicesites_i_right,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/nmismatches_list_right,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/probs_acceptor,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&probs_acceptor);
#ifdef LARGE_GENOMES
Uint8list_free(&ambcoords_acceptor);
@@ -8922,7 +8917,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
donor = Substring_new_donor(/*donor_coord*/splicesites[best_left_j],/*donor_knowni*/best_left_j,
/*splice_pos*/leftpos,nmismatches_shortexon_left,
/*prob*/2.0,/*left*/splicesites[best_left_j]-leftpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
shortexon = Substring_new_shortexon(/*acceptor_coord*/splicesites[j1],/*acceptor_knowni*/j1,
@@ -8930,14 +8925,14 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*acceptor_pos*/leftpos,/*donor_pos*/rightpos,
nmismatches_shortexon_middle,/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/false,/*donor_ambp*/false,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[best_right_j],/*acceptor_knowni*/best_right_j,
/*splice_pos*/rightpos,nmismatches_shortexon_right,
/*prob*/2.0,/*left*/splicesites[best_right_j]-rightpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
if (donor == NULL || shortexon == NULL || acceptor == NULL) {
@@ -8951,13 +8946,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Substring_chimera_prob(acceptor),
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
}
}
Intlist_free(&nmismatches_list_right);
@@ -8996,7 +8990,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
debug4k(printf(" Doing Splicetrie_find_right from rightpos %d (minus)\n",rightpos));
if ((nmismatches_shortexon_middle =
Genome_count_mismatches_substring(query_compress,segmentm_left,/*pos5*/leftpos,/*pos3*/rightpos,
- plusp,genestrand,first_read_p)) <= max_mismatches_allowed - nmismatches_shortexon_left &&
+ plusp,genestrand)) <= max_mismatches_allowed - nmismatches_shortexon_left &&
(splicesites_i_right =
Splicetrie_find_right(&nmismatches_shortexon_right,&nmismatches_list_right,j2,
/*origleft*/segmentm_left,/*pos5*/rightpos,/*pos3*/querylength,segmentm->chrhigh,
@@ -9017,7 +9011,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*acceptor_pos*/rightpos,/*donor_pos*/leftpos,nmismatches_shortexon_middle,
/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/true,/*donor_ambp*/true,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
if (shortexon != NULL) {
@@ -9031,13 +9025,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Doublelist_max(probs_donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Doublelist_max(probs_acceptor),
amb_length_donor,amb_length_acceptor,
- /*amb_prob_donor*/2.0,/*amb_prob_acceptor*/2.0,
ambcoords_donor,ambcoords_acceptor,
/*amb_knowni_donor*/splicesites_i_right,/*amb_knowni_acceptor*/splicesites_i_left,
/*amb_nmismatches_donor*/nmismatches_list_right,/*amb_nmismatches_acceptor*/nmismatches_list_left,
/*amb_probs_donor*/probs_donor,/*amb_probs_acceptor*/probs_acceptor,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&probs_donor);
Doublelist_free(&probs_acceptor);
#ifdef LARGE_GENOMES
@@ -9060,7 +9053,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*acceptor_pos*/rightpos,/*donor_pos*/leftpos,nmismatches_shortexon_middle,
/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/false,/*donor_ambp*/true,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
@@ -9068,7 +9061,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
donor = Substring_new_donor(/*donor_coord*/splicesites[best_right_j],/*donor_knowni*/best_right_j,
/*splice_pos*/rightpos,nmismatches_shortexon_right,
/*prob*/2.0,/*left*/splicesites[best_right_j]-rightpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
if (donor == NULL || shortexon == NULL) {
@@ -9082,13 +9075,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Doublelist_max(probs_acceptor),
/*amb_length_donor*/0,amb_length_acceptor,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/2.0,
/*ambcoords_donor*/NULL,ambcoords_acceptor,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/splicesites_i_left,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/nmismatches_list_left,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/probs_acceptor,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&probs_acceptor);
#ifdef LARGE_GENOMES
Uint8list_free(&ambcoords_acceptor);
@@ -9105,7 +9097,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[best_left_j],/*acceptor_knowni*/best_left_j,
/*splice_pos*/leftpos,nmismatches_shortexon_left,
/*prob*/2.0,/*left*/splicesites[best_left_j]-leftpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
debug4k(printf("shortexon with donor at %d (%llu) ... amb_acceptor at %d (%llu)\n",
@@ -9115,7 +9107,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*acceptor_pos*/rightpos,/*donor_pos*/leftpos,nmismatches_shortexon_middle,
/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/true,/*donor_ambp*/false,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
@@ -9132,13 +9124,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Doublelist_max(probs_donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Substring_chimera_prob(acceptor),
amb_length_donor,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/2.0,/*amb_prob_acceptor*/0.0,
ambcoords_donor,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/splicesites_i_right,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/nmismatches_list_right,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/probs_donor,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
Doublelist_free(&probs_donor);
#ifdef LARGE_GENOMES
Uint8list_free(&ambcoords_donor);
@@ -9153,7 +9144,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[best_left_j],/*acceptor_knowni*/best_left_j,
/*splice_pos*/leftpos,nmismatches_shortexon_left,
/*prob*/2.0,/*left*/splicesites[best_left_j]-leftpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
shortexon = Substring_new_shortexon(/*acceptor_coord*/splicesites[j2],/*acceptor_knowni*/j2,
@@ -9161,14 +9152,14 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
/*acceptor_pos*/rightpos,/*donor_pos*/leftpos,
nmismatches_shortexon_middle,/*acceptor_prob*/2.0,/*donor_prob*/2.0,
/*left*/segmentm_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,/*acceptor_ambp*/false,/*donor_ambp*/false,
segmentm->chrnum,segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
donor = Substring_new_donor(/*donor_coord*/splicesites[best_right_j],/*donor_knowni*/best_right_j,
/*splice_pos*/rightpos,nmismatches_shortexon_right,
/*prob*/2.0,/*left*/splicesites[best_right_j]-rightpos,
- query_compress,querylength,plusp,genestrand,first_read_p,sensedir,segmentm->chrnum,
+ query_compress,querylength,plusp,genestrand,sensedir,segmentm->chrnum,
segmentm->chroffset,segmentm->chrhigh,segmentm->chrlength);
if (acceptor == NULL || shortexon == NULL || donor == NULL) {
@@ -9182,13 +9173,12 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
Substring_chimera_prob(donor),Substring_siteA_prob(shortexon),
Substring_siteD_prob(shortexon),Substring_chimera_prob(acceptor),
/*amb_length_donor*/0,/*amb_length_acceptor*/0,
- /*amb_prob_donor*/0.0,/*amb_prob_acceptor*/0.0,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
/*amb_probs_donor*/NULL,/*amb_probs_acceptor*/NULL,
/*copy_donor_p*/false,/*copy_acceptor_p*/false,/*copy_shortexon_p*/false,
- splicing_penalty,querylength,first_read_p,sensedir,/*sarrayp*/false));
+ splicing_penalty,querylength,sensedir,/*sarrayp*/false));
}
}
Intlist_free(&nmismatches_list_right);
@@ -9210,7 +9200,7 @@ find_doublesplices (int *found_score, List_T hits, List_T *lowprob,
debug4k(printf("Finished find_known_doublesplices with %d hits\n",List_length(hits)));
return hits;
}
-
+#endif
@@ -9222,7 +9212,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
char *queryptr,
#endif
Floors_T floors, int querylength, int query_lastpos, Compress_T query_compress,
- int max_mismatches_allowed, bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
#ifdef DEBUG4E
char *gbuffer;
#endif
@@ -9280,7 +9270,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
/* pos3 was trimpos */
nmismatches_left = Genome_mismatches_left(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug4e(
printf("%d mismatches on left (%d allowed) at:",
@@ -9334,7 +9324,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
if ((hit = Substring_new_donor(/*donor_coord*/splicesites[j],/*donor_knowni*/j,splice_pos,nmismatches,
/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s donor: known at %d (%d mismatches)\n",
@@ -9350,7 +9340,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
if ((hit = Substring_new_acceptor(/*acceptor_coord*/splicesites[j],/*acceptor_knowni*/j,
splice_pos,nmismatches,/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s antiacceptor : known at %d (%d mismatches)\n",
@@ -9368,7 +9358,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
/* pos5 was trimpos+1 */
nmismatches_right = Genome_mismatches_right(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug4e(
printf("%d mismatches on right (%d allowed) at:",nmismatches_right,max_mismatches_allowed);
@@ -9420,7 +9410,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
if ((hit = Substring_new_acceptor(/*acceptor_coord*/splicesites[j],/*acceptor_knowni*/j,
splice_pos,nmismatches,/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s acceptor: known at %d (%d mismatches)\n",
@@ -9436,7 +9426,7 @@ find_spliceends_shortend (List_T **shortend_donors, List_T **shortend_antidonors
if ((hit = Substring_new_donor(/*donor_coord*/splicesites[j],/*donor_knowni*/j,splice_pos,nmismatches,
/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s antidonor: known at %d (%d mismatches)\n",
@@ -9461,7 +9451,7 @@ find_spliceends_distant_dna_plus (List_T **distant_startfrags, List_T **distant_
char *queryptr,
#endif
Floors_T floors, int querylength, int query_lastpos, Compress_T query_compress,
- int max_mismatches_allowed, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, int genestrand) {
#ifdef DEBUG4E
char *gbuffer;
#endif
@@ -9515,7 +9505,7 @@ find_spliceends_distant_dna_plus (List_T **distant_startfrags, List_T **distant_
/* pos3 was trimpos */
nmismatches_left = Genome_mismatches_left(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
debug4e(
printf("%d mismatches on left (%d allowed) at:",
@@ -9545,10 +9535,10 @@ find_spliceends_distant_dna_plus (List_T **distant_startfrags, List_T **distant_
while (splice_pos <= splice_pos_end && nmismatches <= max_mismatches_allowed) {
debug4e(printf(" splice pos %d, nmismatches %d\n",splice_pos,nmismatches));
assert(nmismatches == Genome_count_mismatches_substring(query_compress,segment_left,/*pos5*/0,/*pos3*/splice_pos,
- /*plusp*/true,genestrand,first_read_p));
+ /*plusp*/true,genestrand));
if ((hit = Substring_new_startfrag(/*startfrag_coord*/segment_left + splice_pos,
splice_pos,nmismatches,/*left*/segment_left,query_compress,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> plus startfrag: at %d (%d mismatches)\n",Substring_chimera_pos(hit),nmismatches));
@@ -9570,7 +9560,7 @@ find_spliceends_distant_dna_plus (List_T **distant_startfrags, List_T **distant_
/* pos5 was trimpos+1 */
nmismatches_right = Genome_mismatches_right(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
debug4e(
printf("%d mismatches on right (%d allowed) at:",nmismatches_right,max_mismatches_allowed);
@@ -9601,10 +9591,10 @@ find_spliceends_distant_dna_plus (List_T **distant_startfrags, List_T **distant_
Genome_count_mismatches_substring(query_compress,segment_left,/*pos5*/splice_pos,/*pos3*/querylength,
/*plusp*/true,genestrand,first_read_p)));
assert(nmismatches == Genome_count_mismatches_substring(query_compress,segment_left,/*pos5*/splice_pos,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p));
+ /*plusp*/true,genestrand));
if ((hit = Substring_new_endfrag(/*endfrag_coord*/segment_left + splice_pos,
splice_pos,nmismatches,/*left*/segment_left,query_compress,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> plus endfrag: at %d (%d mismatches)\n",Substring_chimera_pos(hit),nmismatches));
@@ -9634,7 +9624,7 @@ find_spliceends_distant_dna_minus (List_T **distant_startfrags, List_T **distant
char *queryptr,
#endif
Floors_T floors, int querylength, int query_lastpos, Compress_T query_compress,
- int max_mismatches_allowed, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, int genestrand) {
#ifdef DEBUG4E
char *gbuffer;
#endif
@@ -9688,7 +9678,7 @@ find_spliceends_distant_dna_minus (List_T **distant_startfrags, List_T **distant
/* pos3 was trimpos */
nmismatches_left = Genome_mismatches_left(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
debug4e(
printf("%d mismatches on left (%d allowed) at:",
@@ -9718,10 +9708,10 @@ find_spliceends_distant_dna_minus (List_T **distant_startfrags, List_T **distant
while (splice_pos <= splice_pos_end && nmismatches <= max_mismatches_allowed) {
debug4e(printf(" splice pos %d, nmismatches %d\n",splice_pos,nmismatches));
assert(nmismatches == Genome_count_mismatches_substring(query_compress,segment_left,/*pos5*/0,/*pos3*/splice_pos,
- /*plusp*/false,genestrand,first_read_p));
+ /*plusp*/false,genestrand));
if ((hit = Substring_new_endfrag(/*endfrag_coord*/segment_left + splice_pos,
splice_pos,nmismatches,/*left*/segment_left,query_compress,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> minus endfrag: at %d (%d mismatches)\n",Substring_chimera_pos(hit),nmismatches));
@@ -9743,7 +9733,7 @@ find_spliceends_distant_dna_minus (List_T **distant_startfrags, List_T **distant
/* pos5 was trimpos+1 */
nmismatches_right = Genome_mismatches_right(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
debug4e(
printf("%d mismatches on right (%d allowed) at:",nmismatches_right,max_mismatches_allowed);
@@ -9774,10 +9764,10 @@ find_spliceends_distant_dna_minus (List_T **distant_startfrags, List_T **distant
Genome_count_mismatches_substring(query_compress,segment_left,/*pos5*/splice_pos,/*pos3*/querylength,
/*plusp*/false,genestrand,first_read_p)));
assert(nmismatches == Genome_count_mismatches_substring(query_compress,segment_left,/*pos5*/splice_pos,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p));
+ /*plusp*/false,genestrand));
if ((hit = Substring_new_startfrag(/*startfrag_coord*/segment_left + splice_pos,
splice_pos,nmismatches,/*left*/segment_left,query_compress,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> minus startfrag: at %d (%d mismatches)\n",Substring_chimera_pos(hit),nmismatches));
@@ -9811,7 +9801,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
char *queryptr,
#endif
Floors_T floors, int querylength, int query_lastpos, Compress_T query_compress,
- int max_mismatches_allowed, bool plusp, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, bool plusp, int genestrand) {
#ifdef DEBUG4E
char *gbuffer;
#endif
@@ -9889,7 +9879,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
/* pos3 was trimpos */
nmismatches_left = Genome_mismatches_left(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug4e(
printf("%d mismatches on left (%d allowed) at:",
@@ -9971,7 +9961,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
if ((hit = Substring_new_donor(/*donor_coord*/segment_left + splice_pos,/*donor_knowni*/donori_knowni[i],
splice_pos,nmismatches,/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s donor: %f at %d (%d mismatches)\n",
@@ -9990,7 +9980,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_end));
if ((hit = Substring_new_donor(/*donor_coord*/segment_left + splice_pos,/*donor_knowni*/-1,
splice_pos,nmismatches,prob,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s donor: %f at %d (%d mismatches)\n",
@@ -10047,7 +10037,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_end));
if ((hit = Substring_new_acceptor(/*acceptor_coord*/segment_left + splice_pos,/*acceptor_knowni*/antiacceptori_knowni[i],
splice_pos,nmismatches,/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s antiacceptor : %f at %d (%d mismatches)\n",
@@ -10066,7 +10056,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_end));
if ((hit = Substring_new_acceptor(/*acceptor_coord*/segment_left + splice_pos,/*acceptor_knowni*/-1,
splice_pos,nmismatches,prob,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s antiacceptor : %f at %d (%d mismatches)\n",
@@ -10091,7 +10081,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
/* pos5 was trimpos+1 */
nmismatches_right = Genome_mismatches_right(mismatch_positions,max_mismatches_allowed,
query_compress,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug4e(
printf("%d mismatches on right (%d allowed) at:",nmismatches_right,max_mismatches_allowed);
@@ -10173,7 +10163,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_start));
if ((hit = Substring_new_acceptor(/*acceptor_coord*/segment_left + splice_pos,/*acceptor_knowni*/acceptorj_knowni[i],
splice_pos,nmismatches,/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s acceptor: %f at %d (%d mismatches)\n",
@@ -10192,7 +10182,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_start));
if ((hit = Substring_new_acceptor(/*acceptor_coord*/segment_left + splice_pos,/*acceptor_knowni*/-1,
splice_pos,nmismatches,prob,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s acceptor: %f at %d (%d mismatches)\n",
@@ -10249,7 +10239,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_start));
if ((hit = Substring_new_donor(/*donor_coord*/segment_left + splice_pos,/*donor_knowni*/antidonorj_knowni[i],
splice_pos,nmismatches,/*prob*/2.0,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s antidonor: %f at %d (%d mismatches)\n",
@@ -10268,7 +10258,7 @@ find_spliceends_distant_rna (List_T **distant_donors, List_T **distant_antidonor
(unsigned long long) segment_left,splice_pos,nmismatches,splice_pos_start));
if ((hit = Substring_new_donor(/*donor_coord*/segment_left + splice_pos,/*donor_knowni*/-1,
splice_pos,nmismatches,prob,/*left*/segment_left,query_compress,
- querylength,plusp,genestrand,first_read_p,
+ querylength,plusp,genestrand,
sensedir,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength)) != NULL) {
debug4e(printf("=> %s antidonor: %f at %d (%d mismatches)\n",
@@ -10298,7 +10288,7 @@ static List_T
find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
int querylength, int query_lastpos,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
- int max_mismatches_allowed, int genestrand, bool first_read_p) {
+ int max_mismatches_allowed, int genestrand) {
#ifdef DEBUG4T
char *gbuffer;
#endif
@@ -10373,7 +10363,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*//*truncate_pos_left*/querylength,
/*left*/segment_left,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
start_endtype,end_endtype,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
/*sarrayp*/false)) != NULL) {
@@ -10401,7 +10391,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_left = Genome_mismatches_left(mismatch_positions,max_mismatches_allowed,
query_compress_fwd,/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
debug4t(
printf("%d mismatches on left at:",nmismatches_left);
@@ -10417,7 +10407,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_left,max_mismatches_allowed,mismatch_positions[nmismatches_left-1],querylength - max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*//*truncate_pos_left*/querylength,
/*left*/segment_left,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
/*start_endtype*/END,/*end_endtype*/TERM,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10436,7 +10426,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*//*truncate_pos_left*/querylength,
/*left*/segment_left,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
/*start_endtype*/END,/*end_endtype*/TERM,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10464,7 +10454,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_right = Genome_mismatches_right(mismatch_positions,max_mismatches_allowed,
/*query_compress*/query_compress_fwd,
/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
debug4t(
printf("%d mismatches on right at:",nmismatches_right);
@@ -10484,7 +10474,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_right,max_mismatches_allowed,mismatch_positions[nmismatches_right-1],max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*//*truncate_pos_right*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
/*start_endtype*/TERM,/*end_endtype*/END,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10502,7 +10492,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_right,max_mismatches_allowed,mismatch_positions[(nmismatches_right-1)/2],querylength-max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*//*truncate_pos_right*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
/*start_endtype*/TERM,/*end_endtype*/END,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10592,7 +10582,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
start_endtype,end_endtype,segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
/*sarrayp*/false)) != NULL) {
@@ -10621,7 +10611,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_left = Genome_mismatches_left(mismatch_positions,max_mismatches_allowed,
/*query_compress*/query_compress_rev,
/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
debug4t(
printf("%d mismatches on left at:",nmismatches_left);
@@ -10637,7 +10627,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_left,max_mismatches_allowed,mismatch_positions[nmismatches_left-1],querylength - max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*//*querylength-truncate_pos_left*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
/*start_endtype*/TERM,/*end_endtype*/END,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10655,7 +10645,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_left,max_mismatches_allowed,mismatch_positions[(nmismatches_left-1)/2],max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*//*querylength-truncate_pos_left*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
/*start_endtype*/TERM,/*end_endtype*/END,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10682,7 +10672,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_right = Genome_mismatches_right(mismatch_positions,max_mismatches_allowed,
/*query_compress*/query_compress_rev,
/*left*/segment_left,/*pos5*/0,/*pos3*/querylength,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
debug4t(
printf("%d mismatches on right at:",nmismatches_right);
@@ -10698,7 +10688,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_right,max_mismatches_allowed,mismatch_positions[nmismatches_right-1],max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*//*querylength-truncate_pos_right*/querylength,
/*left*/segment_left,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
/*start_endtype*/END,/*end_endtype*/TERM,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10716,7 +10706,7 @@ find_terminals (List_T plus_anchor_segments, List_T minus_anchor_segments,
nmismatches_right,max_mismatches_allowed,mismatch_positions[(nmismatches_right-1)/2],querylength-max_terminal_length));
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*//*querylength-truncate_pos_right*/querylength,
/*left*/segment_left,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
/*start_endtype*/END,/*end_endtype*/TERM,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
@@ -10832,7 +10822,7 @@ find_terminals_by_width_only (struct Segment_T *plus_segments, int plus_nsegment
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,
+ querylength,/*plusp*/true,genestrand,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
/*sarrayp*/false)) != NULL) {
@@ -10864,7 +10854,7 @@ find_terminals_by_width_only (struct Segment_T *plus_segments, int plus_nsegment
if ((hit = Stage3end_new_terminal(/*querystart*/0,/*queryend*/querylength,
/*left*/segment_left,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,
+ querylength,/*plusp*/false,genestrand,
segment->chrnum,segment->chroffset,
segment->chrhigh,segment->chrlength,max_mismatches_allowed,
/*sarrayp*/false)) != NULL) {
@@ -11063,7 +11053,7 @@ find_splicepairs_distant_dna (int *found_score, int *ndistantsplicepairs,
*localsplicing = List_push(*localsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
startfrag,endfrag,/*donor_prob*/0.0,/*acceptor_prob*/0.0,distance,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11074,7 +11064,7 @@ find_splicepairs_distant_dna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
startfrag,endfrag,/*donor_prob*/0.0,/*acceptor_prob*/0.0,distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11154,7 +11144,7 @@ find_splicepairs_distant_dna (int *found_score, int *ndistantsplicepairs,
*localsplicing = List_push(*localsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
startfrag,endfrag,/*donor_prob*/0.0,/*acceptor_prob*/0.0,distance,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11165,7 +11155,7 @@ find_splicepairs_distant_dna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
startfrag,endfrag,/*donor_prob*/0.0,/*acceptor_prob*/0.0,distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11238,7 +11228,7 @@ find_splicepairs_distant_dna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
startfrag,endfrag,/*donor_prob*/0.0,/*acceptor_prob*/0.0,distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11300,7 +11290,7 @@ find_splicepairs_distant_dna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
startfrag,endfrag,/*donor_prob*/0.0,/*acceptor_prob*/0.0,distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11441,7 +11431,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
*localsplicing = List_push(*localsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11452,7 +11442,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11532,7 +11522,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
*localsplicing = List_push(*localsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11543,7 +11533,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11623,7 +11613,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
*localsplicing = List_push(*localsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11634,7 +11624,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11714,7 +11704,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
*localsplicing = List_push(*localsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11725,7 +11715,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11795,7 +11785,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11857,7 +11847,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11920,7 +11910,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -11982,7 +11972,7 @@ find_splicepairs_distant_rna (int *found_score, int *ndistantsplicepairs,
distantsplicing = List_push(distantsplicing,
(void *) Stage3end_new_splice(&(*found_score),nmismatches1,nmismatches2,
donor,acceptor,Substring_chimera_prob(donor),Substring_chimera_prob(acceptor),distance,
- /*shortdistancep*/false,distantsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/false,distantsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12030,8 +12020,8 @@ find_splicepairs_shortend (int *found_score, List_T hits,
Intlist_T nmismatches_list;
Doublelist_T probs_list;
int nmismatches, nmismatches_shortend, nmisses_allowed, support, endlength;
- int amb_length;
#ifdef DEBUG4H
+ int amb_length;
Univcoord_T leftbound, rightbound;
#endif
Univcoord_T bestleft, origleft, chroffset, chrhigh;
@@ -12096,12 +12086,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 1: short-overlap donor_plus: Successful ambiguous from donor #%d with amb_length %d\n",
Substring_splicesites_knowni(donor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,/*acceptor*/NULL,Substring_chimera_prob(donor),Doublelist_max(probs_list),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
/*ambcoords_donor*/NULL,ambcoords,
/*ambi_donor*/NULL,/*ambi_acceptor*/splicesites_i,
/*amb_nmismatches_donor*/NULL,/*nmismatches_acceptor*/nmismatches_list,
@@ -12120,14 +12110,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[bestj],/*acceptor_knowni*/bestj,
Substring_chimera_pos(donor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,/*sensedir*/SENSE_FORWARD,
+ querylength,/*plusp*/true,genestrand,/*sensedir*/SENSE_FORWARD,
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug4h(printf("End 1: short-overlap donor_plus: Successful splice from donor #%d to acceptor #%d\n",
Substring_splicesites_knowni(donor),Substring_splicesites_knowni(acceptor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,acceptor,Substring_chimera_prob(donor),/*acceptor_prob*/2.0,/*distance*/bestleft-origleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12172,12 +12162,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 2: short-overlap acceptor_plus: Successful ambiguous from acceptor #%d with amb_length %d\n",
Substring_splicesites_knowni(acceptor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
/*donor*/NULL,acceptor,Doublelist_max(probs_list),Substring_chimera_prob(acceptor),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
ambcoords,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/splicesites_i,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/nmismatches_list,/*amb_nmismatches_acceptor*/NULL,
@@ -12196,14 +12186,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((donor = Substring_new_donor(/*donor_coord*/splicesites[bestj],/*donor_knowni*/bestj,
Substring_chimera_pos(acceptor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,/*sensedir*/SENSE_FORWARD,
+ querylength,/*plusp*/true,genestrand,/*sensedir*/SENSE_FORWARD,
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug4h(printf("End 2: short-overlap acceptor_plus: Successful splice from acceptor #%d to donor #%d\n",
Substring_splicesites_knowni(acceptor),Substring_splicesites_knowni(donor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
donor,acceptor,/*donor_prob*/2.0,Substring_chimera_prob(acceptor),/*distance*/origleft-bestleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12248,12 +12238,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 3: short-overlap donor_minus: Successful ambiguous from donor #%d with amb_length %d\n",
Substring_splicesites_knowni(donor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,/*acceptor*/NULL,Substring_chimera_prob(donor),Doublelist_max(probs_list),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/splicesites_i,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/nmismatches_list,
@@ -12272,14 +12262,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[bestj],/*acceptor_knowni*/bestj,
querylength-Substring_chimera_pos(donor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,/*sensedir*/SENSE_FORWARD,
+ querylength,/*plusp*/false,genestrand,/*sensedir*/SENSE_FORWARD,
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug4h(printf("End 3: short-overlap donor_minus: Successful splice from donor #%d to acceptor #%d\n",
Substring_splicesites_knowni(donor),Substring_splicesites_knowni(acceptor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,acceptor,Substring_chimera_prob(donor),/*acceptor_prob*/2.0,/*distance*/origleft-bestleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12325,12 +12315,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 4: short-overlap acceptor_minus: Successful ambiguous from acceptor #%d with amb_length %d\n",
Substring_splicesites_knowni(acceptor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
/*donor*/NULL,acceptor,Doublelist_max(probs_list),Substring_chimera_prob(acceptor),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
ambcoords,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/splicesites_i,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/nmismatches_list,/*amb_nmismatches_acceptor*/NULL,
@@ -12349,14 +12339,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((donor = Substring_new_donor(/*donor_coord*/splicesites[bestj],/*donor_knowni*/bestj,
querylength-Substring_chimera_pos(acceptor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,/*sensedir*/SENSE_FORWARD,
+ querylength,/*plusp*/false,genestrand,/*sensedir*/SENSE_FORWARD,
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug4h(printf("End 4: short-overlap acceptor_minus: Successful splice from acceptor #%d to #%d\n",
Substring_splicesites_knowni(acceptor),Substring_splicesites_knowni(donor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
donor,acceptor,/*donor_prob*/2.0,Substring_chimera_prob(acceptor),/*distance*/bestleft-origleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12401,12 +12391,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 5: short-overlap antidonor_plus: Successful ambiguous from antidonor #%d with amb_length %d\n",
Substring_splicesites_knowni(donor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,/*acceptor*/NULL,Substring_chimera_prob(donor),Doublelist_max(probs_list),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/splicesites_i,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/nmismatches_list,
@@ -12425,14 +12415,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[bestj],/*acceptor_knowni*/bestj,
Substring_chimera_pos(donor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,/*sensedir*/SENSE_ANTI,
+ querylength,/*plusp*/true,genestrand,/*sensedir*/SENSE_ANTI,
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug4h(printf("End 5: short-overlap antidonor_plus: Successful splice from antidonor #%d to antiacceptor #%d\n",
Substring_splicesites_knowni(donor),Substring_splicesites_knowni(acceptor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,acceptor,Substring_chimera_prob(donor),/*acceptor_prob*/2.0,/*distance*/origleft-bestleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12478,12 +12468,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 6: short-overlap antiacceptor_plus: Successful ambiguous from antiacceptor #%d with amb_length %d\n",
Substring_splicesites_knowni(acceptor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
/*donor*/NULL,acceptor,Doublelist_max(probs_list),Substring_chimera_prob(acceptor),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
ambcoords,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/splicesites_i,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/nmismatches_list,/*amb_nmismatches_acceptor*/NULL,
@@ -12502,14 +12492,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((donor = Substring_new_donor(/*donor_coord*/splicesites[bestj],/*donor_knowni*/bestj,
Substring_chimera_pos(acceptor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_fwd,
- querylength,/*plusp*/true,genestrand,first_read_p,/*sensedir*/SENSE_ANTI,
+ querylength,/*plusp*/true,genestrand,/*sensedir*/SENSE_ANTI,
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug4h(printf("End 6: short-overlap antiacceptor_plus: Successful splice from antiacceptor #%d to antidonor #%d\n",
Substring_splicesites_knowni(acceptor),Substring_splicesites_knowni(donor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
donor,acceptor,/*donor_prob*/2.0,Substring_chimera_prob(acceptor),/*distance*/bestleft-origleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12555,12 +12545,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 7: short-overlap antidonor_minus: Successful ambiguous from antidonor #%d with amb_length %d\n",
Substring_splicesites_knowni(donor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,/*acceptor*/NULL,Substring_chimera_prob(donor),Doublelist_max(probs_list),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
/*ambcoords_donor*/NULL,ambcoords,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/splicesites_i,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/nmismatches_list,
@@ -12579,14 +12569,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((acceptor = Substring_new_acceptor(/*acceptor_coord*/splicesites[bestj],/*acceptor_knowni*/bestj,
querylength-Substring_chimera_pos(donor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,/*sensedir*/SENSE_ANTI,
+ querylength,/*plusp*/false,genestrand,/*sensedir*/SENSE_ANTI,
Substring_chrnum(donor),Substring_chroffset(donor),
Substring_chrhigh(donor),Substring_chrlength(donor))) != NULL) {
debug4h(printf("End 7: short-overlap antidonor_minus: Successful splice from antidonor #%d to antiacceptor #%d\n",
Substring_splicesites_knowni(donor),Substring_splicesites_knowni(acceptor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches,nmismatches_shortend,
donor,acceptor,Substring_chimera_prob(donor),/*acceptor_prob*/2.0,/*distance*/bestleft-origleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12631,12 +12621,12 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if (endlength < min_shortend || Intlist_length(splicesites_i) > 1) {
ambcoords = lookup_splicesites(&probs_list,splicesites_i,splicesites);
- amb_length = endlength /*- nmismatches_shortend*/;
+ debug4h(amb_length = endlength /*- nmismatches_shortend*/);
debug4h(printf("End 8: short-overlap antiacceptor_minus: Successful ambiguous from antiacceptor #%d with amb_length %d\n",
Substring_splicesites_knowni(acceptor),amb_length));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
/*donor*/NULL,acceptor,Doublelist_max(probs_list),Substring_chimera_prob(acceptor),/*distance*/0U,
- /*shortdistancep*/false,/*penalty*/0,querylength,amb_length,/*amb_prob*/2.0,
+ /*shortdistancep*/false,/*penalty*/0,querylength,
ambcoords,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/splicesites_i,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/nmismatches_list,/*amb_nmismatches_acceptor*/NULL,
@@ -12655,14 +12645,14 @@ find_splicepairs_shortend (int *found_score, List_T hits,
if ((donor = Substring_new_donor(/*donor_coord*/splicesites[bestj],/*donor_knowni*/bestj,
querylength-Substring_chimera_pos(acceptor),nmismatches_shortend,
/*prob*/2.0,/*left*/bestleft,query_compress_rev,
- querylength,/*plusp*/false,genestrand,first_read_p,/*sensedir*/SENSE_ANTI,
+ querylength,/*plusp*/false,genestrand,/*sensedir*/SENSE_ANTI,
Substring_chrnum(acceptor),Substring_chroffset(acceptor),
Substring_chrhigh(acceptor),Substring_chrlength(acceptor))) != NULL) {
debug4h(printf("End 8: short-overlap antiacceptor_minus: Successful splice from antiacceptor #%d to antidonor #%d\n",
Substring_splicesites_knowni(acceptor),Substring_splicesites_knowni(donor)));
hits = List_push(hits,(void *) Stage3end_new_splice(&(*found_score),nmismatches_shortend,nmismatches,
donor,acceptor,/*donor_prob*/2.0,Substring_chimera_prob(acceptor),/*distance*/origleft-bestleft,
- /*shortdistancep*/true,localsplicing_penalty,querylength,/*amb_length*/0,/*amb_prob*/0.0,
+ /*shortdistancep*/true,localsplicing_penalty,querylength,
/*ambcoords_donor*/NULL,/*ambcoords_acceptor*/NULL,
/*amb_knowni_donor*/NULL,/*amb_knowni_acceptor*/NULL,
/*amb_nmismatches_donor*/NULL,/*amb_nmismatches_acceptor*/NULL,
@@ -12820,7 +12810,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
int querylength, int query_lastpos, Floors_T floors,
int indel_penalty_middle, int indel_penalty_end,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
- int fast_level, int genestrand, bool first_read_p) {
+ int fast_level, int genestrand) {
int firstbound, lastbound;
int max_mismatches_allowed;
#if 0
@@ -12867,7 +12857,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
this->plus_positions,
#endif
this->plus_npositions,this->omitted,querylength,query_lastpos,floors,
- /*max_mismatches_allowed*/*done_level,/*plusp*/true);
+ /*plusp*/true);
this->minus_segments = identify_all_segments(&this->minus_nsegments,&(*minus_anchor_segments),
&this->minus_spliceable,&this->minus_nspliceable,
#ifdef LARGE_GENOMES
@@ -12876,17 +12866,17 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
this->minus_positions,
#endif
this->minus_npositions,this->omitted,querylength,query_lastpos,floors,
- /*max_mismatches_allowed*/*done_level,/*plusp*/false);
+ /*plusp*/false);
*subs = find_complete_mm(&(*found_score),&(*nhits),*subs,*plus_anchor_segments,
querylength,/*queryptr:queryuc_ptr,*/
/*query_compress*/query_compress_fwd,
- /*max_mismatches_allowed*/*done_level,/*plusp*/true,genestrand,first_read_p);
+ /*max_mismatches_allowed*/*done_level,/*plusp*/true,genestrand);
*subs = find_complete_mm(&(*found_score),&(*nhits),*subs,*minus_anchor_segments,
querylength,/*queryptr:queryrc,*/
/*query_compress*/query_compress_rev,
- /*max_mismatches_allowed*/*done_level,/*plusp*/false,genestrand,first_read_p);
+ /*max_mismatches_allowed*/*done_level,/*plusp*/false,genestrand);
*segments_computed_p = true;
@@ -12922,7 +12912,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
this->plus_positions,
#endif
this->plus_npositions,this->omitted,querylength,query_lastpos,floors,
- /*max_mismatches_allowed*/*done_level,/*plusp*/true);
+ /*plusp*/true);
this->minus_segments = identify_all_segments(&this->minus_nsegments,&(*minus_anchor_segments),
&this->minus_spliceable,&this->minus_nspliceable,
#ifdef LARGE_GENOMES
@@ -12931,7 +12921,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
this->minus_positions,
#endif
this->minus_npositions,this->omitted,querylength,query_lastpos,floors,
- /*max_mismatches_allowed*/*done_level,/*plusp*/false);
+ /*plusp*/false);
*segments_computed_p = true;
}
@@ -12947,7 +12937,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
queryuc_ptr,queryrc,
#endif
floors,querylength,query_lastpos,query_compress_fwd,query_compress_rev,genome,
- /*indel_mismatches_allowed*/indel_level - indel_penalty,genestrand,first_read_p);
+ /*indel_mismatches_allowed*/indel_level - indel_penalty,genestrand);
if (allow_end_indels_p == true) {
debug(printf("*** Stage 6. End indels with %d-%d mismatches allowed\n",indel_level,indel_penalty));
@@ -12957,7 +12947,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
#endif
querylength,firstbound,lastbound,query_compress_fwd,query_compress_rev,genome,
max_end_insertions,max_end_deletions,min_indel_end_matches,indel_penalty,
- /*indel_mismatches_allowed*/indel_level - indel_penalty,genestrand,first_read_p);
+ /*indel_mismatches_allowed*/indel_level - indel_penalty,genestrand);
}
if (revise_levels_p == true) {
*opt_level = (*found_score < *opt_level) ? *found_score : *opt_level;
@@ -12979,7 +12969,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
queryuc_ptr,queryrc,
#endif
floors,querylength,query_lastpos,query_compress_fwd,query_compress_rev,
- /*indel_mismatches_allowed*/(*done_level) - indel_penalty_middle,genestrand,first_read_p);
+ /*indel_mismatches_allowed*/(*done_level) - indel_penalty_middle,genestrand);
if (revise_levels_p == true) {
*opt_level = (*found_score < *opt_level) ? *found_score : *opt_level;
if ((*done_level = *opt_level + subopt_levels) > user_maxlevel) {
@@ -12997,7 +12987,7 @@ complete_set_mm_indels (int *found_score, bool *segments_computed_p,
#endif
querylength,firstbound,lastbound,query_compress_fwd,query_compress_rev,
max_end_insertions,max_end_deletions,min_indel_end_matches,indel_penalty_end,
- /*indel_mismatches_allowed*/(*done_level) - indel_penalty_end,genestrand,first_read_p);
+ /*indel_mismatches_allowed*/(*done_level) - indel_penalty_end,genestrand);
if (revise_levels_p == true) {
*opt_level = (*found_score < *opt_level) ? *found_score : *opt_level;
if ((*done_level = *opt_level + subopt_levels) > user_maxlevel) {
@@ -13089,6 +13079,7 @@ complete_set_singlesplicing (int *found_score, List_T localsplicing_orig, Floors
}
+#if 0
static List_T
complete_set_doublesplicing (int *found_score, List_T localsplicing_orig, Floors_T floors, T this,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
@@ -13156,6 +13147,8 @@ complete_set_doublesplicing (int *found_score, List_T localsplicing_orig, Floors
return localsplicing;
}
}
+#endif
+
/* Simple table */
typedef struct History_T *History_T;
@@ -13214,7 +13207,7 @@ History_put (History_T this, Univinterval_T interval, List_T gmap_hits) {
}
-/* Also defined in sarray-read.c */
+/* Also defined in sarray-read.c and stage3hr.c */
#define add_bounded(x,plusterm,highbound) ((x + (plusterm) >= highbound) ? (highbound - 1) : x + (plusterm))
#define subtract_bounded(x,minusterm,lowbound) ((x < lowbound + (minusterm)) ? lowbound : x - (minusterm))
@@ -13222,17 +13215,16 @@ History_put (History_T this, Univinterval_T interval, List_T gmap_hits) {
static List_T
run_gmap_for_region (bool *good_start_p, bool *good_end_p, History_T gmap_history,
List_T hits, char *accession, char *queryuc_ptr, int querylength,
- int sense_try, bool favor_right_p, int paired_favor_mode, int zero_offset,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
+ int sense_try, bool favor_right_p,
Univcoord_T mappingstart, Univcoord_T mappingend,
Univcoord_T knownsplice_limit_low, Univcoord_T knownsplice_limit_high,
- bool watsonp, int genestrand, bool first_read_p,
+ bool watsonp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
- Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, int user_maxlevel) {
+ Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
Stage3end_T hit;
#ifdef EXTRACT_GENOMICSEG
char *genomicseg, *genomicseg_alloc;
@@ -13240,7 +13232,6 @@ run_gmap_for_region (bool *good_start_p, bool *good_end_p, History_T gmap_histor
List_T stored_hits;
List_T all_stage2results, p;
- int stage2_source, stage2_indexsize;
Stage2_T stage2;
Univinterval_T interval;
@@ -13256,7 +13247,7 @@ run_gmap_for_region (bool *good_start_p, bool *good_end_p, History_T gmap_histor
Splicetype_T ambig_splicetype_5, ambig_splicetype_3;
double ambig_prob_5, ambig_prob_3;
int ncanonical, nsemicanonical, nnoncanonical;
- int maxintronlen_bound;
+ /* int maxintronlen_bound; */
debug13(printf("Running GMAP at mappingstart %u + %d = mappingend %u, watsonp %d, sense_try %d, querylength %d, limits %u..%u\n",
@@ -13317,22 +13308,20 @@ run_gmap_for_region (bool *good_start_p, bool *good_end_p, History_T gmap_histor
maxintronlen_bound = shortsplicedist;
}
#else
- maxintronlen_bound = shortsplicedist;
+ /* maxintronlen_bound = shortsplicedist; */
#endif
+
/* Note: Use nmatches post-trim to decide if the alignment is high
quality or worth keeping. But if so, then use nmatches_pretrim
for ranking and scoring purposes. */
/* use_shifted_canonical_p == true can be slow and can give wrong answers */
- all_stage2results = Stage2_compute(&stage2_source,&stage2_indexsize,
- /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*query_offset*/0,
+ all_stage2results = Stage2_compute(/*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*query_offset*/0,
/*chrstart*/mappingstart-chroffset,/*chrend*/mappingend-chroffset,
chroffset,chrhigh,/*plusp*/watsonp,genestrand,
-
- oligoindices_major,/*proceed_pctcoverage*/0.5,
- pairpool,diagpool,cellpool,/*localp*/true,
+ oligoindices_major,pairpool,diagpool,cellpool,/*localp*/true,
/*skip_repetitive_p*/true,favor_right_p,/*max_nalignments*/MAX_NALIGNMENTS,
/*debug_graphic_p*/false,/*worker_stopwatch*/NULL,/*diag_debug*/false);
@@ -13394,10 +13383,10 @@ run_gmap_for_region (bool *good_start_p, bool *good_end_p, History_T gmap_histor
if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
ambig_end_length_5,ambig_end_length_3,
ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
+ min_splice_prob,
pairarray,npairs,nsegments,nintrons,nindelbreaks,
/*left*/start,/*genomiclength*/end - start + 1,
- /*plusp*/watsonp,genestrand,first_read_p,
+ /*plusp*/watsonp,genestrand,
accession,querylength,chrnum,chroffset,chrhigh,chrlength,
cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_REGION)) == NULL) {
debug13(printf("Stage3end_new_gmap returns NULL\n"));
@@ -13438,10 +13427,10 @@ run_gmap_for_region (bool *good_start_p, bool *good_end_p, History_T gmap_histor
if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
ambig_end_length_5,ambig_end_length_3,
ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
+ min_splice_prob,
pairarray,npairs,nsegments,nintrons,nindelbreaks,
/*left*/end,/*genomiclength*/start - end + 1,
- /*plusp*/watsonp,genestrand,first_read_p,
+ /*plusp*/watsonp,genestrand,
accession,querylength,chrnum,chroffset,chrhigh,chrlength,
cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_REGION)) == NULL) {
debug13(printf("Stage3end_new_gmap returns NULL\n"));
@@ -13508,7 +13497,7 @@ align_single_hit_with_gmap (Stage3end_T hit, char *queryuc_ptr, int querylength,
Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- int genestrand, bool first_read_p) {
+ int genestrand, bool extend_ends_p) {
/* Both events are tested by Stage3end_anomalous_splice_p */
if (Stage3end_chrnum(hit) == 0) {
/* Translocation */
@@ -13519,16 +13508,24 @@ align_single_hit_with_gmap (Stage3end_T hit, char *queryuc_ptr, int querylength,
return (Stage3end_T) NULL;
} else if (Stage3end_hittype(hit) == GMAP) {
- return (Stage3end_T) NULL;
+ if (Stage3end_plusp(hit) == true) {
+ return Stage3end_gmap_run_gmap_plus(hit,queryuc_ptr,querylength,genestrand,
+ maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ oligoindices_minor,diagpool,cellpool);
+ } else {
+ return Stage3end_gmap_run_gmap_minus(hit,queryuc_ptr,querylength,genestrand,
+ maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ oligoindices_minor,diagpool,cellpool);
+ }
} else if (Stage3end_plusp(hit) == true) {
- return Stage3end_substrings_run_gmap_plus(hit,queryuc_ptr,querylength,genestrand,first_read_p,
+ return Stage3end_substrings_run_gmap_plus(hit,queryuc_ptr,querylength,genestrand,
maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
- oligoindices_minor,diagpool,cellpool);
+ oligoindices_minor,diagpool,cellpool,extend_ends_p);
} else {
- return Stage3end_substrings_run_gmap_minus(hit,queryuc_ptr,querylength,genestrand,first_read_p,
+ return Stage3end_substrings_run_gmap_minus(hit,queryuc_ptr,querylength,genestrand,
maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
- oligoindices_minor,diagpool,cellpool);
+ oligoindices_minor,diagpool,cellpool,extend_ends_p);
}
}
@@ -13728,13 +13725,11 @@ convert_plus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
if (close_mappingstart_p == true && close_mappingend_p == true) {
debug13(printf("Single hit: Running gmap with close mappingstart and close mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,
- close_mappingstart_last,close_mappingend_last,
+ /*sense_try*/0,favor_right_p,close_mappingstart_last,close_mappingend_last,
close_knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_start_p == true && good_end_p == true) {
/* Success */
@@ -13744,46 +13739,42 @@ convert_plus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
if (fallback_mappingend_p == true) {
debug13(printf("Single hit: Re-running gmap with close mappingstart only\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,close_mappingstart_last,mappingend,
+ /*sense_try*/0,favor_right_p,close_mappingstart_last,mappingend,
close_knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else if (good_end_p == true) {
if (fallback_mappingstart_p == true) {
debug13(printf("Single hit: Re-running gmap with close mappingend only\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,mappingstart,close_mappingend_last,
+ /*sense_try*/0,favor_right_p,mappingstart,close_mappingend_last,
knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else {
if (fallback_mappingstart_p == true && fallback_mappingend_p == true) {
debug13(printf("Single hit: Re-running gmap with far mappingstart and mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ /*sense_try*/0,favor_right_p,mappingstart,mappingend,
knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
}
} else if (close_mappingstart_p == true) {
debug13(printf("Single hit: Running gmap with close mappingstart\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,close_mappingstart_last,mappingend,
+ /*sense_try*/0,favor_right_p,close_mappingstart_last,mappingend,
close_knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_start_p == true) {
/* Success */
} else if (gmap_rerun_p == false) {
@@ -13791,23 +13782,21 @@ convert_plus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
} else if (fallback_mappingstart_p == true) {
debug13(printf("Single hit: Re-running gmap with far mappingstart\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ /*sense_try*/0,favor_right_p,mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else if (close_mappingend_p == true) {
debug13(printf("Single hit: Running gmap with close mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,mappingstart,close_mappingend_last,
+ /*sense_try*/0,favor_right_p,mappingstart,close_mappingend_last,
knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_end_p == true) {
/* Success */
} else if (gmap_rerun_p == false) {
@@ -13815,23 +13804,21 @@ convert_plus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
} else if (fallback_mappingend_p == true) {
debug13(printf("Single hit: Re-running gmap with far mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ /*sense_try*/0,favor_right_p,mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else {
debug13(printf("Single hit: Running gmap with far mappingstart and mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ /*sense_try*/0,favor_right_p,mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/true,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/true,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
}
}
@@ -14037,13 +14024,12 @@ convert_minus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
if (close_mappingstart_p == true && close_mappingend_p == true) {
debug13(printf("Single hit: Running gmap with close mappingstart and close mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
- query_compress_fwd,query_compress_rev,
+ /*sense_try*/0,favor_right_p,query_compress_fwd,query_compress_rev,
close_mappingstart_last,close_mappingend_last,
close_knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_start_p == true && good_end_p == true) {
/* Success */
@@ -14053,46 +14039,46 @@ convert_minus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
if (fallback_mappingend_p == true) {
debug13(printf("Single hit: Re-running gmap with close mappingstart only\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,close_mappingstart_last,mappingend,
close_knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else if (good_end_p == true) {
if (fallback_mappingstart_p == true) {
debug13(printf("Single hit: Re-running gmap with close mappingend only\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,mappingstart,close_mappingend_last,
knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else {
if (fallback_mappingstart_p == true && fallback_mappingend_p == true) {
debug13(printf("Single hit: Re-running gmap with far mappingstart and mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,mappingstart,mappingend,
knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
}
} else if (close_mappingstart_p == true) {
debug13(printf("Single hit: Running gmap with close mappingstart\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,close_mappingstart_last,mappingend,
close_knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_start_p == true) {
/* Success */
} else if (gmap_rerun_p == false) {
@@ -14100,23 +14086,23 @@ convert_minus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
} else if (fallback_mappingstart_p == true) {
debug13(printf("Single hit: Re-running gmap with far mappingstart\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else if (close_mappingend_p == true) {
debug13(printf("Single hit: Running gmap with close mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,mappingstart,close_mappingend_last,
knownsplice_limit_low,close_knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_end_p == true) {
/* Success */
} else if (gmap_rerun_p == false) {
@@ -14124,23 +14110,23 @@ convert_minus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
} else if (fallback_mappingend_p == true) {
debug13(printf("Single hit: Re-running gmap with far mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else {
debug13(printf("Single hit: Running gmap with far mappingstart and mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,hits,accession,queryuc_ptr,querylength,
- /*sense_try*/0,favor_right_p,/*paired_favor_mode*/0,/*zero_offset*/0,
+ /*sense_try*/0,favor_right_p,
query_compress_fwd,query_compress_rev,mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- /*plusp*/false,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ /*plusp*/false,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
}
}
@@ -14152,18 +14138,15 @@ convert_minus_segments_to_gmap_via_region (History_T gmap_history, List_T hits,
/* Segment chaining */
static List_T
-convert_plus_segments_to_gmap (History_T gmap_history, List_T hits,
- char *accession, char *queryuc_ptr, int querylength, int query_lastpos,
+convert_plus_segments_to_gmap (List_T hits, char *queryuc_ptr, int querylength, int query_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
char *queryrc, bool invertedp,
#endif
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
List_T anchor_segments, struct Segment_T *plus_segments, int plus_nsegments,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- int user_maxlevel, int genestrand, bool first_read_p,
- bool require_pairing_p) {
+ int genestrand, bool require_pairing_p) {
Univcoord_T chroffset, chrhigh, mappingpos;
Univcoord_T origlow, orighigh;
Univcoord_T close_mappingstart_last, close_mappingend_last,
@@ -14617,8 +14600,7 @@ convert_plus_segments_to_gmap (History_T gmap_history, List_T hits,
seglength = (segment->querypos3 + index1part) - querypos;
Genome_get_segment_blocks_left(gsequence_orig,gsequence_alt,/*right*/chroffset+genomepos+seglength,
seglength,chroffset,/*revcomp*/false);
- debug13(printf("At %u, gsequence_orig %s\n",genomepos,gsequence_orig));
-
+
i = 0;
while (i < seglength && querypos < boundpos && genomepos < min_genomepos) {
c = queryuc_ptr[querypos];
@@ -14750,10 +14732,10 @@ convert_plus_segments_to_gmap (History_T gmap_history, List_T hits,
if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
ambig_end_length_5,ambig_end_length_3,
ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
+ min_splice_prob,
pairarray,npairs,nsegments,nintrons,nindelbreaks,
/*left*/start,/*genomiclength*/end - start + 1,
- /*plusp*/true,genestrand,first_read_p,
+ /*plusp*/true,genestrand,
/*accession*/NULL,querylength,chrnum,chroffset,chrhigh,chrlength,
cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SEGMENTS)) == NULL) {
@@ -14793,18 +14775,15 @@ convert_plus_segments_to_gmap (History_T gmap_history, List_T hits,
/* Segment chaining */
static List_T
-convert_minus_segments_to_gmap (History_T gmap_history, List_T hits,
- char *accession, char *queryuc_ptr, int querylength, int query_lastpos,
+convert_minus_segments_to_gmap (List_T hits, char *queryuc_ptr, int querylength, int query_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
char *queryrc, bool invertedp,
#endif
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
List_T anchor_segments, struct Segment_T *minus_segments, int minus_nsegments,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- int user_maxlevel, int genestrand, bool first_read_p,
- bool require_pairing_p) {
+ int genestrand, bool require_pairing_p) {
Univcoord_T chroffset, chrhigh, mappingpos;
Univcoord_T origlow, orighigh;
Univcoord_T close_mappingstart_last, close_mappingend_last,
@@ -15388,10 +15367,10 @@ convert_minus_segments_to_gmap (History_T gmap_history, List_T hits,
if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
ambig_end_length_5,ambig_end_length_3,
ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
+ min_splice_prob,
pairarray,npairs,nsegments,nintrons,nindelbreaks,
/*left*/end,/*genomiclength*/start - end + 1,
- /*plusp*/false,genestrand,first_read_p,
+ /*plusp*/false,genestrand,
/*accession*/NULL,querylength,chrnum,chroffset,chrhigh,chrlength,
cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SEGMENTS)) == NULL) {
FREE_OUT(pairarray);
@@ -15429,13 +15408,11 @@ convert_minus_segments_to_gmap (History_T gmap_history, List_T hits,
static List_T
-align_singleend_with_gmap (History_T gmap_history, List_T result, T this,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
- char *accession, char *queryuc_ptr, int querylength, int query_lastpos,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+align_singleend_with_gmap (List_T result, char *queryuc_ptr, int querylength,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- int user_maxlevel, int cutoff_level, bool first_read_p) {
+ int user_maxlevel) {
List_T new_result = NULL;
Stage3end_T hit, gmap;
List_T p;
@@ -15499,7 +15476,7 @@ align_singleend_with_gmap (History_T gmap_history, List_T result, T this,
#endif
oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- genestrand,first_read_p)) != NULL) {
+ genestrand,/*extend_ends_p*/false)) != NULL) {
debug13(missing_hit = querylength - Stage3end_nmatches_posttrim(hit));
debug13(missing_gmap = querylength - Stage3end_nmatches_posttrim(gmap));
debug13(printf("GMAP %p with %d matches, %d missing compared with original hit with %d matches, %d missing\n",
@@ -15544,16 +15521,16 @@ align_singleend_with_gmap (History_T gmap_history, List_T result, T this,
/* done_level should probably be renamed final_level. opt_level
should probably be renamed found_level or opt_level. */
static List_T
-align_end (int *cutoff_level, History_T gmap_history, T this,
+align_end (int *cutoff_level, T this,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
- char *accession, char *queryuc_ptr, char *queryrc, int querylength, int query_lastpos,
+ char *queryuc_ptr, char *queryrc, int querylength, int query_lastpos,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int indexdb_size_threshold, Floors_T *floors_array,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- int user_maxlevel, int min_coverage, int indel_penalty_middle, int indel_penalty_end,
+ int user_maxlevel, int indel_penalty_middle, int indel_penalty_end,
int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
bool keep_floors_p, int genestrand, bool first_read_p) {
@@ -15563,7 +15540,6 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
List_T plus_anchor_segments = NULL, minus_anchor_segments = NULL;
List_T p;
Stage3end_T hit, gmap;
- int nmisses_allowed_sarray;
int found_score, done_level, opt_level, fast_level, mismatch_level, nmismatches;
int max_splice_mismatches, i;
int nhits = 0, nsplicepairs = 0;
@@ -15576,6 +15552,9 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
bool segments_computed_p = false;
Indexdb_T plus_indexdb, minus_indexdb;
bool allvalidp;
+#ifndef LARGE_GENOMES
+ int nmisses_allowed_sarray;
+#endif
#ifdef DEBUG13
int missing_hit, missing_gmap;
#endif
@@ -15637,17 +15616,16 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
nhits = 0;
+#ifndef LARGE_GENOMES
nmisses_allowed_sarray = *cutoff_level;
-#ifndef LARGE_GENOMES
if (use_only_sarray_p == true || (use_sarray_p == true && querylength < min_kmer_readlength)) {
hits = Sarray_search_greedy(&(*cutoff_level),
- queryuc_ptr,queryrc,querylength,query_compress_fwd,query_compress_rev,maxpeelback,pairpool,
- dynprogL,dynprogM,dynprogR,oligoindices_minor,diagpool,cellpool,
- nmisses_allowed_sarray,genestrand,first_read_p);
+ queryuc_ptr,queryrc,querylength,query_compress_fwd,query_compress_rev,
+ nmisses_allowed_sarray,genestrand);
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
@@ -15670,10 +15648,8 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
spanningsetp = false; /* Suffix array search replaces spanning set */
debug(printf("Trying suffix array\n"));
- greedy = Sarray_search_greedy(&found_score,
- queryuc_ptr,queryrc,querylength,query_compress_fwd,query_compress_rev,maxpeelback,pairpool,
- dynprogL,dynprogM,dynprogR,oligoindices_minor,diagpool,cellpool,
- nmisses_allowed_sarray,genestrand,first_read_p);
+ greedy = Sarray_search_greedy(&found_score,queryuc_ptr,queryrc,querylength,query_compress_fwd,query_compress_rev,
+ nmisses_allowed_sarray,genestrand);
opt_level = (found_score < opt_level) ? found_score : opt_level;
if ((done_level = opt_level + subopt_levels) > user_maxlevel) {
@@ -15691,8 +15667,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* Search 2: Exact/subs via spanning set */
if (spanningsetp == true) {
- read_oligos(&allvalidp,this,queryuc_ptr,querylength,query_lastpos,/*genestrand*/0,
- /*first_read_p*/true);
+ read_oligos(&allvalidp,this,queryuc_ptr,querylength,query_lastpos,/*genestrand*/0);
/* 1. Exact. Requires compress if cmet or genomealt. Creates and uses spanning set. */
mismatch_level = 0;
@@ -15705,7 +15680,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
} else {
debug(printf("fast_level = %d\n",fast_level));
debug(printf("*** Stage 1. Exact ***\n"));
- subs = find_spanning_exact_matches(&found_score,&nhits,/*hits*/NULL,this,genestrand,first_read_p,
+ subs = find_spanning_exact_matches(&found_score,&nhits,/*hits*/NULL,this,genestrand,
querylength,query_lastpos,plus_indexdb,minus_indexdb,
query_compress_fwd,query_compress_rev);
opt_level = (found_score < opt_level) ? found_score : opt_level;
@@ -15719,7 +15694,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* 2. One mismatch. Requires spanning set and compress. */
if (allvalidp && querylength >= one_miss_querylength && done_level >= 1) {
debug(printf("*** Stage 2. One miss ***\n"));
- subs = find_spanning_onemiss_matches(&found_score,&nhits,subs,this,genestrand,first_read_p,
+ subs = find_spanning_onemiss_matches(&found_score,&nhits,subs,this,genestrand,
querylength,query_compress_fwd,query_compress_rev);
opt_level = (found_score < opt_level) ? found_score : opt_level;
if ((done_level = opt_level + subopt_levels) > user_maxlevel) {
@@ -15733,7 +15708,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
if (allvalidp && done_level >= 2) {
while (mismatch_level <= fast_level && mismatch_level <= done_level) {
debug(printf("*** Stage 3 (level %d). Spanning set mismatches ***\n",mismatch_level));
- subs = find_spanning_multimiss_matches(&found_score,&nhits,subs,this,genestrand,first_read_p,
+ subs = find_spanning_multimiss_matches(&found_score,&nhits,subs,this,genestrand,
NREQUIRED_FAST,querylength,query_compress_fwd,query_compress_rev,
/*nmisses_allowed*/mismatch_level);
opt_level = (found_score < opt_level) ? found_score : opt_level;
@@ -15761,8 +15736,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
if (completesetp == true) {
if (this->read_oligos_p == false) {
- read_oligos(&allvalidp,this,queryuc_ptr,querylength,query_lastpos,/*genestrand*/0,
- /*first_read_p*/true);
+ read_oligos(&allvalidp,this,queryuc_ptr,querylength,query_lastpos,/*genestrand*/0);
}
floors = compute_floors(&any_omitted_p,&alloc_floors_p,floors_array,this,querylength,query_lastpos,
@@ -15778,7 +15752,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
#endif
querylength,query_lastpos,floors,indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
- fast_level,genestrand,first_read_p);
+ fast_level,genestrand);
if (found_score <= done_level) {
debug(printf("Test for completeset: false because found_score %d >done_level %d\n",found_score,done_level));
completesetp = false;
@@ -15816,7 +15790,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
this->plus_positions,
#endif
this->plus_npositions,this->omitted,querylength,query_lastpos,floors,
- /*max_mismatches_allowed*/done_level,/*plusp*/true);
+ /*plusp*/true);
this->minus_segments = identify_all_segments(&this->minus_nsegments,&minus_anchor_segments,
&this->minus_spliceable,&this->minus_nspliceable,
#ifdef LARGE_GENOMES
@@ -15825,7 +15799,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
this->minus_positions,
#endif
this->minus_npositions,this->omitted,querylength,query_lastpos,floors,
- /*max_mismatches_allowed*/done_level,/*plusp*/false);
+ /*plusp*/false);
segments_computed_p = true;
}
@@ -15841,8 +15815,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* Mark ambiguous splices only for single-end reads */
singlesplicing = Stage3end_mark_ambiguous_splices(&ambiguousp,singlesplicing);
#endif
- singlesplicing = Stage3end_optimal_score(singlesplicing,/*cutoff_level*/opt_level,subopt_levels,
- query_compress_fwd,query_compress_rev,querylength,
+ singlesplicing = Stage3end_optimal_score(singlesplicing,query_compress_fwd,query_compress_rev,querylength,
/*keep_gmap_p*/true,/*finalp*/false);
if (singlesplicing) {
@@ -15879,8 +15852,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* Mark ambiguous splices only for single-end reads */
doublesplicing = Stage3end_mark_ambiguous_splices(&ambiguousp,doublesplicing);
#endif
- doublesplicing = Stage3end_optimal_score(doublesplicing,/*cutoff_level*/opt_level,subopt_levels,
- query_compress_fwd,query_compress_rev,querylength,
+ doublesplicing = Stage3end_optimal_score(doublesplicing,query_compress_fwd,query_compress_rev,querylength,
/*keep_gmap_p*/true,/*finalp*/false);
if (doublesplicing) {
@@ -15922,7 +15894,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/*queryptr*/queryuc_ptr,
#endif
floors,querylength,query_lastpos,/*query_compress*/query_compress_fwd,
- max_splice_mismatches,/*plusp*/true,genestrand,first_read_p);
+ max_splice_mismatches,/*plusp*/true,genestrand);
debug(printf("Finished find_spliceends (plus)\n"));
debug(printf("Starting find_spliceends (minus) with %d anchor segments\n",List_length(minus_anchor_segments)));
@@ -15932,7 +15904,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/*queryptr*/queryrc,
#endif
floors,querylength,query_lastpos,/*query_compress*/query_compress_rev,
- max_splice_mismatches,/*plusp*/false,genestrand,first_read_p);
+ max_splice_mismatches,/*plusp*/false,genestrand);
debug(printf("Finished find_spliceends (minus)\n"));
shortendsplicing = find_splicepairs_shortend(&found_score,shortendsplicing,
@@ -16002,7 +15974,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/*queryptr*/queryuc_ptr,
#endif
floors,querylength,query_lastpos,/*query_compress*/query_compress_fwd,
- max_splice_mismatches,genestrand,first_read_p);
+ max_splice_mismatches,genestrand);
debug(printf("Finished find_spliceends_distant_dna_plus\n"));
debug(printf("Starting find_spliceends_distant_dna_minus\n"));
@@ -16011,7 +15983,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/*queryptr*/queryrc,
#endif
floors,querylength,query_lastpos,/*query_compress*/query_compress_rev,
- max_splice_mismatches,genestrand,first_read_p);
+ max_splice_mismatches,genestrand);
debug(printf("Finished find_spliceends_distant_dna_minus\n"));
nmismatches = 0;
@@ -16048,8 +16020,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* Excess distant splicing should be freed already in find_splicepairs_distant_rna */
debug(printf("Entering Stage3end_optimal_score with %d hits\n",List_length(distantsplicing)));
- distantsplicing = Stage3end_optimal_score(distantsplicing,opt_level,subopt_levels,
- query_compress_fwd,query_compress_rev,querylength,
+ distantsplicing = Stage3end_optimal_score(distantsplicing,query_compress_fwd,query_compress_rev,querylength,
/*keep_gmap_p*/true,/*finalp*/false);
debug(printf("Exiting Stage3end_optimal_score with %d hits\n",List_length(distantsplicing)));
@@ -16066,8 +16037,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
if (longsinglesplicing != NULL) {
debug(printf("Entering Stage3end_optimal_score with %d longsinglesplicing hits\n",List_length(longsinglesplicing)));
- longsinglesplicing = Stage3end_optimal_score(longsinglesplicing,opt_level,subopt_levels,
- query_compress_fwd,query_compress_rev,querylength,
+ longsinglesplicing = Stage3end_optimal_score(longsinglesplicing,query_compress_fwd,query_compress_rev,querylength,
/*keep_gmap_p*/true,/*finalp*/false);
debug(printf("Exiting Stage3end_optimal_score with %d hits\n",List_length(longsinglesplicing)));
@@ -16117,7 +16087,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/*queryptr*/queryuc_ptr,
#endif
floors,querylength,query_lastpos,/*query_compress*/query_compress_fwd,
- max_splice_mismatches,/*plusp*/true,genestrand,first_read_p);
+ max_splice_mismatches,/*plusp*/true,genestrand);
debug(printf("Finished find_spliceends_distant_rna (plus)\n"));
@@ -16128,7 +16098,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/*queryptr*/queryrc,
#endif
floors,querylength,query_lastpos,/*query_compress*/query_compress_rev,
- max_splice_mismatches,/*plusp*/false,genestrand,first_read_p);
+ max_splice_mismatches,/*plusp*/false,genestrand);
debug(printf("Finished find_spliceends_distant_rna (minus)\n"));
@@ -16176,8 +16146,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
/* Excess distant splicing should be freed already in find_splicepairs_distant_rna */
debug(printf("Entering Stage3end_optimal_score with %d hits\n",List_length(distantsplicing)));
- distantsplicing = Stage3end_optimal_score(distantsplicing,opt_level,subopt_levels,
- query_compress_fwd,query_compress_rev,querylength,
+ distantsplicing = Stage3end_optimal_score(distantsplicing,query_compress_fwd,query_compress_rev,querylength,
/*keep_gmap_p*/true,/*finalp*/false);
debug(printf("Exiting Stage3end_optimal_score with %d hits\n",List_length(distantsplicing)));
@@ -16194,8 +16163,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
if (longsinglesplicing != NULL) {
debug(printf("Entering Stage3end_optimal_score with %d longsinglesplicing hits\n",List_length(longsinglesplicing)));
- longsinglesplicing = Stage3end_optimal_score(longsinglesplicing,opt_level,subopt_levels,
- query_compress_fwd,query_compress_rev,querylength,
+ longsinglesplicing = Stage3end_optimal_score(longsinglesplicing,query_compress_fwd,query_compress_rev,querylength,
/*keep_gmap_p*/true,/*finalp*/false);
debug(printf("Exiting Stage3end_optimal_score with %d hits\n",List_length(longsinglesplicing)));
@@ -16242,7 +16210,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
terminals = find_terminals(plus_anchor_segments,minus_anchor_segments,
querylength,query_lastpos,
query_compress_fwd,query_compress_rev,
- /*max_mismatches_allowed*/done_level,genestrand,first_read_p);
+ /*max_mismatches_allowed*/done_level,genestrand);
}
debug(printf("Before GMAP:\n"));
@@ -16276,27 +16244,22 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
gmap_hits = (List_T) NULL;
if (gmapp == true) {
- gmap_hits = convert_plus_segments_to_gmap(gmap_history,/*hits*/NULL,
- accession,queryuc_ptr,querylength,query_lastpos,
+ gmap_hits = convert_plus_segments_to_gmap(/*hits*/NULL,queryuc_ptr,querylength,query_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc,Shortread_invertedp(queryseq),
#endif
- query_compress_fwd,query_compress_rev,
-
plus_anchor_segments,this->plus_segments,this->plus_nsegments,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel,genestrand,first_read_p,/*require_pairing_p*/false);
- gmap_hits = convert_minus_segments_to_gmap(gmap_history,/*hits*/gmap_hits,
- accession,queryuc_ptr,querylength,query_lastpos,
+ genestrand,/*require_pairing_p*/false);
+ gmap_hits = convert_minus_segments_to_gmap(/*hits*/gmap_hits,queryuc_ptr,querylength,query_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc,Shortread_invertedp(queryseq),
#endif
- query_compress_fwd,query_compress_rev,
minus_anchor_segments,this->minus_segments,this->minus_nsegments,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel,genestrand,first_read_p,/*require_pairing_p*/false);
+ genestrand,/*require_pairing_p*/false);
opt_level = (found_score < opt_level) ? found_score : opt_level;
if ((done_level = opt_level + subopt_levels) > user_maxlevel) {
@@ -16328,7 +16291,7 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
#endif
oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- genestrand,first_read_p)) != NULL) {
+ genestrand,/*extend_ends_p*/true)) != NULL) {
debug13(missing_hit = querylength - Stage3end_nmatches_posttrim(hit));
debug13(missing_gmap = querylength - Stage3end_nmatches_posttrim(gmap));
debug13(printf("GMAP %p with %d matches, %d missing compared with original terminal with %d matches, %d missing\n",
@@ -16351,36 +16314,33 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
if (gmap_improvement_p == false) {
debug(printf("No GMAP improvement: Before remove_overlaps at cutoff level %d: %d\n",*cutoff_level,List_length(hits)));
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/true,/*finalp*/true);
/* hits = Stage3end_reject_trimlengths(hits); */
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
- debug(printf("After remove_overlaps: %d\n",List_length(hits)));
+ debug(printf("After remove_overlaps (1): %d\n",List_length(hits)));
} else {
debug(printf("GMAP improvement: Before remove_overlaps at cutoff level %d: %d\n",*cutoff_level,List_length(hits)));
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/true,/*finalp*/false);
/* Don't reject based on trimlength until after GMAP improvements */
hits = Stage3end_remove_overlaps(hits,/*finalp*/false);
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/false,/*finalp*/false);
hits = Stage3end_resolve_multimapping(hits);
- debug(printf("After remove_overlaps: %d\n",List_length(hits)));
+ debug(printf("After remove_overlaps (2): %d\n",List_length(hits)));
- hits = align_singleend_with_gmap(gmap_history,hits,this,query_compress_fwd,query_compress_rev,
- accession,queryuc_ptr,querylength,query_lastpos,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel,*cutoff_level,
- first_read_p);
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = align_singleend_with_gmap(hits,queryuc_ptr,querylength,oligoindices_minor,
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/true,/*finalp*/true);
/* hits = Stage3end_reject_trimlengths(hits); */
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
- hits = Stage3end_optimal_score(hits,*cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
}
@@ -16396,15 +16356,14 @@ align_end (int *cutoff_level, History_T gmap_history, T this,
static Stage3end_T *
-single_read (int *npaths, int *first_absmq, int *second_absmq,
+single_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
Shortread_T queryseq, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
int indexdb_size_threshold, Floors_T *floors_array,
double user_maxlevel_float, double user_mincoverage_float,
int indel_penalty_middle, int indel_penalty_end,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
- Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
+ Oligoindex_array_T oligoindices_minor, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
bool keep_floors_p) {
Stage3end_T *stage3array;
@@ -16428,7 +16387,7 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
if (querylength > MAX_READLENGTH) {
fprintf(stderr,"Read %s has length %d > MAX_READLENGTH %d. Either run configure and make again with a higher value of MAX_READLENGTH, or consider using GMAP instead.\n",
Shortread_accession(queryseq),querylength,MAX_READLENGTH);
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
return (Stage3end_T *) NULL;
}
#endif
@@ -16467,24 +16426,25 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
query_lastpos = querylength - index1part;
gmap_history = History_new();
- hits = align_end(&cutoff_level,gmap_history,this,
- query_compress_fwd,query_compress_rev,
- Shortread_accession(queryseq),queryuc_ptr,queryrc,querylength,query_lastpos,
+ hits = align_end(&cutoff_level,this,query_compress_fwd,query_compress_rev,
+ queryuc_ptr,queryrc,querylength,query_lastpos,
indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel,min_coverage,indel_penalty_middle,indel_penalty_end,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ user_maxlevel,indel_penalty_middle,indel_penalty_end,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
keep_floors_p,/*genestrand*/0,/*first_read_p*/true);
hits = Stage3end_filter_coverage(hits,min_coverage);
- if ((*npaths = List_length(hits)) == 0) {
+ if (hits == NULL) {
+ *npaths_primary = *npaths_altloc = 0;
stage3array = (Stage3end_T *) NULL;
} else {
+ Stage3end_count_hits(&(*npaths_primary),&(*npaths_altloc),hits);
stage3array = (Stage3end_T *) List_to_array_out(hits,NULL); List_free(&hits); /* Return value */
- stage3array = Stage3end_eval_and_sort(&(*npaths),&(*first_absmq),&(*second_absmq),
- stage3array,maxpaths_search,queryseq,queryuc_ptr,queryrc,
+ stage3array = Stage3end_eval_and_sort(/*npaths*/(*npaths_primary) + (*npaths_altloc),
+ &(*first_absmq),&(*second_absmq),
+ stage3array,maxpaths_search,queryseq,queryuc_ptr,
query_compress_fwd,query_compress_rev,
quality_string,/*displayp*/true);
}
@@ -16498,14 +16458,14 @@ single_read (int *npaths, int *first_absmq, int *second_absmq,
static Stage3end_T *
-single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_absmq,
+single_read_tolerant_nonstranded (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
Shortread_T queryseq, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
int indexdb_size_threshold, Floors_T *floors_array,
double user_maxlevel_float, double user_mincoverage_float,
int indel_penalty_middle, int indel_penalty_end,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
bool keep_floors_p) {
@@ -16531,7 +16491,7 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
if (querylength > MAX_READLENGTH) {
fprintf(stderr,"Read %s has length %d > MAX_READLENGTH %d. Either run configure and make again with a higher value of MAX_READLENGTH, or consider using GMAP instead.\n",
Shortread_accession(queryseq),querylength,MAX_READLENGTH);
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
return (Stage3end_T *) NULL;
}
#endif
@@ -16572,50 +16532,47 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
#endif
make_complement_buffered(queryrc,queryuc_ptr,querylength);
- if (read_oligos(&allvalidp,this_geneplus,queryuc_ptr,querylength,query_lastpos,/*genestrand*/+1,
- /*first_read_p*/true) > 0) {
- hits_geneplus = align_end(&cutoff_level,gmap_history,this_geneplus,
- query_compress_fwd,query_compress_rev,
- Shortread_accession(queryseq),queryuc_ptr,queryrc,querylength,query_lastpos,
- indexdb_fwd,indexdb_rev,indexdb_size_threshold,
- floors_array,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel,min_coverage,indel_penalty_middle,indel_penalty_end,
+ if (read_oligos(&allvalidp,this_geneplus,queryuc_ptr,querylength,query_lastpos,/*genestrand*/+1) > 0) {
+ hits_geneplus = align_end(&cutoff_level,this_geneplus,query_compress_fwd,query_compress_rev,
+ queryuc_ptr,queryrc,querylength,query_lastpos,
+ indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ user_maxlevel,indel_penalty_middle,indel_penalty_end,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
keep_floors_p,/*genestrand*/+1,/*first_read_p*/true);
}
- if (read_oligos(&allvalidp,this_geneminus,queryuc_ptr,querylength,query_lastpos,/*genestrand*/+2,
- /*first_read_p*/true) > 0) {
- hits_geneminus = align_end(&cutoff_level,gmap_history,this_geneminus,
- query_compress_fwd,query_compress_rev,
- Shortread_accession(queryseq),queryuc_ptr,queryrc,querylength,query_lastpos,
- indexdb_fwd,indexdb_rev,indexdb_size_threshold,
- floors_array,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel,min_coverage,indel_penalty_middle,indel_penalty_end,
+ if (read_oligos(&allvalidp,this_geneminus,queryuc_ptr,querylength,query_lastpos,/*genestrand*/+2) > 0) {
+ hits_geneminus = align_end(&cutoff_level,this_geneminus,query_compress_fwd,query_compress_rev,
+ queryuc_ptr,queryrc,querylength,query_lastpos,
+ indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ user_maxlevel,indel_penalty_middle,indel_penalty_end,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
keep_floors_p,/*genestrand*/+2,/*first_read_p*/true);
}
hits = List_append(hits_geneplus,hits_geneminus);
- hits = Stage3end_optimal_score(hits,cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/true,/*finalp*/true);
/* hits = Stage3end_reject_trimlengths(hits); */
hits = Stage3end_remove_overlaps(hits,/*finalp*/true);
- hits = Stage3end_optimal_score(hits,cutoff_level,subopt_levels,query_compress_fwd,query_compress_rev,
+ hits = Stage3end_optimal_score(hits,query_compress_fwd,query_compress_rev,
querylength,/*keep_gmap_p*/false,/*finalp*/true);
hits = Stage3end_resolve_multimapping(hits);
hits = Stage3end_filter_coverage(hits,min_coverage);
- if ((*npaths = List_length(hits)) == 0) {
+ if (hits == NULL) {
+ *npaths_primary = *npaths_altloc = 0;
stage3array = (Stage3end_T *) NULL;
} else {
+ Stage3end_count_hits(&(*npaths_primary),&(*npaths_altloc),hits);
stage3array = (Stage3end_T *) List_to_array_out(hits,NULL); List_free(&hits); /* Return value */
- stage3array = Stage3end_eval_and_sort(&(*npaths),&(*first_absmq),&(*second_absmq),
- stage3array,maxpaths_search,queryseq,queryuc_ptr,queryrc,
+ stage3array = Stage3end_eval_and_sort(/*npaths*/(*npaths_primary) + (*npaths_altloc),
+ &(*first_absmq),&(*second_absmq),
+ stage3array,maxpaths_search,queryseq,queryuc_ptr,
query_compress_fwd,query_compress_rev,
quality_string,/*displayp*/true);
}
@@ -16630,35 +16587,34 @@ single_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
Stage3end_T *
-Stage1_single_read (int *npaths, int *first_absmq, int *second_absmq,
+Stage1_single_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
Shortread_T queryseq, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
int indexdb_size_threshold, Floors_T *floors_array,
double user_maxlevel_float, double user_mincoverage_float,
int indel_penalty_middle, int indel_penalty_end,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
bool keep_floors_p) {
if (mode == STANDARD || mode == CMET_STRANDED || mode == ATOI_STRANDED || mode == TTOC_STRANDED) {
- return single_read(&(*npaths),&(*first_absmq),&(*second_absmq),
+ return single_read(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),
queryseq,indexdb_fwd,indexdb_rev,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,keep_floors_p);
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,keep_floors_p);
} else if (mode == CMET_NONSTRANDED || mode == ATOI_NONSTRANDED || mode == TTOC_NONSTRANDED) {
- return single_read_tolerant_nonstranded(&(*npaths),&(*first_absmq),&(*second_absmq),queryseq,
+ return single_read_tolerant_nonstranded(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),queryseq,
indexdb_fwd,indexdb_rev,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,keep_floors_p);
} else {
fprintf(stderr,"Do not recognize mode %d\n",mode);
@@ -16679,18 +16635,16 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
#ifdef END_KNOWNSPLICING_SHORTCUT
char *queryrc, bool invertedp,
#endif
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
struct Segment_T *plus_segments, int plus_nsegments,
struct Segment_T *minus_segments, int minus_nsegments,
Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Chrpos_T pairmax, Chrpos_T shortsplicedist, int user_maxlevel,
- int genestrand, bool first_read_p) {
+ Chrpos_T pairmax, Chrpos_T shortsplicedist, int genestrand) {
List_T hits = NULL;
int sensedir, sense_try;
- int zero_offset = 0;
+ /* int zero_offset = 0; */
Univcoord_T segmentstart, segmentend;
Univcoord_T genomicbound, mappingstart, mappingend,
chroffset, chrhigh, mappingpos;
@@ -17440,12 +17394,11 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
debug13(printf("Halfmapping: Running gmap with close mappingstart and close mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,close_mappingstart_last,close_mappingend_last,
+ close_mappingstart_last,close_mappingend_last,
close_knownsplice_limit_low,close_knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_start_p == true && good_end_p == true) {
/* Success */
@@ -17456,12 +17409,11 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
debug13(printf("Halfmapping: Re-running gmap with close mappingstart only\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,close_mappingstart_last,mappingend,
+ close_mappingstart_last,mappingend,
close_knownsplice_limit_low,knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else if (/* require both ends to be good */ 0 && good_end_p == true) {
@@ -17469,24 +17421,22 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
debug13(printf("Halfmapping: Re-running gmap with close mappingend only\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,mappingstart,close_mappingend_last,
+ mappingstart,close_mappingend_last,
knownsplice_limit_low,close_knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else {
if (fallback_mappingstart_p == true && fallback_mappingend_p == true) {
debug13(printf("Halfmapping: Re-running gmap with far mappingstart and mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
}
@@ -17494,12 +17444,11 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
debug13(printf("Halfmapping: Running gmap with close mappingstart\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,close_mappingstart_last,mappingend,
+ close_mappingstart_last,mappingend,
close_knownsplice_limit_low,knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_start_p == true && /* require both ends to be good */ good_end_p == true) {
/* Success */
@@ -17509,24 +17458,22 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
debug13(printf("Halfmapping: Re-running gmap with far mappingstart\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else if (close_mappingend_p == true) {
debug13(printf("Halfmapping: Running gmap with close mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,mappingstart,close_mappingend_last,
+ mappingstart,close_mappingend_last,
knownsplice_limit_low,close_knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
if (good_end_p == true && /* require both ends to be good */ good_start_p == true) {
/* Success */
@@ -17536,24 +17483,22 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
debug13(printf("Halfmapping: Re-running gmap with far mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
} else {
debug13(printf("Halfmapping: Running gmap with far mappingstart and mappingend\n"));
hits = run_gmap_for_region(&good_start_p,&good_end_p,gmap_history,
hits,Shortread_accession(queryseq5),queryuc_ptr,querylength,sense_try,favor_right_p,
- /*paired_favor_mode*/favor_right_p == true ? +1 : -1,zero_offset,
- query_compress_fwd,query_compress_rev,mappingstart,mappingend,
+ mappingstart,mappingend,
knownsplice_limit_low,knownsplice_limit_high,
- watsonp,genestrand,first_read_p,chrnum,chroffset,chrhigh,chrlength,
+ watsonp,genestrand,chrnum,chroffset,chrhigh,chrlength,
oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,user_maxlevel);
+ pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
}
return hits;
@@ -17562,22 +17507,12 @@ align_halfmapping_with_gmap (History_T gmap_history, Stage3end_T hit5, Stage3end
static List_T
align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
- History_T gmap_history_5, History_T gmap_history_3,
- Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
- Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- struct Segment_T **plus_segments_genestrand_5, int *plus_nsegments_genestrand_5,
- struct Segment_T **minus_segments_genestrand_5, int *minus_nsegments_genestrand_5,
- struct Segment_T **plus_segments_genestrand_3, int *plus_nsegments_genestrand_3,
- struct Segment_T **minus_segments_genestrand_3, int *minus_nsegments_genestrand_3,
- Shortread_T queryseq5, Shortread_T queryseq3,
char *queryuc_ptr_5, char *queryuc_ptr_3,
- int querylength5, int querylength3, int query5_lastpos, int query3_lastpos,
- int localsplicing_penalty,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ int querylength5, int querylength3,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Chrpos_T pairmax, int cutoff_level_5, int cutoff_level_3,
- Pairtype_T pairtype, bool expect_concordant_p, bool redo_for_sense_p) {
+ int cutoff_level_5, int cutoff_level_3, bool expect_concordant_p) {
Stage3pair_T newpair, stage3pair;
List_T gmap5_hits = NULL, gmap3_hits = NULL;
Stage3end_T hit5, hit3, gmap5, gmap3;
@@ -17590,6 +17525,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
#endif
+ debug16(printf("Running align_pair_with GMAP on %d results\n",List_length(result)));
debug13(printf("Sorting %d hitpairs by nmatches\n",List_length(result)));
result = Stage3pair_sort_bymatches(result);
@@ -17606,6 +17542,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
/* Was querylength5 - Stage3end_matches(hit5) > 5 */
debug13(printf("Looking at hit5 with nmismatches %d - %d ?<= cutoff_level %d\n",
querylength5,Stage3end_nmatches_posttrim(hit5),cutoff_level_5));
+
#if 0
if (Stage3end_sarrayp(hit5) == true && redo_for_sense_p == false) {
/* Skip */
@@ -17624,7 +17561,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
#endif
if (querylength5 - Stage3end_nmatches_posttrim(hit5) <= cutoff_level_5) {
- /* Skip */
+ /* Skip, because already good enough */
debug13(printf("Skipping hit5 with nmismatches %d - %d <= cutoff_level %d\n",
querylength5,Stage3end_nmatches_posttrim(hit5),cutoff_level_5));
@@ -17635,7 +17572,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
#endif
oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- genestrand,/*first_read_p*/true)) != NULL) {
+ genestrand,/*extend_ends_p*/true)) != NULL) {
debug13(missing_hit = querylength5 - Stage3end_nmatches_posttrim(hit5));
debug13(missing_gmap = querylength5 - Stage3end_nmatches_posttrim(gmap5));
debug13(printf("GMAP %p with %d matches, %d missing compared with original 5' hit with %d matches, %d missing\n",
@@ -17649,7 +17586,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
querylength3,Stage3end_nmatches_posttrim(hit3),cutoff_level_3));
if (querylength3 - Stage3end_nmatches_posttrim(hit3) <= cutoff_level_3) {
- /* Skip */
+ /* Skip, because already good enough */
debug13(printf("Skipping hit3 with nmismatches %d - %d <= cutoff_level %d\n",
querylength3,Stage3end_nmatches_posttrim(hit3),cutoff_level_3));
@@ -17661,7 +17598,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
#endif
oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- genestrand,/*first_read_p*/false)) != NULL) {
+ genestrand,/*extend_ends_p*/true)) != NULL) {
debug13(missing_hit = querylength3 - Stage3end_nmatches_posttrim(hit3));
debug13(missing_gmap = querylength3 - Stage3end_nmatches_posttrim(gmap3));
debug13(printf("GMAP %p with %d matches, %d missing compared with original 3' hit with %d matches, %d missing\n",
@@ -17680,10 +17617,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
gmap3 = (Stage3end_T) List_head(b);
debug13(printf("Imperfect concordant uniq: Double GMAP on hit5 and hit3"));
- if ((newpair = Stage3pair_new(Stage3end_copy(gmap5),Stage3end_copy(gmap3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/UNSPECIFIED,localsplicing_penalty,
+ if ((newpair = Stage3pair_new(Stage3end_copy(gmap5),Stage3end_copy(gmap3),genestrand,/*pairtype*/UNSPECIFIED,
/*private5p*/true,/*private3p*/true,expect_concordant_p)) == NULL) {
/* Stage3end_free(&gmap3); -- done by Stage3pair_new */
/* Stage3end_free(&gmap5); -- done by Stage3pair_new */
@@ -17735,10 +17669,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
gmap5 = (Stage3end_T) List_head(a);
debug13(printf("Imperfect concordant uniq: Single GMAP on hit5"));
- if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/UNSPECIFIED,localsplicing_penalty,
+ if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),genestrand,/*pairtype*/UNSPECIFIED,
/*private5p*/true,/*private3p*/true,expect_concordant_p)) == NULL) {
/* Stage3end_free(&gmap5); -- done by Stage3pair_new */
debug13(printf(" => NULL\n"));
@@ -17776,10 +17707,7 @@ align_pair_with_gmap (Pairtype_T *final_pairtype, List_T result,
gmap3 = (Stage3end_T) List_head(b);
debug13(printf("Imperfect concordant uniq: Single GMAP on hit3"));
- if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/UNSPECIFIED,localsplicing_penalty,
+ if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,genestrand,/*pairtype*/UNSPECIFIED,
/*private5p*/true,/*private3p*/true,expect_concordant_p)) == NULL) {
/* Stage3end_free(&gmap3); -- done by Stage3pair_new */
debug13(printf(" => NULL\n"));
@@ -17915,7 +17843,10 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
History_T gmap_history_5, History_T gmap_history_3, List_T *hits5, List_T *hits3, T this5, T this3,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- char *queryuc_ptr_5, char *queryuc_ptr_3, char *queryrc5, char *queryrc3,
+ char *queryuc_ptr_5, char *queryuc_ptr_3,
+#ifndef LARGE_GENOMES
+ char *queryrc5, char *queryrc3,
+#endif
int querylength5, int querylength3, int query5_lastpos, int query3_lastpos,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int indexdb_size_threshold, Floors_T *floors_array,
@@ -17923,9 +17854,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- int user_maxlevel_5, int user_maxlevel_3, int min_coverage_5, int min_coverage_3,
- int indel_penalty_middle, int indel_penalty_end,
- int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
+ int user_maxlevel_5, int user_maxlevel_3, int indel_penalty_middle, int indel_penalty_end,
+ int localsplicing_penalty, int distantsplicing_penalty,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
Chrpos_T pairmax, int maxpairedpaths, bool keep_floors_p, Shortread_T queryseq5, Shortread_T queryseq3,
int genestrand) {
@@ -17943,7 +17873,6 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
indels3 = NULL, singlesplicing3 = NULL, doublesplicing3 = NULL,
distantsplicing3 = NULL, gmap3_hits = NULL;
List_T longsinglesplicing5 = NULL, longsinglesplicing3 = NULL;
- int nmisses_allowed_sarray_5, nmisses_allowed_sarray_3;
int ignore_found_score, done_level_5, done_level_3, opt_level, fast_level_5, fast_level_3,
mismatch_level_5, mismatch_level_3, nmismatches;
int max_splice_mismatches_5 = -1, max_splice_mismatches_3 = -1, i;
@@ -17960,10 +17889,13 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
bool alloc_floors_p_5 = false, alloc_floors_p_3 = false, floors5_computed_p = false, floors3_computed_p = false,
segments5_computed_p = false, segments3_computed_p = false;
int best_score_paired;
- bool found_terminals_p = false;
+ /* bool found_terminals_p = false; */
int nconcordant = 0, nsamechr = 0;
Indexdb_T plus_indexdb_5, plus_indexdb_3, minus_indexdb_5, minus_indexdb_3;
bool allvalidp5, allvalidp3;
+#ifndef LARGE_GENOMES
+ int nmisses_allowed_sarray_5, nmisses_allowed_sarray_3;
+#endif
if (genestrand == +2) {
@@ -18068,20 +18000,18 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
nhits5 = nhits3 = 0;
+#ifndef LARGE_GENOMES
nmisses_allowed_sarray_5 = *cutoff_level_5;
nmisses_allowed_sarray_3 = *cutoff_level_3;
-#ifndef LARGE_GENOMES
if (use_only_sarray_p == true) {
*hits5 = Sarray_search_greedy(&(*cutoff_level_5),
- queryuc_ptr_5,queryrc5,querylength5,query5_compress_fwd,query5_compress_rev,maxpeelback,pairpool,
- dynprogL,dynprogM,dynprogR,oligoindices_minor,diagpool,cellpool,
- nmisses_allowed_sarray_5,genestrand,/*first_read_p*/true);
+ queryuc_ptr_5,queryrc5,querylength5,query5_compress_fwd,query5_compress_rev,
+ nmisses_allowed_sarray_5,genestrand);
*hits3 = Sarray_search_greedy(&(*cutoff_level_3),
- queryuc_ptr_3,queryrc3,querylength3,query3_compress_fwd,query3_compress_rev,maxpeelback,pairpool,
- dynprogL,dynprogM,dynprogR,oligoindices_minor,diagpool,cellpool,
- nmisses_allowed_sarray_3,genestrand,/*first_read_p*/false);
+ queryuc_ptr_3,queryrc3,querylength3,query3_compress_fwd,query3_compress_rev,
+ nmisses_allowed_sarray_3,genestrand);
/* Need to run Stage3end_remove_duplicates before we append the results together */
hitarray5[HITARRAY_GREEDY] = *hits5;
@@ -18097,11 +18027,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_GREEDY+1,
hitarray3,/*narray3*/HITARRAY_GREEDY+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing sarray, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
debug(printf("SA> found_score = %d, done_level %d,%d\n",*found_score,done_level_5,done_level_3));
@@ -18123,15 +18050,13 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("Trying suffix array on 5' end\n"));
greedy5 = Sarray_search_greedy(&ignore_found_score,
- queryuc_ptr_5,queryrc5,querylength5,query5_compress_fwd,query5_compress_rev,maxpeelback,pairpool,
- dynprogL,dynprogM,dynprogR,oligoindices_minor,diagpool,cellpool,
- nmisses_allowed_sarray_5,genestrand,/*first_read_p*/true);
+ queryuc_ptr_5,queryrc5,querylength5,query5_compress_fwd,query5_compress_rev,
+ nmisses_allowed_sarray_5,genestrand);
debug(printf("Trying suffix array on 3' end\n"));
greedy3 = Sarray_search_greedy(&ignore_found_score,
- queryuc_ptr_3,queryrc3,querylength3,query3_compress_fwd,query3_compress_rev,maxpeelback,pairpool,
- dynprogL,dynprogM,dynprogR,oligoindices_minor,diagpool,cellpool,
- nmisses_allowed_sarray_3,genestrand,/*first_read_p*/false);
+ queryuc_ptr_3,queryrc3,querylength3,query3_compress_fwd,query3_compress_rev,
+ nmisses_allowed_sarray_3,genestrand);
hitarray5[HITARRAY_GREEDY] = greedy5;
hitarray3[HITARRAY_GREEDY] = greedy3;
@@ -18142,11 +18067,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_GREEDY+1,
hitarray3,/*narray3*/HITARRAY_GREEDY+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing sarray, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
@@ -18201,8 +18123,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
if (done_level_5 == 0 && snpp == false) {
debug(printf("Suffix array already found exact matches for 5' end and no SNPs, so spanning set can't do any better\n"));
} else {
- read_oligos(&allvalidp5,this5,queryuc_ptr_5,querylength5,query5_lastpos,genestrand,
- /*first_read_p*/true);
+ read_oligos(&allvalidp5,this5,queryuc_ptr_5,querylength5,query5_lastpos,genestrand);
if (allvalidp5 == false) {
debug(printf("Not all oligos in 5' end are valid, so cannot perform spanning set\n"));
fast_level_5 = -1;
@@ -18211,7 +18132,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("fast_level_5 = %d\n",fast_level_5));
debug(printf("*** Stage 1. Exact ***\n"));
ignore_found_score = *found_score;
- subs5 = find_spanning_exact_matches(&ignore_found_score,&nhits5,subs5,this5,genestrand,/*first_read_p*/true,
+ subs5 = find_spanning_exact_matches(&ignore_found_score,&nhits5,subs5,this5,genestrand,
querylength5,query5_lastpos,plus_indexdb_5,minus_indexdb_5,
query5_compress_fwd,query5_compress_rev);
mismatch_level_5 = 1;
@@ -18223,8 +18144,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
if (done_level_3 == 0 && snpp == false) {
debug(printf("Suffix array already found exact matches for 3' end and no SNPs, so spanning set can't do any better\n"));
} else {
- read_oligos(&allvalidp3,this3,queryuc_ptr_3,querylength3,query3_lastpos,genestrand,
- /*first_read_p*/false);
+ read_oligos(&allvalidp3,this3,queryuc_ptr_3,querylength3,query3_lastpos,genestrand);
if (allvalidp3 == false) {
debug(printf("Not all oligos in 3' end are valid, so cannot perform spanning set\n"));
fast_level_3 = -1;
@@ -18233,7 +18153,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("fast_level_3 = %d\n",fast_level_3));
debug(printf("*** Stage 1. Exact ***\n"));
ignore_found_score = *found_score;
- subs3 = find_spanning_exact_matches(&ignore_found_score,&nhits3,subs3,this3,genestrand,/*first_read_p*/false,
+ subs3 = find_spanning_exact_matches(&ignore_found_score,&nhits3,subs3,this3,genestrand,
querylength3,query3_lastpos,plus_indexdb_3,minus_indexdb_3,
query3_compress_fwd,query3_compress_rev);
mismatch_level_3 = 1;
@@ -18248,11 +18168,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_SUBS+1,
hitarray3,/*narray3*/HITARRAY_SUBS+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing exact, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == true) {
@@ -18277,7 +18194,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("*** Stage 2A. One miss ***\n"));
did_alignment_p = true;
ignore_found_score = *found_score;
- subs5 = find_spanning_onemiss_matches(&ignore_found_score,&nhits5,subs5,this5,genestrand,/*first_read_p*/true,
+ subs5 = find_spanning_onemiss_matches(&ignore_found_score,&nhits5,subs5,this5,genestrand,
querylength5,query5_compress_fwd,query5_compress_rev);
mismatch_level_5 = 2;
}
@@ -18287,7 +18204,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("*** Stage 2B. One miss ***\n"));
did_alignment_p = true;
ignore_found_score = *found_score;
- subs3 = find_spanning_onemiss_matches(&ignore_found_score,&nhits3,subs3,this3,genestrand,/*first_read_p*/false,
+ subs3 = find_spanning_onemiss_matches(&ignore_found_score,&nhits3,subs3,this3,genestrand,
querylength3,query3_compress_fwd,query3_compress_rev);
mismatch_level_3 = 2;
}
@@ -18300,11 +18217,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_SUBS+1,
hitarray3,/*narray3*/HITARRAY_SUBS+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing one mismatch, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == true) {
@@ -18337,7 +18251,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("*** Stage 3A (level %d). Spanning set mismatches ***\n",mismatch_level_5));
did_alignment_p = true;
ignore_found_score = *found_score;
- subs5 = find_spanning_multimiss_matches(&ignore_found_score,&nhits5,subs5,this5,genestrand,/*first_read_p*/true,
+ subs5 = find_spanning_multimiss_matches(&ignore_found_score,&nhits5,subs5,this5,genestrand,
NREQUIRED_FAST,querylength5,query5_compress_fwd,query5_compress_rev,
/*nmisses_allowed*/mismatch_level_5);
mismatch_level_5++;
@@ -18351,7 +18265,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("*** Stage 3B (level %d). Spanning set mismatches ***\n",mismatch_level_3));
did_alignment_p = true;
ignore_found_score = *found_score;
- subs3 = find_spanning_multimiss_matches(&ignore_found_score,&nhits3,subs3,this3,genestrand,/*first_read_p*/true,
+ subs3 = find_spanning_multimiss_matches(&ignore_found_score,&nhits3,subs3,this3,genestrand,
NREQUIRED_FAST,querylength3,query3_compress_fwd,query3_compress_rev,
/*nmisses_allowed*/mismatch_level_3);
mismatch_level_3++;
@@ -18366,11 +18280,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_SUBS+1,
hitarray3,/*narray3*/HITARRAY_SUBS+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing spanning set, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == true) {
@@ -18422,8 +18333,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
if (completeset5p == true) {
debug(printf("Performing complete set analysis on 5' end\n"));
if (this5->read_oligos_p == false) {
- read_oligos(&allvalidp5,this5,queryuc_ptr_5,querylength5,query5_lastpos,genestrand,
- /*first_read_p*/true);
+ read_oligos(&allvalidp5,this5,queryuc_ptr_5,querylength5,query5_lastpos,genestrand);
}
floors5 = compute_floors(&any_omitted_p_5,&alloc_floors_p_5,floors_array,this5,
@@ -18441,7 +18351,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#endif
querylength5,query5_lastpos,floors5,indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
- fast_level_5,genestrand,/*first_read_p*/true);
+ fast_level_5,genestrand);
}
/* 4/5B. Complete set mismatches and indels, omitting frequent oligos */
@@ -18449,8 +18359,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug(printf("Performing complete set analysis on 3' end\n"));
if (this3->read_oligos_p == false) {
- read_oligos(&allvalidp3,this3,queryuc_ptr_3,querylength3,query3_lastpos,genestrand,
- /*first_read_p*/false);
+ read_oligos(&allvalidp3,this3,queryuc_ptr_3,querylength3,query3_lastpos,genestrand);
}
floors3 = compute_floors(&any_omitted_p_3,&alloc_floors_p_3,floors_array,this3,
@@ -18468,7 +18377,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#endif
querylength3,query3_lastpos,floors3,indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
- fast_level_3,genestrand,/*first_read_p*/false);
+ fast_level_3,genestrand);
}
debug(printf("complete: 5' end has %d subs, %d indels, %d single splices\n",
@@ -18487,11 +18396,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_INDELS+1,
hitarray3,/*narray3*/HITARRAY_INDELS+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing complete set mismatches and indels, found %d concordant, %d nsamechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == true) {
@@ -18555,7 +18461,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
this5->plus_positions,
#endif
this5->plus_npositions,this5->omitted,querylength5,query5_lastpos,floors5,
- /*max_mismatches_allowed*/done_level_5,/*plusp*/true);
+ /*plusp*/true);
this5->minus_segments = identify_all_segments(&this5->minus_nsegments,&minus_anchor_segments_5,
&this5->minus_spliceable,&this5->minus_nspliceable,
#ifdef LARGE_GENOMES
@@ -18564,7 +18470,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
this5->minus_positions,
#endif
this5->minus_npositions,this5->omitted,querylength5,query5_lastpos,floors5,
- /*max_mismatches_allowed*/done_level_5,/*plusp*/false);
+ /*plusp*/false);
segments5_computed_p = true;
}
@@ -18609,7 +18515,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
this3->plus_positions,
#endif
this3->plus_npositions,this3->omitted,querylength3,query3_lastpos,floors3,
- /*max_mismatches_allowed*/done_level_3,/*plusp*/true);
+ /*plusp*/true);
this3->minus_segments = identify_all_segments(&this3->minus_nsegments,&minus_anchor_segments_3,
&this3->minus_spliceable,&this3->minus_nspliceable,
#ifdef LARGE_GENOMES
@@ -18618,7 +18524,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
this3->minus_positions,
#endif
this3->minus_npositions,this3->omitted,querylength3,query3_lastpos,floors3,
- /*max_mismatches_allowed*/done_level_3,/*plusp*/false);
+ /*plusp*/false);
segments3_computed_p = true;
}
@@ -18644,11 +18550,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_SINGLESPLICING+1,
hitarray3,/*narray3*/HITARRAY_SINGLESPLICING+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing single splicing, found %d concordant, %d nsamechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == true) {
@@ -18731,11 +18634,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_DOUBLESPLICING+1,
hitarray3,/*narray3*/HITARRAY_DOUBLESPLICING+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing double splicing, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == true) {
@@ -18805,30 +18705,22 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
pairmax);
if (gmap5p == true) {
- gmap5_hits = convert_plus_segments_to_gmap(gmap_history_5,/*hits*/NULL,
- Shortread_accession(queryseq5),
- queryuc_ptr_5,querylength5,query5_lastpos,
+ gmap5_hits = convert_plus_segments_to_gmap(/*hits*/NULL,queryuc_ptr_5,querylength5,query5_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc5,Shortread_invertedp(queryseq5),
#endif
- query5_compress_fwd,query5_compress_rev,
plus_anchor_segments_5,this5->plus_segments,this5->plus_nsegments,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_5,genestrand,/*first_read_p*/true,
- /*require_pairing_p*/true);
- gmap5_hits = convert_minus_segments_to_gmap(gmap_history_5,/*hits*/gmap5_hits,
- Shortread_accession(queryseq5),
- queryuc_ptr_5,querylength5,query5_lastpos,
+ genestrand,/*require_pairing_p*/true);
+ gmap5_hits = convert_minus_segments_to_gmap(/*hits*/gmap5_hits,queryuc_ptr_5,querylength5,query5_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc5,Shortread_invertedp(queryseq5),
#endif
- query5_compress_fwd,query5_compress_rev,
minus_anchor_segments_5,this5->minus_segments,this5->minus_nsegments,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_5,genestrand,/*first_read_p*/true,
- /*require_pairing_p*/true);
+ genestrand,/*require_pairing_p*/true);
#if 0
/* Note: cannot use hitarray after we have removed overlapping alignments. Have to point to hits5 and hits3 and set narray5 = narray3 = 1 */
hitarray5[HITARRAY_SEGMENTS_GMAP] = gmap5_hits;
@@ -18838,30 +18730,22 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
}
if (gmap3p == true) {
- gmap3_hits = convert_plus_segments_to_gmap(gmap_history_3,/*hits*/NULL,
- Shortread_accession(queryseq3),
- queryuc_ptr_3,querylength3,query3_lastpos,
+ gmap3_hits = convert_plus_segments_to_gmap(/*hits*/NULL,queryuc_ptr_3,querylength3,query3_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc3,Shortread_invertedp(queryseq3),
#endif
- query3_compress_fwd,query3_compress_rev,
plus_anchor_segments_3,this3->plus_segments,this3->plus_nsegments,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_3,genestrand,/*first_read_p*/false,
- /*require_pairing_p*/true);
- gmap3_hits = convert_minus_segments_to_gmap(gmap_history_3,/*hits*/gmap3_hits,
- Shortread_accession(queryseq3),
- queryuc_ptr_3,querylength3,query3_lastpos,
+ genestrand,/*require_pairing_p*/true);
+ gmap3_hits = convert_minus_segments_to_gmap(/*hits*/gmap3_hits,queryuc_ptr_3,querylength3,query3_lastpos,
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc3,Shortread_invertedp(queryseq3),
#endif
- query3_compress_fwd,query3_compress_rev,
minus_anchor_segments_3,this3->minus_segments,this3->minus_nsegments,
- oligoindices_major,oligoindices_minor,
+ oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_3,genestrand,/*first_read_p*/false,
- /*require_pairing_p*/true);
+ genestrand,/*require_pairing_p*/true);
#if 0
/* Note: cannot use hitarray after we have removed overlapping alignments. Have to point to hits5 and hits3 and set narray5 = narray3 = 1 */
hitarray3[HITARRAY_SEGMENTS_GMAP] = gmap3_hits;
@@ -18872,18 +18756,15 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
}
if (gmap5_hits != NULL || gmap3_hits != NULL) {
- found_terminals_p = true;
+ /* found_terminals_p = true; */
debug4t(printf("Running Stage3_pair_up_concordant\n"));
/* Note: cannot use hitarray after we have removed overlapping alignments */
hitpairs = Stage3_pair_up_concordant(&(*abort_pairing_p),&(*found_score),&nconcordant,&nsamechr,
&(*samechr),&(*conc_transloc),
hitpairs,/*hitarray5*/&(*hits5),/*narray5*/1,
/*hitarray3*/&(*hits3),/*narray3*/1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("11> After pairing GMAP, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == false) {
@@ -18944,7 +18825,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/*queryptr*/queryuc_ptr_5,
#endif
floors5,querylength5,query5_lastpos,/*query_compress*/query5_compress_fwd,
- max_splice_mismatches_5,/*plusp*/true,genestrand,/*first_read_p*/true);
+ max_splice_mismatches_5,/*plusp*/true,genestrand);
debug(printf("Finished find_spliceends (plus)\n"));
debug(printf("Starting find_spliceends (minus) on 5' end with %d anchor segments\n",List_length(minus_anchor_segments_5)));
@@ -18954,7 +18835,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/*queryptr*/queryrc5,
#endif
floors5,querylength5,query5_lastpos,/*query_compress*/query5_compress_rev,
- max_splice_mismatches_5,/*plusp*/false,genestrand,/*first_read_p*/true);
+ max_splice_mismatches_5,/*plusp*/false,genestrand);
debug(printf("Finished find_spliceends (minus)\n"));
@@ -19046,7 +18927,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/*queryptr*/queryuc_ptr_3,
#endif
floors3,querylength3,query3_lastpos,/*query_compress*/query3_compress_fwd,
- max_splice_mismatches_3,/*plusp*/true,genestrand,/*first_read_p*/false);
+ max_splice_mismatches_3,/*plusp*/true,genestrand);
debug(printf("Finished find_spliceends (plus)\n"));
debug(printf("Starting find_spliceends (minus) on 3' end with %d anchor segments\n",List_length(minus_anchor_segments_3)));
@@ -19056,7 +18937,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/*queryptr*/queryrc3,
#endif
floors3,querylength3,query3_lastpos,/*query_compress*/query3_compress_rev,
- max_splice_mismatches_3,/*plusp*/false,genestrand,/*first_read_p*/false);
+ max_splice_mismatches_3,/*plusp*/false,genestrand);
debug(printf("Finished find_spliceends (minus)\n"));
/* 11B. Distant splicing */
@@ -19137,11 +19018,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,/*hitarray5*/&(*hits5),/*narray5*/1,
/*hitarray3*/&(*hits3),/*narray3*/1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("10> After pairing long single splicing, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
@@ -19178,11 +19056,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,/*hitarray5*/&(*hits5),/*narray5*/1,
/*hitarray3*/&(*hits3),/*narray3*/1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("11> After pairing distant splicing, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
@@ -19204,24 +19079,21 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
terminals5 = find_terminals(plus_anchor_segments_5,minus_anchor_segments_5,
querylength5,query5_lastpos,
query5_compress_fwd,query5_compress_rev,
- /*max_mismatches_allowed*/done_level_5,genestrand,/*first_read_p*/true);
+ /*max_mismatches_allowed*/done_level_5,genestrand);
*hits5 = List_append(*hits5,terminals5);
terminals3 = find_terminals(plus_anchor_segments_3,minus_anchor_segments_3,
querylength3,query3_lastpos,
query3_compress_fwd,query3_compress_rev,
- /*max_mismatches_allowed*/done_level_3,genestrand,/*first_read_p*/false);
+ /*max_mismatches_allowed*/done_level_3,genestrand);
*hits3 = List_append(*hits3,terminals3);
hitpairs = Stage3_pair_up_concordant(&(*abort_pairing_p),&(*found_score),&nconcordant,&nsamechr,
&(*samechr),&(*conc_transloc),
hitpairs,/*hitarray5*/&(*hits5),/*narray5*/1,
/*hitarray3*/&(*hits3),/*narray3*/1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing terminals, found %d concordant, %d nsamechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
}
@@ -19265,7 +19137,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
if (gmap3p == true) {
debug(printf("Before remove_overlaps of 5' at cutoff level %d: %d hits\n",*cutoff_level_5,List_length(*hits5)));
*hits5 = Stage3end_sort_bymatches(Stage3end_remove_overlaps(*hits5,/*finalp*/false));
- debug(printf("After remove_overlaps: %d\n",List_length(*hits5)));
+ debug(printf("After remove_overlaps (3): %d\n",List_length(*hits5)));
i = 0;
best_score_paired = Stage3end_best_score_paired(*hits5);
@@ -19282,12 +19154,10 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc3,Shortread_invertedp(queryseq3),
#endif
- query3_compress_fwd,query3_compress_rev,
this3->plus_segments,this3->plus_nsegments,this3->minus_segments,this3->minus_nsegments,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,shortsplicedist,user_maxlevel_5,genestrand,
- /*first_read_p*/false);
+ pairmax,shortsplicedist,genestrand);
for (a = halfmapping3; a != NULL; a = List_next(a)) {
gmap3 = (Stage3end_T) List_head(a);
debug13(printf("=> Successful pairsearch GMAP on hit3 with score %d and nmatches %d\n",
@@ -19298,10 +19168,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug13(printf("Score is only %d vs cutoff level %d\n",Stage3end_score(gmap3),*cutoff_level_3));
Stage3end_free(&gmap3);
- } else if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,localsplicing_penalty,
+ } else if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,genestrand,/*pairtype*/CONCORDANT,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/true)) == NULL) {
debug13(printf( "newpair is NULL\n"));
/* Stage3end_free(&gmap3); -- done by Stage3pair_new */
@@ -19330,10 +19197,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
Stage3pair_free(&newpair);
}
#else
- if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,localsplicing_penalty,
+ if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,genestrand,/*pairtype*/CONCORDANT,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/true)) == NULL) {
debug13(printf( "newpair is NULL\n"));
/* Stage3end_free(&gmap3); -- done by Stage3pair_new */
@@ -19353,7 +19217,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
if (gmap5p == true) {
debug(printf("Before remove_overlaps of 3' at cutoff level %d: %d hits\n",*cutoff_level_3,List_length(*hits3)));
*hits3 = Stage3end_sort_bymatches(Stage3end_remove_overlaps(*hits3,/*finalp*/false));
- debug(printf("After remove_overlaps: %d\n",List_length(*hits3)));
+ debug(printf("After remove_overlaps (4): %d\n",List_length(*hits3)));
i = 0;
best_score_paired = Stage3end_best_score_paired(*hits3);
@@ -19370,12 +19234,10 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc5,Shortread_invertedp(queryseq5),
#endif
- query5_compress_fwd,query5_compress_rev,
this5->plus_segments,this5->plus_nsegments,this5->minus_segments,this5->minus_nsegments,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,shortsplicedist,user_maxlevel_5,genestrand,
- /*first_read_p*/true);
+ pairmax,shortsplicedist,genestrand);
for (a = halfmapping5; a != NULL; a = List_next(a)) {
gmap5 = (Stage3end_T) List_head(a);
debug13(printf("=> Successful pairsearch GMAP on hit5 with score %d and nmatches %d\n",
@@ -19387,10 +19249,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug13(printf("Score is only %d vs cutoff level %d\n",Stage3end_score(gmap5),*cutoff_level_5));
Stage3end_free(&gmap5);
- } else if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,localsplicing_penalty,
+ } else if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),genestrand,/*pairtype*/CONCORDANT,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/true)) == NULL) {
debug13(printf( "newpair is NULL\n"));
/* Stage3end_free(&gmap5); -- done by Stage3pair_new */
@@ -19418,10 +19277,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
Stage3pair_free(&newpair);
}
#else
- if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,localsplicing_penalty,
+ if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),genestrand,/*pairtype*/CONCORDANT,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/true)) == NULL) {
debug13(printf( "newpair is NULL\n"));
/* Stage3end_free(&gmap5); -- done by Stage3pair_new */
@@ -19474,8 +19330,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
queryuc_ptr_5,
#endif
floors5,querylength5,query5_lastpos,/*query_compress*/query5_compress_fwd,
- /*max_mismatches_allowed*/max_splice_mismatches_5,/*plusp*/true,genestrand,
- /*first_read_p*/true);
+ /*max_mismatches_allowed*/max_splice_mismatches_5,/*plusp*/true,genestrand);
find_spliceends_shortend(&antidonors_minus_5,&donors_minus_5,&antiacceptors_minus_5,&acceptors_minus_5,
minus_anchor_segments_5,
@@ -19483,8 +19338,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/*queryptr*/queryrc5,
#endif
floors5,querylength5,query5_lastpos,/*query_compress*/query5_compress_rev,
- /*max_mismatches_allowed*/max_splice_mismatches_5,/*plusp*/false,genestrand,
- /*first_read_p*/true);
+ /*max_mismatches_allowed*/max_splice_mismatches_5,/*plusp*/false,genestrand);
ignore_found_score = *found_score;
singlesplicing5 = find_splicepairs_shortend(&ignore_found_score,/*hits*/singlesplicing5,
@@ -19527,8 +19381,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
queryuc_ptr_3,
#endif
floors3,querylength3,query3_lastpos,/*query_compress*/query3_compress_fwd,
- /*max_mismatches_allowed*/max_splice_mismatches_3,/*plusp*/true,genestrand,
- /*first_read_p*/false);
+ /*max_mismatches_allowed*/max_splice_mismatches_3,/*plusp*/true,genestrand);
find_spliceends_shortend(&antidonors_minus_3,&donors_minus_3,&antiacceptors_minus_3,&acceptors_minus_3,
minus_anchor_segments_3,
@@ -19536,8 +19389,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
/*queryptr*/queryrc3,
#endif
floors3,querylength3,query3_lastpos,/*query_compress*/query3_compress_rev,
- /*max_mismatches_allowed*/max_splice_mismatches_3,/*plusp*/false,genestrand,
- /*first_read_p*/false);
+ /*max_mismatches_allowed*/max_splice_mismatches_3,/*plusp*/false,genestrand);
ignore_found_score = *found_score;
singlesplicing3 = find_splicepairs_shortend(&ignore_found_score,/*hits*/singlesplicing3,
@@ -19557,11 +19409,8 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
&(*samechr),&(*conc_transloc),
hitpairs,hitarray5,/*narray5*/HITARRAY_DOUBLESPLICING+1,
hitarray3,/*narray3*/HITARRAY_DOUBLESPLICING+1,
- *cutoff_level_5,*cutoff_level_3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- querylength5,querylength3,maxpairedpaths,localsplicing_penalty,
- genestrand);
+ *cutoff_level_5,*cutoff_level_3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
debug(printf("After pairing short-overlap splicing, found %d concordant, %d samechr, found_score %d\n",
nconcordant,nsamechr,*found_score));
if (*abort_pairing_p == false) {
@@ -19637,11 +19486,11 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#if 1
debug13(printf("Before remove_overlaps of 5' at cutoff level %d: %d hits\n",*cutoff_level_5,List_length(*hits5)));
*hits5 = Stage3end_sort_bymatches(Stage3end_remove_overlaps(*hits5,/*finalp*/false));
- debug13(printf("After remove_overlaps: %d\n",List_length(*hits5)));
+ debug13(printf("After remove_overlaps (5): %d\n",List_length(*hits5)));
debug13(printf("Before remove_overlaps of 3' at cutoff level %d: %d hits\n",*cutoff_level_3,List_length(*hits3)));
*hits3 = Stage3end_sort_bymatches(Stage3end_remove_overlaps(*hits3,/*finalp*/false));
- debug13(printf("After remove_overlaps: %d\n",List_length(*hits3)));
+ debug13(printf("After remove_overlaps (6): %d\n",List_length(*hits3)));
#else
/* Focus on those terminals not yet processed */
terminals5 = Stage3end_sort_by_paired_seenp(terminals5);
@@ -19660,12 +19509,10 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc3,Shortread_invertedp(queryseq3),
#endif
- query3_compress_fwd,query3_compress_rev,
this3->plus_segments,this3->plus_nsegments,this3->minus_segments,this3->minus_nsegments,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,shortsplicedist,user_maxlevel_3,genestrand,
- /*first_read_p*/false);
+ pairmax,shortsplicedist,genestrand);
for (a = halfmapping3; a != NULL; a = List_next(a)) {
gmap3 = (Stage3end_T) List_head(a);
@@ -19674,10 +19521,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
if (Stage3end_score(gmap3) > *cutoff_level_3 + gmap_allowance) {
debug13(printf("Score is only %d vs cutoff level %d\n",Stage3end_score(gmap3),*cutoff_level_3));
Stage3end_free(&gmap3);
- } else if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,localsplicing_penalty,
+ } else if ((newpair = Stage3pair_new(Stage3end_copy(hit5),gmap3,genestrand,/*pairtype*/CONCORDANT,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/true)) == NULL) {
/* Stage3end_free(&gmap3); -- done by Stage3pair_new */
#if 0
@@ -19706,12 +19550,10 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
#ifdef END_KNOWNSPLICING_SHORTCUT
queryrc5,Shortread_invertedp(queryseq5),
#endif
- query5_compress_fwd,query5_compress_rev,
this5->plus_segments,this5->plus_nsegments,this5->minus_segments,this5->minus_nsegments,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,shortsplicedist,user_maxlevel_5,genestrand,
- /*first_read_p*/true);
+ pairmax,shortsplicedist,genestrand);
for (a = halfmapping5; a != NULL; a = List_next(a)) {
gmap5 = (Stage3end_T) List_head(a);
debug13(printf("=> Successful terminal GMAP on hit5 %p with score %d and nmatches %d. Copying hit3 %p\n",
@@ -19720,10 +19562,7 @@ align_pair (bool *abort_pairing_p, int *found_score, int *cutoff_level_5, int *c
debug13(printf("Score is only %d vs cutoff level %d\n",Stage3end_score(gmap5),*cutoff_level_5));
Stage3end_free(&gmap5);
- } else if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,localsplicing_penalty,
+ } else if ((newpair = Stage3pair_new(gmap5,Stage3end_copy(hit3),genestrand,/*pairtype*/CONCORDANT,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/true)) == NULL) {
/* Stage3end_free(&gmap5); -- done by Stage3pair_new */
#if 0
@@ -19874,9 +19713,8 @@ paired_results_free (T this5, T this3, List_T hitpairs, List_T samechr, List_T c
}
static void
-realign_separately (Stage3end_T **stage3array5, int *nhits5, int *first_absmq5, int *second_absmq5,
- Stage3end_T **stage3array3, int *nhits3, int *first_absmq3, int *second_absmq3,
- History_T gmap_history_5, History_T gmap_history_3,
+realign_separately (Stage3end_T **stage3array5, int *nhits5_primary, int *nhits5_altloc, int *first_absmq5, int *second_absmq5,
+ Stage3end_T **stage3array3, int *nhits3_primary, int *nhits3_altloc, int *first_absmq3, int *second_absmq3,
T this5, T this3, Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
Shortread_T queryseq5, char *queryuc_ptr_5, char *queryrc5, char *quality_string_5, int querylength5, int query5_lastpos,
@@ -19887,7 +19725,7 @@ realign_separately (Stage3end_T **stage3array5, int *nhits5, int *first_absmq5,
int indel_penalty_middle, int indel_penalty_end,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
bool keep_floors_p, int genestrand) {
@@ -19896,60 +19734,58 @@ realign_separately (Stage3end_T **stage3array5, int *nhits5, int *first_absmq5,
bool allvalidp5, allvalidp3;
/* Re-align 5' end as a single end */
- if (read_oligos(&allvalidp5,this5,queryuc_ptr_5,querylength5,query5_lastpos,genestrand,
- /*first_read_p*/true) == 0) {
+ if (read_oligos(&allvalidp5,this5,queryuc_ptr_5,querylength5,query5_lastpos,genestrand) == 0) {
debug(printf("Aborting because no hits found anywhere\n"));
singlehits5 = (List_T) NULL;
} else {
- singlehits5 = align_end(&cutoff_level_5,gmap_history_5,this5,
- query5_compress_fwd,query5_compress_rev,
- Shortread_accession(queryseq5),queryuc_ptr_5,queryrc5,querylength5,query5_lastpos,
- indexdb_fwd,indexdb_rev,indexdb_size_threshold,
- floors_array,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_5,min_coverage_5,indel_penalty_middle,indel_penalty_end,
+ singlehits5 = align_end(&cutoff_level_5,this5,query5_compress_fwd,query5_compress_rev,
+ queryuc_ptr_5,queryrc5,querylength5,query5_lastpos,
+ indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ user_maxlevel_5,indel_penalty_middle,indel_penalty_end,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
keep_floors_p,genestrand,/*first_read_p*/true);
}
singlehits5 = Stage3end_filter_coverage(singlehits5,min_coverage_5);
- if ((*nhits5 = List_length(singlehits5)) == 0) {
+ if (singlehits5 == NULL) {
+ *nhits5_primary = *nhits5_altloc = 0;
*stage3array5 = (Stage3end_T *) NULL;
} else {
+ Stage3end_count_hits(&(*nhits5_primary),&(*nhits5_altloc),singlehits5);
*stage3array5 = (Stage3end_T *) List_to_array_out(singlehits5,NULL); List_free(&singlehits5); /* Return value */
- *stage3array5 = Stage3end_eval_and_sort(&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- *stage3array5,maxpaths_search,queryseq5,queryuc_ptr_5,queryrc5,
- query5_compress_fwd,query5_compress_rev,
+ *stage3array5 = Stage3end_eval_and_sort((*nhits5_primary) + (*nhits5_altloc),
+ &(*first_absmq5),&(*second_absmq5),*stage3array5,maxpaths_search,
+ queryseq5,queryuc_ptr_5,query5_compress_fwd,query5_compress_rev,
quality_string_5,/*displayp*/true);
}
/* Re-align 3' end as a single end */
- if (read_oligos(&allvalidp3,this3,queryuc_ptr_3,querylength3,query3_lastpos,genestrand,
- /*first_read_p*/false) == 0) {
+ if (read_oligos(&allvalidp3,this3,queryuc_ptr_3,querylength3,query3_lastpos,genestrand) == 0) {
debug(printf("Aborting because no hits found anywhere\n"));
singlehits3 = (List_T) NULL;
} else {
- singlehits3 = align_end(&cutoff_level_3,gmap_history_3,this3,
- query3_compress_fwd,query3_compress_rev,
- Shortread_accession(queryseq5),queryuc_ptr_3,queryrc3,querylength3,query3_lastpos,
- indexdb_fwd,indexdb_rev,indexdb_size_threshold,
- floors_array,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_3,min_coverage_3,indel_penalty_middle,indel_penalty_end,
+ singlehits3 = align_end(&cutoff_level_3,this3,query3_compress_fwd,query3_compress_rev,
+ queryuc_ptr_3,queryrc3,querylength3,query3_lastpos,
+ indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ user_maxlevel_3,indel_penalty_middle,indel_penalty_end,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
keep_floors_p,genestrand,/*first_read_p*/false);
}
singlehits3 = Stage3end_filter_coverage(singlehits3,min_coverage_3);
- if ((*nhits3 = List_length(singlehits3)) == 0) {
+ if (singlehits3 == NULL) {
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array3 = (Stage3end_T *) NULL;
} else {
+ Stage3end_count_hits(&(*nhits3_primary),&(*nhits3_altloc),singlehits3);
*stage3array3 = (Stage3end_T *) List_to_array_out(singlehits3,NULL); List_free(&singlehits3); /* Return value */
- *stage3array3 = Stage3end_eval_and_sort(&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- *stage3array3,maxpaths_search,queryseq3,queryuc_ptr_3,queryrc3,
- query3_compress_fwd,query3_compress_rev,
+ *stage3array3 = Stage3end_eval_and_sort((*nhits3_primary) + (*nhits3_altloc),
+ &(*first_absmq3),&(*second_absmq3),*stage3array3,maxpaths_search,
+ queryseq3,queryuc_ptr_3,query3_compress_fwd,query3_compress_rev,
quality_string_3,/*displayp*/true);
}
@@ -19959,28 +19795,23 @@ realign_separately (Stage3end_T **stage3array5, int *nhits5, int *first_absmq5,
/* Have three lists: hitpairs, samechr, and conc_transloc => result */
static Stage3pair_T *
-consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
- Stage3end_T **stage3array5, int *nhits5, int *first_absmq5, int *second_absmq5,
- Stage3end_T **stage3array3, int *nhits3, int *first_absmq3, int *second_absmq3,
+consolidate_paired_results (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
+ Stage3end_T **stage3array5, int *nhits5_primary, int *nhits5_altloc, int *first_absmq5, int *second_absmq5,
+ Stage3end_T **stage3array3, int *nhits3_primary, int *nhits3_altloc, int *first_absmq3, int *second_absmq3,
List_T hitpairs, List_T samechr, List_T conc_transloc,
- List_T hits5, List_T hits3, History_T gmap_history_5, History_T gmap_history_3,
+ List_T hits5, List_T hits3,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- struct Segment_T **plus_segments_genestrand_5, int *plus_nsegments_genestrand_5,
- struct Segment_T **minus_segments_genestrand_5, int *minus_nsegments_genestrand_5,
- struct Segment_T **plus_segments_genestrand_3, int *plus_nsegments_genestrand_3,
- struct Segment_T **minus_segments_genestrand_3, int *minus_nsegments_genestrand_3,
-
- Shortread_T queryseq5, char *queryuc_ptr_5, char *queryrc5,
- char *quality_string_5, int querylength5, int query5_lastpos,
- Shortread_T queryseq3, char *queryuc_ptr_3, char *queryrc3,
- char *quality_string_3, int querylength3, int query3_lastpos,
-
- int cutoff_level_5, int cutoff_level_3, int min_coverage_5, int min_coverage_3, int localsplicing_penalty,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+
+ Shortread_T queryseq5, char *queryuc_ptr_5,
+ char *quality_string_5, int querylength5,
+ Shortread_T queryseq3, char *queryuc_ptr_3,
+ char *quality_string_3, int querylength3,
+
+ int cutoff_level_5, int cutoff_level_3, int min_coverage_5, int min_coverage_3,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
- Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Chrpos_T pairmax, int user_maxlevel_5, int user_maxlevel_3) {
+ Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR) {
Stage3pair_T *stage3pairarray, stage3pair, newpair;
Stage3end_T hit5, hit3;
List_T result, singlehits5, singlehits3, p;
@@ -20014,12 +19845,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
if (gmap_improvement_p == false) {
debug16(printf("No GMAP improvement: Before removing overlaps, %d results\n",List_length(hitpairs)));
- result = Stage3pair_optimal_score(hitpairs,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(hitpairs,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/true);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
@@ -20029,12 +19860,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
} else {
debug16(printf("GMAP improvement: Before removing overlaps, %d results\n",List_length(hitpairs)));
- result = Stage3pair_optimal_score(hitpairs,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(hitpairs,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/false);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/false);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/false);
@@ -20042,48 +19873,29 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
/* result = Stage3pair_sort_distance(result); */
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
- result = align_pair_with_gmap(&(*final_pairtype),result,gmap_history_5,gmap_history_3,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,
- minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,
- minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryseq3,queryuc_ptr_5,queryuc_ptr_3,
- querylength5,querylength3,query5_lastpos,query3_lastpos,
- localsplicing_penalty,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,cutoff_level_5,cutoff_level_3,
- /*pairtype*/CONCORDANT,/*expect_concordant_p*/true,
- /*redo_for_sense_p*/false);
+ result = align_pair_with_gmap(&(*final_pairtype),result,
+ queryuc_ptr_5,queryuc_ptr_3,querylength5,querylength3,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ cutoff_level_5,cutoff_level_3,/*expect_concordant_p*/true);
if (Stage3pair_sense_consistent_p(result) == false) {
- result = align_pair_with_gmap(&(*final_pairtype),result,gmap_history_5,gmap_history_3,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,
- minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,
- minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryseq3,queryuc_ptr_5,queryuc_ptr_3,
- querylength5,querylength3,query5_lastpos,query3_lastpos,
- localsplicing_penalty,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,cutoff_level_5,cutoff_level_3,
- /*pairtype*/CONCORDANT,/*expect_concordant_p*/true,
- /*redo_for_sense_p*/true);
- }
-
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = align_pair_with_gmap(&(*final_pairtype),result,
+ queryuc_ptr_5,queryuc_ptr_3,querylength5,querylength3,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ cutoff_level_5,cutoff_level_3,/*expect_concordant_p*/true);
+ }
+
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/true);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
+
+ /* TODO: Resolve terminals by doing full GMAP, and then redo optimal_score */
+
result = Stage3pair_resolve_multimapping(result);
}
@@ -20104,50 +19916,39 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
if (gmap_improvement_p == false) {
debug16(printf("No GMAP improvement: Before removing overlaps, %d results\n",List_length(samechr)));
- result = Stage3pair_optimal_score(samechr,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(samechr,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/true);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
result = Stage3pair_resolve_multimapping(result);
} else {
debug16(printf("GMAP improvement: Before removing overlaps, %d results\n",List_length(samechr)));
- result = Stage3pair_optimal_score(samechr,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(samechr,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/false);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/false);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/false);
result = Stage3pair_resolve_multimapping(result);
- result = align_pair_with_gmap(&(*final_pairtype),result,gmap_history_5,gmap_history_3,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,
- minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,
- minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryseq3,queryuc_ptr_5,queryuc_ptr_3,
- querylength5,querylength3,query5_lastpos,query3_lastpos,
- localsplicing_penalty,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,cutoff_level_5,cutoff_level_3,
- /*pairtype*/PAIRED_UNSPECIFIED,/*expect_concordant_p*/false,
- /*redo_for_sense_p*/false);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = align_pair_with_gmap(&(*final_pairtype),result,
+ queryuc_ptr_5,queryuc_ptr_3,querylength5,querylength3,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ cutoff_level_5,cutoff_level_3,/*expect_concordant_p*/false);
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/true);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
@@ -20176,12 +19977,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
}
List_free(&samechr);
- result = Stage3pair_optimal_score(conc_transloc,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(conc_transloc,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/true);
result = Stage3pair_remove_overlaps(result,/*translocp*/true,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
@@ -20256,7 +20057,7 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
if (gmap_improvement_p == false) {
debug16(printf("No GMAP improvement: Before removing overlaps, %d results\n",List_length(result)));
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
@@ -20265,9 +20066,9 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
} else {
- debug16(printf("GMAP improvement: Before removing overlaps, %d results\n",List_length(results)));
+ debug16(printf("GMAP improvement: Before removing overlaps, %d results\n",List_length(result)));
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/false);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/false);
@@ -20275,45 +20076,23 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
/* result = Stage3pair_sort_distance(result); */
debug16(printf("After removing overlaps, %d results\n",List_length(result)));
- result = align_pair_with_gmap(&(*final_pairtype),result,gmap_history_5,gmap_history_3,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,
- minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,
- minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryseq3,queryuc_ptr_5,queryuc_ptr_3,
- querylength5,querylength3,query5_lastpos,query3_lastpos,
- localsplicing_penalty,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,cutoff_level_5,cutoff_level_3,
- /*pairtype*/CONCORDANT,/*expect_concordant_p*/true,
- /*redo_for_sense_p*/false);
+ result = align_pair_with_gmap(&(*final_pairtype),result,
+ queryuc_ptr_5,queryuc_ptr_3,querylength5,querylength3,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ cutoff_level_5,cutoff_level_3,/*expect_concordant_p*/true);
if (Stage3pair_sense_consistent_p(result) == false) {
- result = align_pair_with_gmap(&(*final_pairtype),result,gmap_history_5,gmap_history_3,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,
- minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,
- minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryseq3,queryuc_ptr_5,queryuc_ptr_3,
- querylength5,querylength3,query5_lastpos,query3_lastpos,
- localsplicing_penalty,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- pairmax,cutoff_level_5,cutoff_level_3,
- /*pairtype*/CONCORDANT,/*expect_concordant_p*/true,
- /*redo_for_sense_p*/true);
+ result = align_pair_with_gmap(&(*final_pairtype),result,
+ queryuc_ptr_5,queryuc_ptr_3,querylength5,querylength3,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ cutoff_level_5,cutoff_level_3,/*expect_concordant_p*/true);
}
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/true,/*finalp*/true);
result = Stage3pair_remove_overlaps(result,/*translocp*/false,/*finalp*/true);
- result = Stage3pair_optimal_score(result,/*cutoff*/1000000,subopt_levels,
+ result = Stage3pair_optimal_score(result,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,/*keep_gmap_p*/false,/*finalp*/true);
@@ -20335,21 +20114,21 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
if (result == NULL) {
- singlehits5 = Stage3end_optimal_score(hits5,cutoff_level_5,subopt_levels,query5_compress_fwd,query5_compress_rev,
+ singlehits5 = Stage3end_optimal_score(hits5,query5_compress_fwd,query5_compress_rev,
querylength5,/*keep_gmap_p*/true,/*finalp*/true);
/* singlehits5 = Stage3end_reject_trimlengths(singlehits5); */
singlehits5 = Stage3end_linearize_5(singlehits5);
singlehits5 = Stage3end_remove_overlaps(singlehits5,/*finalp*/true);
- singlehits5 = Stage3end_optimal_score(singlehits5,cutoff_level_5,subopt_levels,query5_compress_fwd,query5_compress_rev,
+ singlehits5 = Stage3end_optimal_score(singlehits5,query5_compress_fwd,query5_compress_rev,
querylength5,/*keep_gmap_p*/false,/*finalp*/true);
singlehits5 = Stage3end_resolve_multimapping(singlehits5);
- singlehits3 = Stage3end_optimal_score(hits3,cutoff_level_3,subopt_levels,query3_compress_fwd,query3_compress_rev,
+ singlehits3 = Stage3end_optimal_score(hits3,query3_compress_fwd,query3_compress_rev,
querylength3,/*keep_gmap_p*/true,/*finalp*/true);
/* singlehits3 = Stage3end_reject_trimlengths(singlehits3); */
singlehits3 = Stage3end_linearize_3(singlehits3);
singlehits3 = Stage3end_remove_overlaps(singlehits3,/*finalp*/true);
- singlehits3 = Stage3end_optimal_score(singlehits3,cutoff_level_3,subopt_levels,query3_compress_fwd,query3_compress_rev,
+ singlehits3 = Stage3end_optimal_score(singlehits3,query3_compress_fwd,query3_compress_rev,
querylength3,/*keep_gmap_p*/false,/*finalp*/true);
singlehits3 = Stage3end_resolve_multimapping(singlehits3);
@@ -20360,19 +20139,23 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
(pairtype = Stage3_determine_pairtype(hit5=(Stage3end_T) List_head(singlehits5),hit3=(Stage3end_T) List_head(singlehits3))) != UNPAIRED) {
/* Convert unpaired uniq to a paired uniq */
debug16(printf("Converting unpaired uniq to paired uniq, with initial pairtype %s\n",Pairtype_string(pairtype)));
- if ((newpair = Stage3pair_new(hit5,hit3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,
- /*genestrand*/0,pairtype,localsplicing_penalty,
+ if ((newpair = Stage3pair_new(hit5,hit3,/*genestrand*/0,pairtype,
/*private5p*/false,/*private3p*/false,
/*expect_concordant_p*/pairtype == CONCORDANT ? true : false)) != NULL) {
stage3pairarray = (Stage3pair_T *) CALLOC_OUT(1,sizeof(Stage3pair_T));
stage3pairarray[0] = newpair;
- *nhits5 = *nhits3 = 0;
+ *nhits5_primary = *nhits5_altloc = 0;
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
- *npaths = 1;
+ if (Stage3pair_altlocp(newpair) == true) {
+ *npaths_primary = 0;
+ *npaths_altloc = 1;
+ } else {
+ *npaths_primary = 1;
+ *npaths_altloc = 0;
+ }
if (pairtype == CONCORDANT) {
debug16(printf("final pairtype is CONCORDANT\n"));
*final_pairtype = CONCORDANT;
@@ -20381,9 +20164,9 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
*final_pairtype = PAIRED_UNSPECIFIED;
}
Stage3pair_privatize(stage3pairarray,/*npairs*/1);
- Stage3pair_eval_and_sort(&(*npaths),&(*first_absmq),&(*second_absmq),
- stage3pairarray,maxpaths_search,queryseq5,queryseq3,
- queryuc_ptr_5,queryrc5,queryuc_ptr_3,queryrc3,
+ Stage3pair_eval_and_sort(/*npaths*/(*npaths_primary) + (*npaths_altloc),
+ &(*first_absmq),&(*second_absmq),stage3pairarray,maxpaths_search,queryseq5,queryseq3,
+ queryuc_ptr_5,queryuc_ptr_3,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
quality_string_5,quality_string_3);
@@ -20395,11 +20178,12 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
}
/* Fall through: halfmapping or unpaired */
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
*final_pairtype = UNPAIRED;
singlehits5 = Stage3end_filter_coverage(singlehits5,min_coverage_5);
- if ((*nhits5 = List_length(singlehits5)) == 0) {
+ if (singlehits5 == NULL) {
+ *nhits5_primary = *nhits5_altloc = 0;
*stage3array5 = (Stage3end_T *) NULL;
} else {
#if 0
@@ -20407,13 +20191,14 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
#else
singlehits5 = Stage3end_remove_circular_alias(singlehits5); /* Contains a call to unalias_circular */
singlehits5 = Stage3end_remove_duplicates(singlehits5); /* Aliases can cause duplicates */
- *nhits5 = List_length(singlehits5);
+ Stage3end_count_hits(&(*nhits5_primary),&(*nhits5_altloc),singlehits5);
#endif
*stage3array5 = (Stage3end_T *) List_to_array_out(singlehits5,NULL); List_free(&singlehits5); /* Return value */
}
singlehits3 = Stage3end_filter_coverage(singlehits3,min_coverage_3);
- if ((*nhits3 = List_length(singlehits3)) == 0) {
+ if (singlehits3 == NULL) {
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array3 = (Stage3end_T *) NULL;
} else {
#if 0
@@ -20421,47 +20206,44 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
#else
singlehits3 = Stage3end_remove_circular_alias(singlehits3); /* Contains a call to unalias_circular */
singlehits3 = Stage3end_remove_duplicates(singlehits3); /* Aliases can cause duplicates */
- *nhits3 = List_length(singlehits3);
+ Stage3end_count_hits(&(*nhits3_primary),&(*nhits3_altloc),singlehits3);
#endif
*stage3array3 = (Stage3end_T *) List_to_array_out(singlehits3,NULL); List_free(&singlehits3); /* Return value */
}
- if (*nhits5 > 0) {
- if (*nhits3 == 1) {
- /* Use single 3' hit to guide sorting of multiple 5' hits */
- *stage3array5 = Stage3end_eval_and_sort_guided(&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- /*guide*/(*stage3array3)[0],
+ if ((*nhits5_primary) + (*nhits5_altloc) > 0) {
+ if ((*nhits3_primary) + (*nhits3_altloc) == 1) {
+ /* Use single 3' hit to guide sorting of multiple 5' hits */
+ *stage3array5 = Stage3end_eval_and_sort_guided((*nhits5_primary) + (*nhits5_altloc),
+ &(*first_absmq5),&(*second_absmq5),/*guide*/(*stage3array3)[0],
*stage3array5,maxpaths_search,queryseq5,
- queryuc_ptr_5,queryrc5,
- query5_compress_fwd,query5_compress_rev,
+ queryuc_ptr_5,query5_compress_fwd,query5_compress_rev,
quality_string_5,/*displayp*/true);
} else {
- *stage3array5 = Stage3end_eval_and_sort(&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- *stage3array5,maxpaths_search,queryseq5,
- queryuc_ptr_5,queryrc5,
- query5_compress_fwd,query5_compress_rev,
+ *stage3array5 = Stage3end_eval_and_sort((*nhits5_primary) + (*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ *stage3array5,maxpaths_search,queryseq5,
+ queryuc_ptr_5,query5_compress_fwd,query5_compress_rev,
quality_string_5,/*displayp*/true);
}
}
- if (*nhits3 > 0) {
- if (*nhits5 == 1) {
+ if ((*nhits3_primary) + (*nhits3_altloc) > 0) {
+ if ((*nhits5_primary) + (*nhits5_altloc) == 1) {
/* Use single 5' hit to guide sorting of multiple 3' hits */
- *stage3array3 = Stage3end_eval_and_sort_guided(&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- /*guide*/(*stage3array5)[0],
+ *stage3array3 = Stage3end_eval_and_sort_guided((*nhits3_primary) + (*nhits3_altloc),
+ &(*first_absmq3),&(*second_absmq3),/*guide*/(*stage3array5)[0],
*stage3array3,maxpaths_search,queryseq3,
- queryuc_ptr_3,queryrc3,
- query3_compress_fwd,query3_compress_rev,
+ queryuc_ptr_3,query3_compress_fwd,query3_compress_rev,
quality_string_3,/*displayp*/true);
} else {
- *stage3array3 = Stage3end_eval_and_sort(&(*nhits3),&(*first_absmq3),&(*second_absmq3),
+ *stage3array3 = Stage3end_eval_and_sort((*nhits3_primary) + (*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
*stage3array3,maxpaths_search,queryseq3,
- queryuc_ptr_3,queryrc3,
- query3_compress_fwd,query3_compress_rev,
+ queryuc_ptr_3,query3_compress_fwd,query3_compress_rev,
quality_string_3,/*displayp*/true);
}
}
- debug16(printf("Result is NULL, and we have %d hits on 5' end and %d hits on 3' end\n",*nhits5,*nhits3));
+ debug16(printf("Result is NULL, and we have %d hits on 5' end and %d hits on 3' end\n",
+ (*nhits5_primary) + (*nhits5_altloc),(*nhits3_primary) + (*nhits3_altloc)));
return (Stage3pair_T *) NULL;
} else {
@@ -20469,28 +20251,32 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
List_length(result)));
result = Stage3pair_filter_coverage(result,min_coverage_5,min_coverage_3);
- if ((*npaths = List_length(result)) == 0) {
+ if (result == NULL) {
+ *npaths_primary = *npaths_altloc = 0;
stage3list_gc(&hits3);
stage3list_gc(&hits5);
- *nhits5 = *nhits3 = 0;
+ *nhits5_primary = *nhits5_altloc = 0;
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
} else {
/* result != NULL */
/* Concordant, paired, or transloc pairs found. Remove single hits. */
+ Stage3pair_count_hits(&(*npaths_primary),&(*npaths_altloc),result);
stage3pairarray = (Stage3pair_T *) List_to_array_out(result,NULL); List_free(&result); /* Return value */
- Stage3pair_privatize(stage3pairarray,*npaths);
- Stage3pair_eval_and_sort(&(*npaths),&(*first_absmq),&(*second_absmq),
- stage3pairarray,maxpaths_search,queryseq5,queryseq3,
- queryuc_ptr_5,queryrc5,queryuc_ptr_3,queryrc3,
+ Stage3pair_privatize(stage3pairarray,/*npaths*/(*npaths_primary) + (*npaths_altloc));
+ Stage3pair_eval_and_sort(/*npaths*/(*npaths_primary) + (*npaths_altloc),
+ &(*first_absmq),&(*second_absmq),stage3pairarray,maxpaths_search,queryseq5,queryseq3,
+ queryuc_ptr_5,queryuc_ptr_3,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
quality_string_5,quality_string_3);
stage3list_gc(&hits3);
stage3list_gc(&hits5);
- *nhits5 = *nhits3 = 0;
+ *nhits5_primary = *nhits5_altloc = 0;
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return stage3pairarray;
}
@@ -20499,9 +20285,9 @@ consolidate_paired_results (int *npaths, int *first_absmq, int *second_absmq, Pa
static Stage3pair_T *
-paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
- Stage3end_T **stage3array5, int *nhits5, int *first_absmq5, int *second_absmq5,
- Stage3end_T **stage3array3, int *nhits3, int *first_absmq3, int *second_absmq3,
+paired_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
+ Stage3end_T **stage3array5, int *nhits5_primary, int *nhits5_altloc, int *first_absmq5, int *second_absmq5,
+ Stage3end_T **stage3array3, int *nhits3_primary, int *nhits3_altloc, int *first_absmq3, int *second_absmq3,
Shortread_T queryseq5, Shortread_T queryseq3,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int indexdb_size_threshold,
Floors_T *floors_array,
@@ -20542,7 +20328,9 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
if (querylength5 > MAX_READLENGTH || querylength3 > MAX_READLENGTH) {
fprintf(stderr,"Paired-read %s has lengths %d and %d > MAX_READLENGTH %d. Either run configure and make again with a higher value of MAX_READLENGTH, or consider using GMAP instead.\n",
Shortread_accession(queryseq5),querylength5,querylength3,MAX_READLENGTH);
- *npaths = *nhits5 = *nhits3 = 0;
+ *npaths_primary = *npaths_altloc = 0;
+ *nhits5_primary = *nhits5_altloc = 0;
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
}
@@ -20600,16 +20388,18 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
&samechr,&conc_transloc,gmap_history_5,gmap_history_3,
&hits5,&hits3,this5,this3,query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
- queryuc_ptr_5,queryuc_ptr_3,queryrc5,queryrc3,
+ queryuc_ptr_5,queryuc_ptr_3,
+#ifndef LARGE_GENOMES
+ queryrc5,queryrc3,
+#endif
querylength5,querylength3,query5_lastpos,query3_lastpos,
indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_5,user_maxlevel_3,min_coverage_5,min_coverage_3,
- indel_penalty_middle,indel_penalty_end,
- localsplicing_penalty,distantsplicing_penalty,min_shortend,
+ user_maxlevel_5,user_maxlevel_3,indel_penalty_middle,indel_penalty_end,
+ localsplicing_penalty,distantsplicing_penalty,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
pairmax,maxpairedpaths,keep_floors_p,queryseq5,queryseq3,/*genestrand*/0);
@@ -20620,9 +20410,9 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
this5 = Stage1_new(querylength5);
this3 = Stage1_new(querylength3);
- realign_separately(stage3array5,&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- stage3array3,&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- gmap_history_5,gmap_history_3,this5,this3,
+ realign_separately(stage3array5,&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ stage3array3,&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
+ this5,this3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
@@ -20631,11 +20421,10 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
keep_floors_p,/*genestrand*/0);
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
*final_pairtype = UNPAIRED;
History_free(&gmap_history_3);
History_free(&gmap_history_5);
@@ -20649,19 +20438,15 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
} else {
stage3pairarray =
- consolidate_paired_results(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
- &(*stage3array5),&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- &(*stage3array3),&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- hitpairs,samechr,conc_transloc,hits5,hits3,gmap_history_5,gmap_history_3,
+ consolidate_paired_results(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
+ &(*stage3array5),&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ &(*stage3array3),&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
+ hitpairs,samechr,conc_transloc,hits5,hits3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
- &this5->plus_segments,&this5->plus_nsegments,&this5->minus_segments,&this5->minus_nsegments,
- &this3->plus_segments,&this3->plus_nsegments,&this3->minus_segments,&this3->minus_nsegments,
- queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
- queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
+ queryseq5,queryuc_ptr_5,quality_string_5,querylength5,
+ queryseq3,queryuc_ptr_3,quality_string_3,querylength3,
cutoff_level_5,cutoff_level_3,min_coverage_5,min_coverage_3,
- localsplicing_penalty,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,user_maxlevel_5,user_maxlevel_3);
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
History_free(&gmap_history_3);
History_free(&gmap_history_5);
@@ -20677,9 +20462,9 @@ paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final
static Stage3pair_T *
-paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
- Stage3end_T **stage3array5, int *nhits5, int *first_absmq5, int *second_absmq5,
- Stage3end_T **stage3array3, int *nhits3, int *first_absmq3, int *second_absmq3,
+paired_read_tolerant_nonstranded (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
+ Stage3end_T **stage3array5, int *nhits5_primary, int *nhits5_altloc, int *first_absmq5, int *second_absmq5,
+ Stage3end_T **stage3array3, int *nhits3_primary, int *nhits3_altloc, int *first_absmq3, int *second_absmq3,
Shortread_T queryseq5, Shortread_T queryseq3,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int indexdb_size_threshold,
Floors_T *floors_array,
@@ -20709,10 +20494,6 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
int maxpairedpaths = maxpaths_search; /* 100000 */
#endif
bool abort_pairing_p_geneplus, abort_pairing_p_geneminus;
- struct Segment_T *plus_segments_genestrand_5[3], *minus_segments_genestrand_5[3],
- *plus_segments_genestrand_3[3], *minus_segments_genestrand_3[3];
- int plus_nsegments_genestrand_5[3], minus_nsegments_genestrand_5[3],
- plus_nsegments_genestrand_3[3], minus_nsegments_genestrand_3[3];
#ifdef HAVE_ALLOCA
char *queryrc5, *queryrc3;
@@ -20728,7 +20509,9 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
if (querylength5 > MAX_READLENGTH || querylength3 > MAX_READLENGTH) {
fprintf(stderr,"Paired-read %s has lengths %d and %d > MAX_READLENGTH %d. Either run configure and make again with a higher value of MAX_READLENGTH, or consider using GMAP instead.\n",
Shortread_accession(queryseq5),querylength5,querylength3,MAX_READLENGTH);
- *npaths = *nhits5 = *nhits3 = 0;
+ *npaths_primary = *npaths_altloc = 0;
+ *nhits5_primary = *nhits5_altloc = 0;
+ *nhits3_primary = *nhits3_altloc = 0;
*stage3array5 = *stage3array3 = (Stage3end_T *) NULL;
return (Stage3pair_T *) NULL;
}
@@ -20791,16 +20574,18 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
gmap_history_5,gmap_history_3,
&hits_geneplus_5,&hits_geneplus_3,this_geneplus_5,this_geneplus_3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
- queryuc_ptr_5,queryuc_ptr_3,queryrc5,queryrc3,
+ queryuc_ptr_5,queryuc_ptr_3,
+#ifndef LARGE_GENOMES
+ queryrc5,queryrc3,
+#endif
querylength5,querylength3,query5_lastpos,query3_lastpos,
indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_5,user_maxlevel_3,min_coverage_5,min_coverage_3,
- indel_penalty_middle,indel_penalty_end,
- localsplicing_penalty,distantsplicing_penalty,min_shortend,
+ user_maxlevel_5,user_maxlevel_3,indel_penalty_middle,indel_penalty_end,
+ localsplicing_penalty,distantsplicing_penalty,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
pairmax,maxpairedpaths,keep_floors_p,
queryseq5,queryseq3,/*genestrand*/+1);
@@ -20812,16 +20597,18 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
gmap_history_5,gmap_history_3,
&hits_geneminus_5,&hits_geneminus_3,this_geneminus_5,this_geneminus_3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
- queryuc_ptr_5,queryuc_ptr_3,queryrc5,queryrc3,
+ queryuc_ptr_5,queryuc_ptr_3,
+#ifndef LARGE_GENOMES
+ queryrc5,queryrc3,
+#endif
querylength5,querylength3,query5_lastpos,query3_lastpos,
indexdb_fwd,indexdb_rev,indexdb_size_threshold,floors_array,
oligoindices_major,oligoindices_minor,
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
- user_maxlevel_5,user_maxlevel_3,min_coverage_5,min_coverage_3,
- indel_penalty_middle,indel_penalty_end,
- localsplicing_penalty,distantsplicing_penalty,min_shortend,
+ user_maxlevel_5,user_maxlevel_3,indel_penalty_middle,indel_penalty_end,
+ localsplicing_penalty,distantsplicing_penalty,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
pairmax,maxpairedpaths,keep_floors_p,queryseq5,queryseq3,/*genestrand*/+2);
@@ -20836,9 +20623,9 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
this_geneplus_5 = Stage1_new(querylength5);
this_geneplus_3 = Stage1_new(querylength3);
- realign_separately(stage3array5,&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- stage3array3,&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- gmap_history_5,gmap_history_3,this_geneplus_5,this_geneplus_3,
+ realign_separately(stage3array5,&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ stage3array3,&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
+ this_geneplus_5,this_geneplus_3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
@@ -20847,11 +20634,10 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
keep_floors_p,/*genestrand*/+1);
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
*final_pairtype = UNPAIRED;
History_free(&gmap_history_3);
History_free(&gmap_history_5);
@@ -20864,30 +20650,17 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
return (Stage3pair_T *) NULL;
} else {
- plus_segments_genestrand_5[+1] = this_geneplus_5->plus_segments;
- plus_nsegments_genestrand_5[+1] = this_geneplus_5->plus_nsegments;
- minus_segments_genestrand_5[+1] = this_geneplus_5->minus_segments;
- minus_nsegments_genestrand_5[+1] = this_geneplus_5->minus_nsegments;
-
- plus_segments_genestrand_3[+1] = this_geneplus_3->plus_segments;
- plus_nsegments_genestrand_3[+1] = this_geneplus_3->plus_nsegments;
- minus_segments_genestrand_3[+1] = this_geneplus_3->minus_segments;
- minus_nsegments_genestrand_3[+1] = this_geneplus_3->minus_nsegments;
-
stage3pairarray =
- consolidate_paired_results(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
- &(*stage3array5),&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- &(*stage3array3),&(*nhits3),&(*first_absmq3),&(*second_absmq3),
+ consolidate_paired_results(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
+ &(*stage3array5),&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ &(*stage3array3),&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
hitpairs_geneplus,samechr_geneplus,conc_transloc_geneplus,
- hits_geneplus_5,hits_geneplus_3,gmap_history_5,gmap_history_3,
+ hits_geneplus_5,hits_geneplus_3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
- queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
+ queryseq5,queryuc_ptr_5,quality_string_5,querylength5,
+ queryseq3,queryuc_ptr_3,quality_string_3,querylength3,
cutoff_level_5,cutoff_level_3,min_coverage_5,min_coverage_3,
- localsplicing_penalty,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,user_maxlevel_5,user_maxlevel_3);
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
History_free(&gmap_history_3);
History_free(&gmap_history_5);
Compress_free(&query5_compress_fwd);
@@ -20910,9 +20683,9 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
this_geneminus_5 = Stage1_new(querylength5);
this_geneminus_3 = Stage1_new(querylength3);
- realign_separately(stage3array5,&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- stage3array3,&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- gmap_history_5,gmap_history_3,this_geneminus_5,this_geneminus_3,
+ realign_separately(stage3array5,&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ stage3array3,&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
+ this_geneminus_5,this_geneminus_3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
@@ -20921,11 +20694,10 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,distantsplicing_penalty,min_shortend,
- oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,
keep_floors_p,/*genestrand*/+2);
- *npaths = 0;
+ *npaths_primary = *npaths_altloc = 0;
*final_pairtype = UNPAIRED;
History_free(&gmap_history_3);
History_free(&gmap_history_5);
@@ -20938,30 +20710,17 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
return (Stage3pair_T *) NULL;
} else {
- plus_segments_genestrand_5[+2] = this_geneminus_5->plus_segments;
- plus_nsegments_genestrand_5[+2] = this_geneminus_5->plus_nsegments;
- minus_segments_genestrand_5[+2] = this_geneminus_5->minus_segments;
- minus_nsegments_genestrand_5[+2] = this_geneminus_5->minus_nsegments;
-
- plus_segments_genestrand_3[+2] = this_geneminus_3->plus_segments;
- plus_nsegments_genestrand_3[+2] = this_geneminus_3->plus_nsegments;
- minus_segments_genestrand_3[+2] = this_geneminus_3->minus_segments;
- minus_nsegments_genestrand_3[+2] = this_geneminus_3->minus_nsegments;
-
stage3pairarray =
- consolidate_paired_results(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
- &(*stage3array5),&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- &(*stage3array3),&(*nhits3),&(*first_absmq3),&(*second_absmq3),
+ consolidate_paired_results(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
+ &(*stage3array5),&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ &(*stage3array3),&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
hitpairs_geneminus,samechr_geneminus,conc_transloc_geneminus,
- hits_geneminus_5,hits_geneminus_3,gmap_history_5,gmap_history_3,
+ hits_geneminus_5,hits_geneminus_3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
- queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
+ queryseq5,queryuc_ptr_5,quality_string_5,querylength5,
+ queryseq3,queryuc_ptr_3,quality_string_3,querylength3,
cutoff_level_5,cutoff_level_3,min_coverage_5,min_coverage_3,
- localsplicing_penalty,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,user_maxlevel_5,user_maxlevel_3);
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
History_free(&gmap_history_3);
History_free(&gmap_history_5);
Compress_free(&query5_compress_fwd);
@@ -20980,39 +20739,16 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
hits5 = List_append(hits_geneplus_5,hits_geneminus_5);
hits3 = List_append(hits_geneplus_3,hits_geneminus_3);
- plus_segments_genestrand_5[+1] = this_geneplus_5->plus_segments;
- plus_nsegments_genestrand_5[+1] = this_geneplus_5->plus_nsegments;
- minus_segments_genestrand_5[+1] = this_geneplus_5->minus_segments;
- minus_nsegments_genestrand_5[+1] = this_geneplus_5->minus_nsegments;
-
- plus_segments_genestrand_3[+1] = this_geneplus_3->plus_segments;
- plus_nsegments_genestrand_3[+1] = this_geneplus_3->plus_nsegments;
- minus_segments_genestrand_3[+1] = this_geneplus_3->minus_segments;
- minus_nsegments_genestrand_3[+1] = this_geneplus_3->minus_nsegments;
-
- plus_segments_genestrand_5[+2] = this_geneminus_5->plus_segments;
- plus_nsegments_genestrand_5[+2] = this_geneminus_5->plus_nsegments;
- minus_segments_genestrand_5[+2] = this_geneminus_5->minus_segments;
- minus_nsegments_genestrand_5[+2] = this_geneminus_5->minus_nsegments;
-
- plus_segments_genestrand_3[+2] = this_geneminus_3->plus_segments;
- plus_nsegments_genestrand_3[+2] = this_geneminus_3->plus_nsegments;
- minus_segments_genestrand_3[+2] = this_geneminus_3->minus_segments;
- minus_nsegments_genestrand_3[+2] = this_geneminus_3->minus_nsegments;
-
stage3pairarray =
- consolidate_paired_results(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
- &(*stage3array5),&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- &(*stage3array3),&(*nhits3),&(*first_absmq3),&(*second_absmq3),
- hitpairs,samechr,conc_transloc,hits5,hits3,gmap_history_5,gmap_history_3,
+ consolidate_paired_results(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
+ &(*stage3array5),&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ &(*stage3array3),&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
+ hitpairs,samechr,conc_transloc,hits5,hits3,
query5_compress_fwd,query5_compress_rev,query3_compress_fwd,query3_compress_rev,
- plus_segments_genestrand_5,plus_nsegments_genestrand_5,minus_segments_genestrand_5,minus_nsegments_genestrand_5,
- plus_segments_genestrand_3,plus_nsegments_genestrand_3,minus_segments_genestrand_3,minus_nsegments_genestrand_3,
- queryseq5,queryuc_ptr_5,queryrc5,quality_string_5,querylength5,query5_lastpos,
- queryseq3,queryuc_ptr_3,queryrc3,quality_string_3,querylength3,query3_lastpos,
+ queryseq5,queryuc_ptr_5,quality_string_5,querylength5,
+ queryseq3,queryuc_ptr_3,quality_string_3,querylength3,
cutoff_level_5,cutoff_level_3,min_coverage_5,min_coverage_3,
- localsplicing_penalty,oligoindices_major,oligoindices_minor,
- pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,user_maxlevel_5,user_maxlevel_3);
+ oligoindices_minor,pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR);
History_free(&gmap_history_3);
History_free(&gmap_history_5);
Compress_free(&query5_compress_fwd);
@@ -21029,9 +20765,9 @@ paired_read_tolerant_nonstranded (int *npaths, int *first_absmq, int *second_abs
Stage3pair_T *
-Stage1_paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
- Stage3end_T **stage3array5, int *nhits5, int *first_absmq5, int *second_absmq5,
- Stage3end_T **stage3array3, int *nhits3, int *first_absmq3, int *second_absmq3,
+Stage1_paired_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
+ Stage3end_T **stage3array5, int *nhits5_primary, int *nhits5_altloc, int *first_absmq5, int *second_absmq5,
+ Stage3end_T **stage3array3, int *nhits3_primary, int *nhits3_altloc, int *first_absmq3, int *second_absmq3,
Shortread_T queryseq5, Shortread_T queryseq3,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int indexdb_size_threshold,
Floors_T *floors_array,
@@ -21044,9 +20780,9 @@ Stage1_paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T
Chrpos_T pairmax, bool keep_floors_p) {
if (mode == STANDARD || mode == CMET_STRANDED || mode == ATOI_STRANDED || mode == TTOC_STRANDED) {
- return paired_read(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
- &(*stage3array5),&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- &(*stage3array3),&(*nhits3),&(*first_absmq3),&(*second_absmq3),
+ return paired_read(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
+ &(*stage3array5),&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ &(*stage3array3),&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
queryseq5,queryseq3,indexdb_fwd,indexdb_rev,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
@@ -21055,9 +20791,9 @@ Stage1_paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T
pairpool,diagpool,cellpool,dynprogL,dynprogM,dynprogR,pairmax,keep_floors_p);
} else if (mode == CMET_NONSTRANDED || mode == ATOI_NONSTRANDED || mode == TTOC_NONSTRANDED) {
- return paired_read_tolerant_nonstranded(&(*npaths),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
- &(*stage3array5),&(*nhits5),&(*first_absmq5),&(*second_absmq5),
- &(*stage3array3),&(*nhits3),&(*first_absmq3),&(*second_absmq3),
+ return paired_read_tolerant_nonstranded(&(*npaths_primary),&(*npaths_altloc),&(*first_absmq),&(*second_absmq),&(*final_pairtype),
+ &(*stage3array5),&(*nhits5_primary),&(*nhits5_altloc),&(*first_absmq5),&(*second_absmq5),
+ &(*stage3array3),&(*nhits3_primary),&(*nhits3_altloc),&(*first_absmq3),&(*second_absmq3),
queryseq5,queryseq3,indexdb_fwd,indexdb_rev,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
@@ -21089,8 +20825,8 @@ Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_
Chrpos_T *splicedists_in, int nsplicesites_in,
bool novelsplicingp_in, bool knownsplicingp_in, bool find_dna_chimeras_p_in,
- bool distances_observed_p_in, int subopt_levels_in,
- Chrpos_T max_middle_insertions_in, Chrpos_T max_middle_deletions_in,
+ bool distances_observed_p_in, int subopt_levels_in, int min_indel_end_matches_in,
+ int max_middle_insertions_in, int max_middle_deletions_in,
Chrpos_T shortsplicedist_in, Chrpos_T shortsplicedist_known_in, Chrpos_T shortsplicedist_novelend_in,
Chrpos_T min_intronlength_in,
@@ -21122,8 +20858,13 @@ Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_
Univ_IIT_intervals_setup(&chroffsets,&chrhighs,&chrlengths,chromosome_iit,nchromosomes,circular_typeint);
}
- leftreadshift = 32 - index1part - index1part; /* For 12-mers, 8 */
- oligobase_mask = ~(~0UL << 2*index1part); /* For 12-mers, was 0x00FFFFFF */
+#ifdef HAVE_64_BIT
+ leftreadshift = 64 - index1part - index1part;
+ oligobase_mask = ~(~0ULL << 2*index1part);
+#else
+ leftreadshift = 32 - index1part - index1part;
+ oligobase_mask = ~(~0U << 2*index1part);
+#endif
one_miss_querylength = spansize + spansize - (index1interval - 1); /* For 12-mers, 22 */
#if 0
@@ -21149,7 +20890,8 @@ Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_
distances_observed_p = distances_observed_p_in;
subopt_levels = subopt_levels_in;
- max_middle_insertions = max_middle_insertions_in;
+ min_indel_end_matches = min_indel_end_matches_in;
+ max_middle_insertions_default = max_middle_insertions_in;
max_middle_deletions = max_middle_deletions_in;
shortsplicedist = shortsplicedist_in;
@@ -21157,11 +20899,11 @@ Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_
shortsplicedist_novelend = shortsplicedist_novelend_in;
overall_max_distance = shortsplicedist;
- if (max_middle_deletions > overall_max_distance) {
+ if (max_middle_deletions > (int) overall_max_distance) {
overall_max_distance = max_middle_deletions;
}
- if (max_middle_insertions > overall_max_distance) {
- overall_max_distance = max_middle_insertions;
+ if (max_middle_insertions_default > (int) overall_max_distance) {
+ overall_max_distance = max_middle_insertions_default;
}
min_intronlength = min_intronlength_in;
diff --git a/src/stage1hr.h b/src/stage1hr.h
index 5bd43f6..72a45d4 100644
--- a/src/stage1hr.h
+++ b/src/stage1hr.h
@@ -1,4 +1,4 @@
-/* $Id: stage1hr.h 186090 2016-03-17 22:21:17Z twu $ */
+/* $Id: stage1hr.h 186091 2016-03-17 22:23:16Z twu $ */
#ifndef STAGE1HR_INCLUDED
#define STAGE1HR_INCLUDED
@@ -56,22 +56,22 @@ Stage1_free (T *old, int querylength);
extern Stage3end_T *
-Stage1_single_read (int *npaths, int *first_absmq, int *second_absmq,
+Stage1_single_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq,
Shortread_T queryseq, Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev,
int indexdb_size_threshold, Floors_T *floors_array,
double user_maxlevel_float, double user_mincoverage_float,
int indel_penalty_middle, int indel_penalty_end,
bool allow_end_indels_p, int max_end_insertions, int max_end_deletions, int min_indel_end_matches,
int localsplicing_penalty, int distantsplicing_penalty, int min_shortend,
- Oligoindex_array_T oligoindices_major, Oligoindex_array_T oligoindices_minor,
+ Oligoindex_array_T oligoindices_minor,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
bool keep_floors_p);
extern Stage3pair_T *
-Stage1_paired_read (int *npaths, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
- Stage3end_T **stage3array5, int *nhits5, int *first_absmq5, int *second_absmq5,
- Stage3end_T **stage3array3, int *nhits3, int *first_absmq3, int *second_absmq3,
+Stage1_paired_read (int *npaths_primary, int *npaths_altloc, int *first_absmq, int *second_absmq, Pairtype_T *final_pairtype,
+ Stage3end_T **stage3array5, int *nhits5_primary, int *nhits5_altloc, int *first_absmq5, int *second_absmq5,
+ Stage3end_T **stage3array3, int *nhits3_primary, int *nhits3_altloc, int *first_absmq3, int *second_absmq3,
Shortread_T queryseq5, Shortread_T queryseq3,
Indexdb_T indexdb_fwd, Indexdb_T indexdb_rev, int indexdb_size_threshold,
Floors_T *floors_array,
@@ -96,8 +96,8 @@ Stage1hr_setup (bool use_sarray_p_in, bool use_only_sarray_p_in, int index1part_
Chrpos_T *splicedists_in, int nsplicesites_in,
bool novelsplicingp_in, bool knownsplicingp_in, bool find_dna_chimeras_p_in,
- bool distances_observed_p_in, int subopt_levels_in,
- Chrpos_T max_middle_insertions_in, Chrpos_T max_middle_deletions_in,
+ bool distances_observed_p_in, int subopt_levels_in, int min_indel_end_matches_in,
+ int max_middle_insertions_in, int max_middle_deletions_in,
Chrpos_T shortsplicedist_in, Chrpos_T shortsplicedist_known_in, Chrpos_T shortsplicedist_novelend_in,
Chrpos_T min_intronlength_in,
diff --git a/src/stage2.c b/src/stage2.c
index 5298112..6a88290 100644
--- a/src/stage2.c
+++ b/src/stage2.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage2.c 186092 2016-03-17 22:28:37Z twu $";
+static char rcsid[] = "$Id: stage2.c 186093 2016-03-17 22:29:54Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -791,7 +791,7 @@ score_querypos_lookback_one (
int **active, int *firstactive,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
int indexsize, Intlist_T processed,
- bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool anchoredp, bool localp, bool splicingp,
bool use_canonical_p, int non_canonical_penalty) {
Link_T prevlink;
struct Link_T *prev_links;
@@ -810,7 +810,8 @@ score_querypos_lookback_one (
#endif
bool donep;
int prev_querypos, prevhit;
- Chrpos_T prevposition, gendistance;
+ Chrpos_T prevposition;
+ int gendistance;
Univcoord_T prevpos, currpos;
int querydistance, diffdistance, lookback, nlookback, nseen, indexsize_nt, indexsize_query;
/* int querydist_penalty; */
@@ -939,7 +940,7 @@ score_querypos_lookback_one (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = position - prevposition;
- assert(gendistance > (Chrpos_T) querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
+ assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
diffdistance = gendistance - querydistance; /* No need for abs() */
fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
@@ -1059,12 +1060,8 @@ score_querypos_lookback_one (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = position - prevposition;
- /* diffdistance = abs(gendistance - querydistance); */
- if (gendistance > querydistance) {
- diffdistance = gendistance - querydistance;
- } else {
- diffdistance = querydistance - gendistance;
- }
+ /* was abs(gendistance - querydistance) */
+ diffdistance = gendistance > querydistance ? (gendistance - querydistance) : (querydistance - gendistance);
#ifdef BAD_GMAX
fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
@@ -1171,7 +1168,7 @@ score_querypos_lookback_mult (
int **active, int *firstactive,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
int indexsize, Intlist_T processed,
- bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool anchoredp, bool localp, bool splicingp,
bool use_canonical_p, int non_canonical_penalty) {
Link_T prevlink, currlink;
Intlist_T last_item, p;
@@ -1185,16 +1182,16 @@ score_querypos_lookback_mult (
int best_fwd_rootposition;
int best_fwd_score, fwd_score;
int best_fwd_prevpos, best_fwd_prevhit;
- bool donep;
#ifdef DEBUG9
int best_fwd_tracei;
int best_fwd_intronnfwd, best_fwd_intronnrev, best_fwd_intronnunk;
int canonicalsgn = 0;
#endif
int adj_querypos, adj_querydistance, prev_querypos, prevhit, adj_frontier, *frontier;
- Chrpos_T prevposition, position, gendistance;
+ Chrpos_T prevposition, position;
+ int gendistance;
Univcoord_T prevpos, currpos;
- int querydistance, diffdistance, lookback, nlookback, indexsize_nt, indexsize_query;
+ int querydistance, diffdistance, indexsize_nt, indexsize_query;
int max_nseen, max_adjacent_nseen, max_nonadjacent_nseen, nseen;
int querydist_credit;
int enough_consecutive = 32;
@@ -1450,7 +1447,7 @@ score_querypos_lookback_mult (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = position - prevposition;
- assert(gendistance > (Chrpos_T) querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
+ assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
diffdistance = gendistance - querydistance; /* No need for abs() */
fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
@@ -1567,12 +1564,8 @@ score_querypos_lookback_mult (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = position - prevposition;
- /* diffdistance = abs(gendistance - querydistance); */
- if (gendistance > querydistance) {
- diffdistance = gendistance - querydistance;
- } else {
- diffdistance = querydistance - gendistance;
- }
+ /* was abs(gendistance - querydistance) */
+ diffdistance = gendistance > querydistance ? (gendistance - querydistance) : (querydistance - gendistance);
#ifdef BAD_GMAX
fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
@@ -1672,7 +1665,7 @@ score_querypos_lookforward_one (
int **active, int *firstactive,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
int indexsize, Intlist_T processed,
- bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool anchoredp, bool localp, bool splicingp,
bool use_canonical_p, int non_canonical_penalty) {
Link_T prevlink;
struct Link_T *prev_links;
@@ -1690,7 +1683,8 @@ score_querypos_lookforward_one (
#endif
bool donep;
int prev_querypos, prevhit;
- Chrpos_T prevposition, gendistance;
+ Chrpos_T prevposition;
+ int gendistance;
Univcoord_T prevpos, currpos;
int querydistance, diffdistance, lookback, nlookback, nseen, indexsize_nt, indexsize_query;
/* int querydist_penalty; */
@@ -1817,7 +1811,7 @@ score_querypos_lookforward_one (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = prevposition - position;
- assert(gendistance > (Chrpos_T) querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
+ assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
diffdistance = gendistance - querydistance; /* No need for abs() */
fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
@@ -1936,12 +1930,8 @@ score_querypos_lookforward_one (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = prevposition - position;
- /* diffdistance = abs(gendistance - querydistance); */
- if (gendistance > querydistance) {
- diffdistance = gendistance - querydistance;
- } else {
- diffdistance = querydistance - gendistance;
- }
+ /* was abs(gendistance - querydistance) */
+ diffdistance = gendistance > querydistance ? (gendistance - querydistance) : (querydistance - gendistance);
#ifdef BAD_GMAX
fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
@@ -2044,7 +2034,7 @@ score_querypos_lookforward_mult (
int **active, int *firstactive,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
int indexsize, Intlist_T processed,
- bool anchoredp, bool localp, bool splicingp, bool skip_repetitive_p,
+ bool anchoredp, bool localp, bool splicingp,
bool use_canonical_p, int non_canonical_penalty) {
Link_T prevlink, currlink;
Intlist_T last_item, p;
@@ -2058,16 +2048,16 @@ score_querypos_lookforward_mult (
int best_fwd_rootposition;
int best_fwd_score, fwd_score;
int best_fwd_prevpos, best_fwd_prevhit;
- bool donep;
#ifdef DEBUG9
int best_fwd_tracei;
int best_fwd_intronnfwd, best_fwd_intronnrev, best_fwd_intronnunk;
int canonicalsgn = 0;
#endif
int adj_querypos, adj_querydistance, prev_querypos, prevhit, adj_frontier, *frontier;
- Chrpos_T prevposition, position, gendistance;
+ Chrpos_T prevposition, position;
+ int gendistance;
Univcoord_T prevpos, currpos;
- int querydistance, diffdistance, lookback, nlookback, indexsize_nt, indexsize_query;
+ int querydistance, diffdistance, indexsize_nt, indexsize_query;
int max_nseen, max_adjacent_nseen, max_nonadjacent_nseen, nseen;
int querydist_credit;
int enough_consecutive = 32;
@@ -2322,7 +2312,7 @@ score_querypos_lookforward_mult (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = prevposition - position;
- assert(gendistance > (Chrpos_T) querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
+ assert(gendistance > querydistance); /* True because gendistance > EQUAL_DISTANCE_NOT_SPLICING + querydistance */
diffdistance = gendistance - querydistance; /* No need for abs() */
fwd_score = prevlink->fwd_score + querydist_credit /*- querydist_penalty*/;
@@ -2439,12 +2429,8 @@ score_querypos_lookforward_mult (
prevlink = &(/*links[prev_querypos]*/prev_links[prevhit]);
gendistance = prevposition - position;
- /* diffdistance = abs(gendistance - querydistance); */
- if (gendistance > querydistance) {
- diffdistance = gendistance - querydistance;
- } else {
- diffdistance = querydistance - gendistance;
- }
+ /* was abs(gendistance - querydistance) */
+ diffdistance = gendistance > querydistance ? (gendistance - querydistance) : (querydistance - gendistance);
#ifdef BAD_GMAX
fwd_score = prevlink->fwd_score + querydist_credit - (diffdistance/ONE + 1) /*- querydist_penalty*/;
@@ -2535,8 +2521,7 @@ score_querypos_lookforward_mult (
static void
revise_active_lookback (int **active, int *firstactive, int *nactive,
- int low_hit, int high_hit, struct Link_T **links, int querypos,
- Chrpos_T **mappings) {
+ int low_hit, int high_hit, struct Link_T **links, int querypos) {
int best_score, threshold, score;
int hit, *ptr;
@@ -2614,8 +2599,7 @@ revise_active_lookback (int **active, int *firstactive, int *nactive,
static void
revise_active_lookforward (int **active, int *firstactive, int *nactive,
- int low_hit, int high_hit, struct Link_T **links, int querypos,
- Chrpos_T **mappings) {
+ int low_hit, int high_hit, struct Link_T **links, int querypos) {
int best_score, threshold, score;
int hit, *ptr;
@@ -2969,13 +2953,13 @@ Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, i
static Cell_T *
Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, int queryend, int *npositions,
- int indexsize, int bestscore, bool favor_right_p, Cellpool_T cellpool) {
+ bool favor_right_p, Cellpool_T cellpool) {
Cell_T *sorted, *cells;
List_T celllist = NULL;
int querypos, hit;
int rootposition, last_rootposition;
int best_score_for_root;
- int ngood, ncells, i, k;
+ int ncells, i, k;
ncells = 0;
for (querypos = querystart; querypos <= queryend; querypos++) {
@@ -3045,6 +3029,7 @@ Linkmatrix_get_cells_fwd (int *nunique, struct Link_T **links, int querystart, i
#endif
+#if 0
static Cell_T *
Linkmatrix_get_cells_both (int *nunique, struct Link_T **links, int querystart, int queryend, int *npositions,
int indexsize, int bestscore, bool favor_right_p, Cellpool_T cellpool) {
@@ -3154,6 +3139,7 @@ Linkmatrix_get_cells_both (int *nunique, struct Link_T **links, int querystart,
return sorted;
}
}
+#endif
@@ -3319,7 +3305,7 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
}
#endif
}
- revise_active_lookback(active,firstactive,nactive,0,npositions[querypos],links,querypos,mappings);
+ revise_active_lookback(active,firstactive,nactive,0,npositions[querypos],links,querypos);
}
grand_fwd_score = 0;
@@ -3409,7 +3395,7 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
currlink,querypos,querystart,queryend,position,
links,mappings,active,firstactive,chroffset,chrhigh,plusp,
indexsize,processed,
- anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ anchoredp,localp,splicingp,use_canonical_p,
non_canonical_penalty);
if (currlink->fwd_score > 0) {
@@ -3432,7 +3418,7 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
/*positions*/&(mappings[querypos][low_hit]),
links,mappings,active,firstactive,chroffset,chrhigh,plusp,
indexsize,processed,
- anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ anchoredp,localp,splicingp,use_canonical_p,
non_canonical_penalty);
debug9(printf("Checking hits from low_hit %d to high_hit %d\n",low_hit,high_hit));
@@ -3550,11 +3536,14 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
#endif
}
- revise_active_lookback(active,firstactive,nactive,low_hit,high_hit,links,querypos,mappings);
+ revise_active_lookback(active,firstactive,nactive,low_hit,high_hit,links,querypos);
/* Need to push querypos, even if firstactive[querypos] == -1 */
- debug6(printf("Pushing querypos %d onto processed\n",querypos));
- processed = Intlist_push(processed,querypos);
+ /* Want to skip npositions[querypos] == 0, so we can find adjacent despite mismatch or overabundance */
+ if (npositions[querypos] > 0) {
+ debug6(printf("Pushing querypos %d onto processed\n",querypos));
+ processed = Intlist_push(processed,querypos);
+ }
querypos = next_querypos;
}
}
@@ -3584,14 +3573,14 @@ align_compute_scores_lookback (int *ncells, struct Link_T **links, Chrpos_T **ma
#ifdef SEPARATE_FWD_REV
if (splicingp == false || use_canonical_p == false) {
cells = Linkmatrix_get_cells_fwd(&(*ncells),links,querystart,queryend,npositions,
- indexsize,best_overall_score,favor_right_p,cellpool);
+ favor_right_p,cellpool);
} else {
cells = Linkmatrix_get_cells_both(&(*ncells),links,querystart,queryend,npositions,
indexsize,best_overall_score,favor_right_p,cellpool);
}
#else
cells = Linkmatrix_get_cells_fwd(&(*ncells),links,querystart,queryend,npositions,
- indexsize,best_overall_score,favor_right_p,cellpool);
+ favor_right_p,cellpool);
#endif
debug9(FREE(oligo));
@@ -3727,7 +3716,7 @@ traceback_one (int querypos, int hit, struct Link_T **links, Chrpos_T **mappings
static List_T
traceback_one_snps (int querypos, int hit, struct Link_T **links, Chrpos_T **mappings,
- char *queryseq_ptr, char *queryuc_ptr,
+ char *queryseq_ptr,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
#ifdef DEBUG0
@@ -3759,7 +3748,7 @@ traceback_one_snps (int querypos, int hit, struct Link_T **links, Chrpos_T **map
path = Pairpool_push(path,pairpool,querypos*3,position,/*cdna*/c2,MATCH_COMP,c2,c2_alt,
/*dynprogindex*/0);
#else
- /* genomic nucleotide same as queryseq */
+ /* genomic nucleotide or SNP same as queryseq */
c2 = get_genomic_nt(&c2_alt,position,chroffset,chrhigh,watsonp);
path = Pairpool_push(path,pairpool,querypos,position,queryseq_ptr[querypos],MATCH_COMP,c2,c2_alt,
/*dynprogindex*/0);
@@ -3884,7 +3873,7 @@ align_compute_lookback (Chrpos_T **mappings, int *npositions, int totalpositions
debug11(printf("Starting subpath %d for rootposition %d with score %d, querypos %d, hit %d, position %u\n",
i,cell->rootposition,cell->score,querypos,hit,mappings[querypos][hit]));
- all_paths = List_push(all_paths,(void *) traceback_one_snps(querypos,hit,links,mappings,queryseq_ptr,queryuc_ptr,
+ all_paths = List_push(all_paths,(void *) traceback_one_snps(querypos,hit,links,mappings,queryseq_ptr,
chroffset,chrhigh,/*watsonp*/plusp,
#ifdef DEBUG0
indexsize,
@@ -4087,7 +4076,7 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
}
#endif
}
- revise_active_lookforward(active,firstactive,nactive,0,npositions[querypos],links,querypos,mappings);
+ revise_active_lookforward(active,firstactive,nactive,0,npositions[querypos],links,querypos);
}
@@ -4178,7 +4167,7 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
links,mappings,active,firstactive,
chroffset,chrhigh,plusp,
indexsize,processed,
- anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ anchoredp,localp,splicingp,use_canonical_p,
non_canonical_penalty);
if (currlink->fwd_score > 0) {
@@ -4201,7 +4190,7 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
/*positions*/&(mappings[querypos][low_hit]),
links,mappings,active,firstactive,chroffset,chrhigh,plusp,
indexsize,processed,
- anchoredp,localp,splicingp,skip_repetitive_p,use_canonical_p,
+ anchoredp,localp,splicingp,use_canonical_p,
non_canonical_penalty);
debug9(printf("Checking hits from high_hit %d to low_hit %d\n",high_hit,low_hit));
@@ -4319,11 +4308,14 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
#endif
}
- revise_active_lookforward(active,firstactive,nactive,low_hit,high_hit,links,querypos,mappings);
+ revise_active_lookforward(active,firstactive,nactive,low_hit,high_hit,links,querypos);
/* Need to push querypos, even if firstactive[querypos] == -1 */
- debug6(printf("Pushing querypos %d onto processed\n",querypos));
- processed = Intlist_push(processed,querypos);
+ /* Want to skip npositions[querypos] == 0, so we can find adjacent despite mismatch or overabundance */
+ if (npositions[querypos] > 0) {
+ debug6(printf("Pushing querypos %d onto processed\n",querypos));
+ processed = Intlist_push(processed,querypos);
+ }
querypos = next_querypos;
}
}
@@ -4354,14 +4346,14 @@ align_compute_scores_lookforward (int *ncells, struct Link_T **links, Chrpos_T *
#ifdef SEPARATE_FWD_REV
if (splicingp == false || use_canonical_p == false) {
cells = Linkmatrix_get_cells_fwd(&(*ncells),links,querystart,queryend,npositions,
- indexsize,best_overall_score,favor_right_p,cellpool);
+ favor_right_p,cellpool);
} else {
cells = Linkmatrix_get_cells_both(&(*ncells),links,querystart,queryend,npositions,
indexsize,best_overall_score,favor_right_p,cellpool);
}
#else
cells = Linkmatrix_get_cells_fwd(&(*ncells),links,querystart,queryend,npositions,
- indexsize,best_overall_score,favor_right_p,cellpool);
+ favor_right_p,cellpool);
#endif
debug9(FREE(oligo));
@@ -4452,7 +4444,7 @@ align_compute_lookforward (Chrpos_T **mappings, int *npositions, int totalpositi
}
if (snps_p == true) {
- all_paths = List_push(all_paths,(void *) traceback_one_snps(querypos,hit,links,mappings,queryseq_ptr,queryuc_ptr,
+ all_paths = List_push(all_paths,(void *) traceback_one_snps(querypos,hit,links,mappings,queryseq_ptr,
chroffset,chrhigh,/*watsonp*/plusp,
#ifdef DEBUG0
indexsize,
@@ -4500,7 +4492,7 @@ align_compute_lookforward (Chrpos_T **mappings, int *npositions, int totalpositi
}
-
+#if 0
/* Modified from stage3.c */
static void
get_splicesite_probs (double *left_prob, double *right_prob,
@@ -4561,7 +4553,7 @@ get_splicesite_probs (double *left_prob, double *right_prob,
return;
}
-
+#endif
/* queryseq_ptr is NULL for PMAP. querypos here is in nt. */
@@ -4573,12 +4565,11 @@ convert_to_nucleotides (List_T path,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
int query_offset, Pairpool_T pairpool, int indexsize_nt,
bool include_gapholders_p) {
- List_T pairs = NULL, pairptr;
+ List_T pairs = NULL;
Pair_T pair;
int querypos, lastquerypos, queryjump, genomejump, fill, default_fill;
int genomepos, lastgenomepos;
char c, c_alt;
- double left_prob, right_prob;
debug5(printf("Beginning convert_to_nucleotides with %d pairs. query_offset = %d, indexsize_nt = %d\n",
List_length(path),query_offset,indexsize_nt));
@@ -4845,7 +4836,7 @@ convert_to_nucleotides_snps (List_T path,
Univcoord_T chroffset, Univcoord_T chrhigh, bool watsonp,
int query_offset, Pairpool_T pairpool, int indexsize_nt,
bool include_gapholders_p) {
- List_T pairs = NULL, pairptr;
+ List_T pairs = NULL;
Pair_T pair;
int querypos, genomepos, lastquerypos, lastgenomepos, queryjump, genomejump, fill, default_fill;
char c, c_alt;
@@ -5109,7 +5100,7 @@ Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
Diagpool_T diagpool, bool debug_graphic_p) {
int ncovered;
int source;
- int indexsize;
+ /* int indexsize; */
Oligoindex_T oligoindex;
Chrpos_T **mappings;
bool *coveredp, oned_matrix_p;
@@ -5154,17 +5145,19 @@ Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
diagonals = (List_T) NULL;
while (source < Oligoindex_array_length(oligoindices) && pct_coverage < SUFF_PCTCOVERAGE_OLIGOINDEX) {
oligoindex = Oligoindex_array_elt(oligoindices,source);
- indexsize = Oligoindex_indexsize(oligoindex); /* Different sources can have different indexsizes */
+ /* indexsize = Oligoindex_indexsize(oligoindex); */ /* Different sources can have different indexsizes */
#ifdef PMAP
if (plusp == true) {
Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
/*mappingend*/chroffset+chrend,/*plusp*/true,
- queryuc_ptr,querylength,/*chrpos*/chrstart);
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart);
} else {
/* Need to add 1 to mappingend to cover same range as plusp */
Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
/*mappingend*/chroffset+chrend+1,/*plusp*/false,
- queryuc_ptr,querylength,/*chrpos*/(chrhigh-chroffset)-chrend);
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend);
}
#else
@@ -5235,14 +5228,13 @@ Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
List_T
-Stage2_compute (int *stage2_source, int *stage2_indexsize,
- char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+Stage2_compute (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
#ifndef GSNAP
- Stage2_alloc_T stage2_alloc,
+ Stage2_alloc_T stage2_alloc, double proceed_pctcoverage,
#endif
- Oligoindex_array_T oligoindices, double proceed_pctcoverage,
+ Oligoindex_array_T oligoindices,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
bool localp, bool skip_repetitive_p,
bool favor_right_p, int max_nalignments, bool debug_graphic_p,
@@ -5259,14 +5251,19 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
int *npositions, totalpositions;
Chrpos_T *minactive, *maxactive;
int *firstactive, *nactive;
- int ncovered;
- double pct_coverage;
int maxnconsecutive;
/* double diag_runtime; */
List_T diagonals;
int anchor_querypos, querystart, queryend;
+ Chrpos_T anchor_position;
+#ifdef GSNAP
Univcoord_T mappingstart, mappingend;
- Chrpos_T anchor_position, chrpos, mappinglength;
+ Chrpos_T chrpos, mappinglength;
+#else
+ double pct_coverage;
+ int ncovered;
+#endif
+
#ifndef USE_DIAGPOOL
List_T p;
@@ -5328,7 +5325,6 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
maxnconsecutive = 0;
source = 0;
- pct_coverage = 0.0;
#ifdef USE_DIAGPOOL
Diagpool_reset(diagpool);
#endif
@@ -5363,21 +5359,17 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
/* printf("indexsize = %d\n",indexsize); */
-#ifdef PMAP
- Oligoindex_pmap_tally(oligoindex,mappingstart,mappingend,plusp,
- queryuc_ptr,querylength,chrpos);
-#else
Oligoindex_hr_tally(oligoindex,mappingstart,mappingend,plusp,
queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
chrpos,genestrand);
-#endif
diagonals = Oligoindex_get_mappings(diagonals,coveredp,mappings,npositions,&totalpositions,
&oned_matrix_p,&maxnconsecutive,oligoindices,oligoindex,queryuc_ptr,
/*querystart*/0,/*queryend*/querylength,querylength,
chrstart,chrend,chroffset,chrhigh,plusp,diagpool);
#else
-
+ /* GMAP */
+ pct_coverage = 0.0;
while (source < Oligoindex_array_length(oligoindices) && pct_coverage < SUFF_PCTCOVERAGE_OLIGOINDEX) {
oligoindex = Oligoindex_array_elt(oligoindices,source);
indexsize = Oligoindex_indexsize(oligoindex); /* Different sources can have different indexsizes */
@@ -5386,11 +5378,13 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
if (plusp == true) {
Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
/*mappingend*/chroffset+chrend,/*plusp*/true,
- queryuc_ptr,querylength,/*chrpos*/chrstart);
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart);
} else {
Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
/*mappingend*/chroffset+chrend+1,/*plusp*/false,
- queryuc_ptr,querylength,/*chrpos*/(chrhigh-chroffset)-chrend);
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend);
}
#else
@@ -5447,8 +5441,8 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
#endif
- *stage2_source = source;
- *stage2_indexsize = indexsize;
+ /* *stage2_source = source; */
+ /* *stage2_indexsize = indexsize; */
#ifdef PMAP
indexsize_nt = 3*indexsize;
#else
@@ -5737,6 +5731,7 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
#endif
}
+ debug0(printf("Done with stage2. Returning %d results\n",List_length(all_stage2results)));
return all_stage2results;
}
@@ -5745,14 +5740,12 @@ Stage2_compute (int *stage2_source, int *stage2_indexsize,
/* Since this stage2 is called from stage3 with a small segment of the
query, we can use alloca instead of stage2_alloc */
List_T
-Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
- char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+Stage2_compute_one (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
- Oligoindex_array_T oligoindices, double proceed_pctcoverage,
+ Oligoindex_array_T oligoindices,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
- bool localp,
- bool skip_repetitive_p, bool use_shifted_canonical_p,
+ bool localp, bool skip_repetitive_p,
bool favor_right_p, bool debug_graphic_p) {
List_T pairs, all_paths;
List_T middle, path;
@@ -5799,11 +5792,13 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
if (plusp == true) {
Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
/*mappingend*/chroffset+chrend,/*plusp*/true,
- queryuc_ptr,querylength,/*chrpos*/chrstart);
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart);
} else {
Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
/*mappingend*/chroffset+chrend+1,/*plusp*/false,
- queryuc_ptr,querylength,/*chrpos*/(chrhigh-chroffset)-chrend);
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend);
}
#else
@@ -5824,15 +5819,15 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
diagonals = Oligoindex_get_mappings(diagonals,coveredp,mappings,npositions,&totalpositions,
&oned_matrix_p,&maxnconsecutive,oligoindices,oligoindex,queryuc_ptr,
- /*querstart*/0,/*queryend*/querylength,querylength,
+ /*querystart*/0,/*queryend*/querylength,querylength,
chrstart,chrend,chroffset,chrhigh,plusp,diagpool);
pct_coverage = Diag_update_coverage(coveredp,&ncovered,diagonals,querylength);
debug(printf("Stage2_compute: source = %d, ncovered = %d, pct_coverage = %f\n",source,ncovered,pct_coverage));
source++;
}
- *stage2_source = source;
- *stage2_indexsize = indexsize;
+ /* *stage2_source = source; */
+ /* *stage2_indexsize = indexsize; */
#ifdef PMAP
indexsize_nt = 3*indexsize;
#else
@@ -5845,8 +5840,8 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
middle = (List_T) NULL;
} else {
- debug(printf("Proceeding because maxnconsecutive is %d and pct_coverage is %f > %f or ncovered = %d > %d\n",
- maxnconsecutive,pct_coverage,proceed_pctcoverage,ncovered,SUFF_NCOVERED));
+ debug(printf("Proceeding because pct_coverage is %f > %f or ncovered = %d > %d\n",
+ maxnconsecutive,pct_coverage,ncovered,SUFF_NCOVERED));
debug(printf("Performing diag on genomiclength %u\n",chrend-chrstart));
Diag_max_bounds(minactive,maxactive,querylength,chrstart,chrend,chroffset,chrhigh,plusp);
@@ -5914,3 +5909,380 @@ Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
return List_reverse(middle);
}
+
+
+/* Called by GSNAP for ends of substring alignments */
+List_T
+Stage2_compute_starts (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+ Chrpos_T chrstart, Chrpos_T chrend,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
+ Oligoindex_array_T oligoindices,
+ Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool localp,
+ bool skip_repetitive_p,
+ bool favor_right_p, int max_nalignments, bool debug_graphic_p) {
+ List_T all_results;
+ List_T pairs, all_paths, p;
+ List_T path;
+ int indexsize, indexsize_nt;
+ Oligoindex_T oligoindex;
+ Chrpos_T **mappings;
+ bool *coveredp, oned_matrix_p;
+ int source;
+ int *npositions, totalpositions;
+ Chrpos_T *minactive, *maxactive;
+ int *firstactive, *nactive;
+ int ncovered;
+ double pct_coverage;
+ int maxnconsecutive;
+ /* double diag_runtime; */
+ List_T diagonals;
+
+
+ debug(printf("Entered Stage2_compute_starts with chrstart %u and chrend %u\n",chrstart,chrend));
+
+ coveredp = (bool *) CALLOCA(querylength,sizeof(bool));
+ mappings = (Chrpos_T **) MALLOCA(querylength * sizeof(Chrpos_T *));
+ npositions = (int *) CALLOCA(querylength,sizeof(int));
+ minactive = (unsigned int *) MALLOCA(querylength * sizeof(unsigned int));
+ maxactive = (unsigned int *) MALLOCA(querylength * sizeof(unsigned int));
+ firstactive = (int *) MALLOCA(querylength * sizeof(int));
+ nactive = (int *) MALLOCA(querylength * sizeof(int));
+
+ totalpositions = 0;
+ maxnconsecutive = 0;
+
+ source = 0;
+ pct_coverage = 0.0;
+#ifdef USE_DIAGPOOL
+ Diagpool_reset(diagpool);
+#endif
+ Cellpool_reset(cellpool);
+ diagonals = (List_T) NULL;
+ while (source < Oligoindex_array_length(oligoindices) && pct_coverage < SUFF_PCTCOVERAGE_OLIGOINDEX) {
+ oligoindex = Oligoindex_array_elt(oligoindices,source);
+ indexsize = Oligoindex_indexsize(oligoindex); /* Different sources can have different indexsizes */
+
+#ifdef PMAP
+ if (plusp == true) {
+ Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend,/*plusp*/true,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart);
+ } else {
+ Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend+1,/*plusp*/false,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend);
+ }
+
+#else
+
+ if (plusp == true) {
+ Oligoindex_hr_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend,/*plusp*/true,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart,genestrand);
+ } else {
+ Oligoindex_hr_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend+1,/*plusp*/false,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend,genestrand);
+ }
+
+#endif
+
+ diagonals = Oligoindex_get_mappings(diagonals,coveredp,mappings,npositions,&totalpositions,
+ &oned_matrix_p,&maxnconsecutive,oligoindices,oligoindex,queryuc_ptr,
+ /*querystart*/0,/*queryend*/querylength,querylength,
+ chrstart,chrend,chroffset,chrhigh,plusp,diagpool);
+ pct_coverage = Diag_update_coverage(coveredp,&ncovered,diagonals,querylength);
+ debug(printf("Stage2_compute: source = %d, ncovered = %d, pct_coverage = %f\n",source,ncovered,pct_coverage));
+
+ source++;
+ }
+ /* *stage2_source = source; */
+ /* *stage2_indexsize = indexsize; */
+#ifdef PMAP
+ indexsize_nt = 3*indexsize;
+#else
+ indexsize_nt = indexsize;
+#endif
+
+
+ if (totalpositions == 0) {
+ debug(printf("Quitting because totalpositions is zero\n"));
+ all_results = (List_T) NULL;
+
+ } else {
+ debug(printf("Proceeding because maxnconsecutive is %d and pct_coverage is %f or ncovered = %d > %d\n",
+ maxnconsecutive,pct_coverage,ncovered,SUFF_NCOVERED));
+
+ debug(printf("Performing diag on genomiclength %u\n",chrend-chrstart));
+ Diag_max_bounds(minactive,maxactive,querylength,chrstart,chrend,chroffset,chrhigh,plusp);
+
+ if ((all_paths = align_compute_lookforward(mappings,npositions,totalpositions,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
+ queryseq_ptr,queryuc_ptr,querylength,
+ /*querystart*/0,/*queryend*/querylength-1,
+ chroffset,chrhigh,plusp,
+ indexsize,pairpool,
+ /*anchoredp*/false,/*anchor_querypos*/0,/*anchor_position*/0,
+ localp,skip_repetitive_p,use_canonical_middle_p,NON_CANONICAL_PENALTY_MIDDLE,
+ favor_right_p,max_nalignments,debug_graphic_p)) == NULL) {
+ all_results = (List_T) NULL;
+
+ } else if (snps_p == true) {
+ all_results = (List_T) NULL;
+ for (p = all_paths; p != NULL; p = List_next(p)) {
+ path = List_head(p);
+ pairs = convert_to_nucleotides_snps(path,
+#ifndef PMAP
+ queryseq_ptr,queryuc_ptr,
+#endif
+ chroffset,chrhigh,/*watsonp*/plusp,
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
+ path = List_reverse(pairs);
+ debug0(printf("START\n"));
+ debug0(Pair_dump_list(path,true));
+ all_results = List_push(all_results,(void *) path);
+ }
+
+ } else {
+ all_results = (List_T) NULL;
+ for (p = all_paths; p != NULL; p = List_next(p)) {
+ path = List_head(p);
+ pairs = convert_to_nucleotides(path,
+#ifndef PMAP
+ queryseq_ptr,queryuc_ptr,
+#endif
+ chroffset,chrhigh,/*watsonp*/plusp,
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
+ path = List_reverse(pairs);
+ debug0(printf("START\n"));
+ debug0(Pair_dump_list(path,true));
+ all_results = List_push(all_results,(void *) path);
+ }
+ }
+
+ List_free(&all_paths);
+ }
+
+ FREEA(nactive);
+ FREEA(firstactive);
+ FREEA(maxactive);
+ FREEA(minactive);
+ FREEA(npositions);
+ FREEA(coveredp);
+ FREEA(mappings); /* Don't need to free contents of mappings */
+
+#if 1
+ for (source = 0; source < Oligoindex_array_length(oligoindices); source++) {
+ oligoindex = Oligoindex_array_elt(oligoindices,source);
+ Oligoindex_untally(oligoindex,queryuc_ptr,querylength);
+ }
+#endif
+
+#ifdef USE_DIAGPOOL
+ /* No need to free diagonals */
+#else
+ for (p = diagonals; p != NULL; p = List_next(p)) {
+ diag = (Diag_T) List_head(p);
+ Diag_free(&diag);
+ }
+ List_free(&diagonals);
+#endif
+
+ return all_results;
+}
+
+
+/* Called by GSNAP for ends of substring alignments */
+List_T
+Stage2_compute_ends (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+ Chrpos_T chrstart, Chrpos_T chrend,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
+ Oligoindex_array_T oligoindices,
+ Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool localp,
+ bool skip_repetitive_p,
+ bool favor_right_p, int max_nalignments, bool debug_graphic_p) {
+ List_T all_results;
+ List_T pairs, all_paths, p;
+ List_T path;
+ int indexsize, indexsize_nt;
+ Oligoindex_T oligoindex;
+ Chrpos_T **mappings;
+ bool *coveredp, oned_matrix_p;
+ int source;
+ int *npositions, totalpositions;
+ Chrpos_T *minactive, *maxactive;
+ int *firstactive, *nactive;
+ int ncovered;
+ double pct_coverage;
+ int maxnconsecutive;
+ /* double diag_runtime; */
+ List_T diagonals;
+
+
+ debug(printf("Entered Stage2_compute_ends with chrstart %u and chrend %u\n",chrstart,chrend));
+
+ coveredp = (bool *) CALLOCA(querylength,sizeof(bool));
+ mappings = (Chrpos_T **) MALLOCA(querylength * sizeof(Chrpos_T *));
+ npositions = (int *) CALLOCA(querylength,sizeof(int));
+ minactive = (unsigned int *) MALLOCA(querylength * sizeof(unsigned int));
+ maxactive = (unsigned int *) MALLOCA(querylength * sizeof(unsigned int));
+ firstactive = (int *) MALLOCA(querylength * sizeof(int));
+ nactive = (int *) MALLOCA(querylength * sizeof(int));
+
+ totalpositions = 0;
+ maxnconsecutive = 0;
+
+ source = 0;
+ pct_coverage = 0.0;
+#ifdef USE_DIAGPOOL
+ Diagpool_reset(diagpool);
+#endif
+ Cellpool_reset(cellpool);
+ diagonals = (List_T) NULL;
+ while (source < Oligoindex_array_length(oligoindices) && pct_coverage < SUFF_PCTCOVERAGE_OLIGOINDEX) {
+ oligoindex = Oligoindex_array_elt(oligoindices,source);
+ indexsize = Oligoindex_indexsize(oligoindex); /* Different sources can have different indexsizes */
+
+#ifdef PMAP
+ if (plusp == true) {
+ Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend,/*plusp*/true,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart);
+ } else {
+ Oligoindex_pmap_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend+1,/*plusp*/false,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend);
+ }
+
+#else
+
+ if (plusp == true) {
+ Oligoindex_hr_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend,/*plusp*/true,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/chrstart,genestrand);
+ } else {
+ Oligoindex_hr_tally(oligoindex,/*mappingstart*/chroffset+chrstart,
+ /*mappingend*/chroffset+chrend+1,/*plusp*/false,
+ queryuc_ptr,/*querystart*/0,/*queryend*/querylength,
+ /*chrpos*/(chrhigh-chroffset)-chrend,genestrand);
+ }
+
+#endif
+
+ diagonals = Oligoindex_get_mappings(diagonals,coveredp,mappings,npositions,&totalpositions,
+ &oned_matrix_p,&maxnconsecutive,oligoindices,oligoindex,queryuc_ptr,
+ /*querystart*/0,/*queryend*/querylength,querylength,
+ chrstart,chrend,chroffset,chrhigh,plusp,diagpool);
+ pct_coverage = Diag_update_coverage(coveredp,&ncovered,diagonals,querylength);
+ debug(printf("Stage2_compute: source = %d, ncovered = %d, pct_coverage = %f\n",source,ncovered,pct_coverage));
+
+ source++;
+ }
+ /* *stage2_source = source; */
+ /* *stage2_indexsize = indexsize; */
+#ifdef PMAP
+ indexsize_nt = 3*indexsize;
+#else
+ indexsize_nt = indexsize;
+#endif
+
+
+ if (totalpositions == 0) {
+ debug(printf("Quitting because totalpositions is zero\n"));
+ all_results = (List_T) NULL;
+
+ } else {
+ debug(printf("Proceeding because maxnconsecutive is %d and pct_coverage is %f or ncovered = %d > %d\n",
+ maxnconsecutive,pct_coverage,ncovered,SUFF_NCOVERED));
+
+ debug(printf("Performing diag on genomiclength %u\n",chrend-chrstart));
+ Diag_max_bounds(minactive,maxactive,querylength,chrstart,chrend,chroffset,chrhigh,plusp);
+
+ if ((all_paths = align_compute_lookback(mappings,npositions,totalpositions,
+ oned_matrix_p,minactive,maxactive,firstactive,nactive,cellpool,
+ queryseq_ptr,queryuc_ptr,querylength,
+ /*querystart*/0,/*queryend*/querylength-1,
+ chroffset,chrhigh,plusp,
+ indexsize,pairpool,
+ /*anchoredp*/false,/*anchor_querypos*/0,/*anchor_position*/0,
+ localp,skip_repetitive_p,use_canonical_middle_p,NON_CANONICAL_PENALTY_MIDDLE,
+ favor_right_p,max_nalignments,debug_graphic_p)) == NULL) {
+ all_results = (List_T) NULL;
+
+ } else if (snps_p == true) {
+ all_results = (List_T) NULL;
+ for (p = all_paths; p != NULL; p = List_next(p)) {
+ pairs = List_head(p);
+ path = List_reverse(pairs);
+ pairs = convert_to_nucleotides_snps(path,
+#ifndef PMAP
+ queryseq_ptr,queryuc_ptr,
+#endif
+ chroffset,chrhigh,/*watsonp*/plusp,
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
+ debug0(printf("END\n"));
+ debug0(Pair_dump_list(pairs,true));
+ all_results = List_push(all_results,(void *) pairs);
+ }
+
+ } else {
+ all_results = (List_T) NULL;
+ for (p = all_paths; p != NULL; p = List_next(p)) {
+ pairs = List_head(p);
+ path = List_reverse(pairs);
+ pairs = convert_to_nucleotides(path,
+#ifndef PMAP
+ queryseq_ptr,queryuc_ptr,
+#endif
+ chroffset,chrhigh,/*watsonp*/plusp,
+ query_offset,pairpool,indexsize_nt,
+ /*include_gapholders_p*/false);
+ debug0(printf("END\n"));
+ debug0(Pair_dump_list(pairs,true));
+ all_results = List_push(all_results,(void *) pairs);
+ }
+ }
+
+ List_free(&all_paths);
+ }
+
+ FREEA(nactive);
+ FREEA(firstactive);
+ FREEA(maxactive);
+ FREEA(minactive);
+ FREEA(npositions);
+ FREEA(coveredp);
+ FREEA(mappings); /* Don't need to free contents of mappings */
+
+#if 1
+ for (source = 0; source < Oligoindex_array_length(oligoindices); source++) {
+ oligoindex = Oligoindex_array_elt(oligoindices,source);
+ Oligoindex_untally(oligoindex,queryuc_ptr,querylength);
+ }
+#endif
+
+#ifdef USE_DIAGPOOL
+ /* No need to free diagonals */
+#else
+ for (p = diagonals; p != NULL; p = List_next(p)) {
+ diag = (Diag_T) List_head(p);
+ Diag_free(&diag);
+ }
+ List_free(&diagonals);
+#endif
+
+ return all_results;
+}
+
diff --git a/src/stage2.h b/src/stage2.h
index c11d1c5..f0b4ff5 100644
--- a/src/stage2.h
+++ b/src/stage2.h
@@ -1,4 +1,4 @@
-/* $Id: stage2.h 166641 2015-05-29 21:13:04Z twu $ */
+/* $Id: stage2.h 184442 2016-02-17 21:04:54Z twu $ */
#ifndef STAGE2_INCLUDED
#define STAGE2_INCLUDED
@@ -18,7 +18,6 @@ typedef struct Stage2_T *Stage2_T;
#include "oligoindex_hr.h"
#endif
-
extern void
Stage2_alloc_free (Stage2_alloc_T *old);
extern Stage2_alloc_T
@@ -54,28 +53,45 @@ Stage2_scan (int *stage2_source, char *queryuc_ptr, int querylength,
Diagpool_T diagpool, bool debug_graphic_p);
extern List_T
-Stage2_compute (int *stage2_source, int *stage2_indexsize,
- char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+Stage2_compute (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
#ifndef GSNAP
- Stage2_alloc_T stage2_alloc,
+ Stage2_alloc_T stage2_alloc, double proceed_pctcoverage,
#endif
- Oligoindex_array_T oligoindices, double proceed_pctcoverage,
+ Oligoindex_array_T oligoindices,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
bool localp, bool skip_repetitive_p,
bool favor_right_p, int max_nalignments, bool debug_graphic_p,
Stopwatch_T stopwatch, bool diag_debug);
extern List_T
-Stage2_compute_one (int *stage2_source, int *stage2_indexsize,
- char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+Stage2_compute_one (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
Chrpos_T chrstart, Chrpos_T chrend,
Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
- Oligoindex_array_T oligoindices, double proceed_pctcoverage,
+ Oligoindex_array_T oligoindices,
Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
bool localp, bool skip_repetitive_p,
- bool use_shifted_canonical_p, bool favor_right_p, bool debug_graphic_p);
+ bool favor_right_p, bool debug_graphic_p);
+
+extern List_T
+Stage2_compute_starts (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+ Chrpos_T chrstart, Chrpos_T chrend,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
+ Oligoindex_array_T oligoindices,
+ Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool localp, bool skip_repetitive_p,
+ bool favor_right_p, int max_nalignments, bool debug_graphic_p);
+
+extern List_T
+Stage2_compute_ends (char *queryseq_ptr, char *queryuc_ptr, int querylength, int query_offset,
+ Chrpos_T chrstart, Chrpos_T chrend,
+ Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
+ Oligoindex_array_T oligoindices,
+ Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool localp, bool skip_repetitive_p,
+ bool favor_right_p, int max_nalignments, bool debug_graphic_p);
+
#undef T
#endif
diff --git a/src/stage3.c b/src/stage3.c
index ed3b9ac..a6501e6 100644
--- a/src/stage3.c
+++ b/src/stage3.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3.c 174482 2015-09-22 00:58:39Z twu $";
+static char rcsid[] = "$Id: stage3.c 184517 2016-02-18 17:44:24Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -90,8 +90,13 @@ static char rcsid[] = "$Id: stage3.c 174482 2015-09-22 00:58:39Z twu $";
#define PROB_SIGDIFF 0.5
#define END_SPLICESITE_SEARCH 10
-#define END_SPLICESITE_PROB 0.95
+#define END_SPLICESITE_PROB_MATCH 0.90
+#define END_SPLICESITE_PROB_MISMATCH 0.95
+
+#if 0
+/* No longer used. Not sure why it was used before */
#define END_SPLICESITE_EXON_LENGTH 100 /* If shorter than this, then don't look for end splice site */
+#endif
/* For Stage3_bad_stretch_p */
@@ -291,6 +296,10 @@ static int acceptor_typeint;
static Univcoord_T *splicesites;
+static bool *altlocp;
+static Univcoord_T *alias_starts;
+static Univcoord_T *alias_ends;
+
static int min_intronlength;
static int max_deletionlength;
static int min_indel_end_matches;
@@ -315,7 +324,7 @@ void
Stage3_setup (bool splicingp_in, bool novelsplicingp_in, bool require_splicedir_p_in,
IIT_T splicesites_iit_in, int *splicesites_divint_crosstable_in,
int donor_typeint_in, int acceptor_typeint_in,
- Univcoord_T *splicesites_in,
+ Univcoord_T *splicesites_in, bool *altlocp_in, Univcoord_T *alias_starts_in, Univcoord_T *alias_ends_in,
int min_intronlength_in, int max_deletionlength_in, int min_indel_end_matches_in,
int maxpeelback_distalmedial_in, int nullgap_in,
int extramaterial_end_in, int extramaterial_paired_in,
@@ -333,6 +342,10 @@ Stage3_setup (bool splicingp_in, bool novelsplicingp_in, bool require_splicedir_
splicesites = splicesites_in;
+ altlocp = altlocp_in;
+ alias_starts = alias_starts_in;
+ alias_ends = alias_ends_in;
+
min_intronlength = min_intronlength_in;
max_deletionlength = max_deletionlength_in;
min_indel_end_matches = min_indel_end_matches_in;
@@ -430,16 +443,15 @@ struct T {
int relaastart;
int relaaend;
+#if 0
int stage2_source;
int stage2_indexsize;
-#if 0
double stage2_diag_runtime;
double stage2_align_runtime;
double stage2_mapfraction;
int stage2_maxconsecutive;
-#endif
-
double stage3_runtime;
+#endif
bool joinable_left_p;
bool joinable_right_p;
@@ -583,6 +595,18 @@ Stage3_chrnum (T this) {
return this->chrnum;
}
+bool
+Stage3_altloc_chr (Univcoord_T *alias_start, Univcoord_T *alias_end, T this) {
+#if 0
+ *alias_start = alias_starts[this->chrnum];
+ *alias_end = alias_ends[this->chrnum];
+ return altlocp[this->chrnum];
+#else
+ return false;
+#endif
+}
+
+
Chrpos_T
Stage3_chrstart (T this) {
return Pair_genomepos(&(this->pairarray[0]));
@@ -1649,9 +1673,11 @@ assign_gap_types (List_T path, int cdna_direction, bool watsonp, char *queryseq_
case GTAG_FWD: pair->comp = FWD_CANONICAL_INTRON_COMP; break;
case GCAG_FWD: pair->comp = FWD_GCAG_INTRON_COMP; break;
case ATAC_FWD: pair->comp = FWD_ATAC_INTRON_COMP; break;
+#ifndef PMAP
case ATAC_REV: pair->comp = REV_ATAC_INTRON_COMP; break;
case GCAG_REV: pair->comp = REV_GCAG_INTRON_COMP; break;
case GTAG_REV: pair->comp = REV_CANONICAL_INTRON_COMP; break;
+#endif
case NONINTRON: pair->comp = NONINTRON_COMP; break;
default:
printf("Unexpected intron type %d\n",introntype);
@@ -1913,9 +1939,11 @@ assign_intron_probs (List_T path, int cdna_direction, bool watsonp,
case GTAG_FWD: pair->comp = FWD_CANONICAL_INTRON_COMP; break;
case GCAG_FWD: pair->comp = FWD_GCAG_INTRON_COMP; break;
case ATAC_FWD: pair->comp = FWD_ATAC_INTRON_COMP; break;
+#ifndef PMAP
case ATAC_REV: pair->comp = REV_ATAC_INTRON_COMP; break;
case GCAG_REV: pair->comp = REV_GCAG_INTRON_COMP; break;
case GTAG_REV: pair->comp = REV_CANONICAL_INTRON_COMP; break;
+#endif
case NONINTRON: pair->comp = NONINTRON_COMP; break;
default:
printf("Unexpected intron type %d\n",introntype);
@@ -2679,6 +2707,8 @@ clean_path_end3 (List_T path, int ambig_end_length_3) {
while (path != NULL) {
lastpair = path->first;
if (lastpair->querypos % 3 == 2) {
+ debug(printf("Ending clean_path_end3\n"));
+ debug(Pair_dump_list(path,true));
return path;
} else {
debug(printf("PMAP popping querypos %d to get to codon boundary\n",lastpair->querypos));
@@ -2689,6 +2719,7 @@ clean_path_end3 (List_T path, int ambig_end_length_3) {
}
debug(printf("Ending clean_path_end3\n"));
+ debug(Pair_dump_list(path,true));
return path;
}
@@ -2739,6 +2770,8 @@ clean_path_end3_gap_indels (List_T path) {
Pair_T lastpair;
debug(printf("Starting clean_path_end3_gap_indels\n"));
+ debug(Pair_dump_list(path,true));
+
/* Remove any remaining gap/indels at 3' end, which can happen rarely */
if (path != NULL) {
lastpair = path->first;
@@ -2759,6 +2792,8 @@ clean_path_end3_gap_indels (List_T path) {
while (path != NULL) {
lastpair = path->first;
if (lastpair->querypos % 3 == 2) {
+ debug(printf("Ending clean_path_end3_gap_indels\n"));
+ debug(Pair_dump_list(path,true));
return path;
} else {
debug(printf("PMAP popping querypos %d to get to codon boundary\n",lastpair->querypos));
@@ -2768,6 +2803,7 @@ clean_path_end3_gap_indels (List_T path) {
#endif
debug(printf("Ending clean_path_end3_gap_indels\n"));
+ debug(Pair_dump_list(path,true));
return path;
}
@@ -3482,7 +3518,7 @@ sufficient_splice_prob_local (int support, int nmatches, int nmismatches, double
-#ifdef GSNAP
+#if 0
static int
exon_length_5 (List_T pairs) {
int exon_length = 0;
@@ -3505,7 +3541,7 @@ exon_length_5 (List_T pairs) {
#endif
-#ifdef GSNAP
+#if 0
static int
exon_length_3 (List_T path) {
int exon_length = 0;
@@ -4548,7 +4584,26 @@ make_pairarrays_chimera (T this_left, T this_right,
}
-
+void
+Stage3_count_paths (int *npaths_primary, int *npaths_altloc, List_T stage3list) {
+ T this;
+
+ *npaths_primary = *npaths_altloc = 0;
+
+ while (stage3list != NULL) {
+ this = (T) List_head(stage3list);
+ if (altlocp[this->chrnum] == true) {
+ (*npaths_altloc) += 1;
+ } else {
+ (*npaths_primary) += 1;
+ }
+ stage3list = List_next(stage3list);
+ }
+
+ return;
+}
+
+
#define MAPQ_MAXIMUM_SCORE 40
void
@@ -4641,9 +4696,9 @@ Stage3_recompute_coverage (List_T stage3list, Sequence_T queryseq) {
static List_T
pick_cdna_direction (int *winning_cdna_direction, int *sensedir,
List_T pairs_fwd, List_T pairs_rev, double defect_rate_fwd, double defect_rate_rev,
- int ncanonical_fwd, int nsemicanonical_fwd,
+ int nknown_fwd, int ncanonical_fwd, int nsemicanonical_fwd,
int nnoncanonical_fwd, int nbadintrons_fwd,
- int ncanonical_rev, int nsemicanonical_rev,
+ int nknown_rev, int ncanonical_rev, int nsemicanonical_rev,
int nnoncanonical_rev, int nbadintrons_rev,
double max_intron_score_fwd, double avg_donor_score_fwd, double avg_acceptor_score_fwd,
double max_intron_score_rev, double avg_donor_score_rev, double avg_acceptor_score_rev,
@@ -4658,13 +4713,13 @@ pick_cdna_direction (int *winning_cdna_direction, int *sensedir,
if (pairs_fwd) {
/* canonical_score_fwd = ncanonical_fwd - nbadintrons_fwd + nsemicanonical_fwd - nnoncanonical_fwd; */
- debug11(printf("ncanonical_fwd %d, nbadintrons_fwd %d, nsemicanonical_fwd %d, nnoncanonical_fwd %d\n",
- ncanonical_fwd,nbadintrons_fwd,nsemicanonical_fwd,nnoncanonical_fwd));
+ debug11(printf("nknown_fwd %d, ncanonical_fwd %d, nbadintrons_fwd %d, nsemicanonical_fwd %d, nnoncanonical_fwd %d\n",
+ nknown_fwd,ncanonical_fwd,nbadintrons_fwd,nsemicanonical_fwd,nnoncanonical_fwd));
}
if (pairs_rev) {
/* canonical_score_rev = ncanonical_rev - nbadintrons_rev + nsemicanonical_rev - nnoncanonical_rev; */
- debug11(printf("ncanonical_rev %d, nbadintrons_rev %d, nsemicanonical_rev %d, nnoncanonical_rev %d\n",
- ncanonical_rev,nbadintrons_rev,nsemicanonical_rev,nnoncanonical_rev));
+ debug11(printf("nknown_rev %d, ncanonical_rev %d, nbadintrons_rev %d, nsemicanonical_rev %d, nnoncanonical_rev %d\n",
+ nknown_rev,ncanonical_rev,nbadintrons_rev,nsemicanonical_rev,nnoncanonical_rev));
}
if (pairs_fwd == NULL && pairs_rev == NULL) {
@@ -4728,6 +4783,16 @@ pick_cdna_direction (int *winning_cdna_direction, int *sensedir,
/* intronscores reveal a clear sensedir */
*winning_cdna_direction = -1;
+ } else if (nknown_fwd > 0 && nknown_rev == 0) {
+ debug11(printf("nknown_fwd %d && nknown_rev %d, so fwd wins\n",
+ nknown_fwd,nknown_rev));
+ *winning_cdna_direction = +1;
+
+ } else if (nknown_rev > 0 && nknown_fwd == 0) {
+ debug11(printf("nknown_fwd %d && nknown_rev %d, so rev wins\n",
+ nknown_fwd,nknown_rev));
+ *winning_cdna_direction = -1;
+
} else if (ncanonical_fwd > 0 && ncanonical_rev == 0) {
debug11(printf("ncanonical_fwd %d && ncanonical_rev %d, so fwd wins\n",
ncanonical_fwd,ncanonical_rev));
@@ -4947,11 +5012,10 @@ initial_cdna_direction (List_T pairs_fwd, List_T pairs_rev,
T
Stage3_new (struct Pair_T *pairarray, List_T pairs, int npairs, int goodness, int cdna_direction, int sensedir,
- int stage2_source, int stage2_indexsize,
int matches, int unknowns, int mismatches, int qopens, int qindels,
int topens, int tindels, int ncanonical, int nsemicanonical, int nnoncanonical,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
- bool watsonp, int querylength, int skiplength, int trimlength, double stage3_runtime,
+ bool watsonp, int querylength, int skiplength, int trimlength,
int straintype, char *strain, IIT_T altstrain_iit) {
T new;
Pair_T start, end;
@@ -5032,8 +5096,8 @@ Stage3_new (struct Pair_T *pairarray, List_T pairs, int npairs, int goodness, in
new->translation_end = 0;
new->translation_length = 0;
- new->stage2_source = stage2_source;
- new->stage2_indexsize = stage2_indexsize;
+ /* new->stage2_source = stage2_source; */
+ /* new->stage2_indexsize = stage2_indexsize; */
new->straintype = straintype;
new->strain = strain;
@@ -5049,7 +5113,7 @@ Stage3_new (struct Pair_T *pairarray, List_T pairs, int npairs, int goodness, in
new->genomicstart = chroffset + Pair_genomepos(start);
new->genomicend = chroffset + Pair_genomepos(end);
- new->stage3_runtime = stage3_runtime;
+ /* new->stage3_runtime = stage3_runtime; */
new->trimmed_coverage = (double) (end->querypos - start->querypos + 1)/(double) (trimlength + skiplength);
@@ -5198,21 +5262,21 @@ Stage3_translate_cdna_via_reference (T this, T reference, bool literalrefp) {
if (reference->cdna_direction < 0) {
Translation_via_reference(&this->relaastart,&this->relaaend,
this->pairarray,this->npairs,this->watsonp,/*backwardsp*/true,/*revcompp*/true,
- reference->pairarray,reference->npairs,reference->watsonp,fixshiftp);
+ reference->pairarray,reference->npairs,reference->watsonp);
} else {
Translation_via_reference(&this->relaastart,&this->relaaend,
this->pairarray,this->npairs,this->watsonp,/*backwardsp*/false,/*revcompp*/false,
- reference->pairarray,reference->npairs,reference->watsonp,fixshiftp);
+ reference->pairarray,reference->npairs,reference->watsonp);
}
} else {
if (reference->cdna_direction < 0) {
Translation_via_reference(&this->relaastart,&this->relaaend,
this->pairarray,this->npairs,this->watsonp,/*backwardsp*/false,/*revcompp*/false,
- reference->pairarray,reference->npairs,reference->watsonp,fixshiftp);
+ reference->pairarray,reference->npairs,reference->watsonp);
} else {
Translation_via_reference(&this->relaastart,&this->relaaend,
this->pairarray,this->npairs,this->watsonp,/*backwardsp*/true,/*revcompp*/true,
- reference->pairarray,reference->npairs,reference->watsonp,fixshiftp);
+ reference->pairarray,reference->npairs,reference->watsonp);
}
}
@@ -5400,12 +5464,11 @@ Stage3_print_pathsummary (Filestring_T fp, T this, int pathnum, Univ_IIT_T chrom
dbversion,Sequence_fulllength_given(queryseq),Sequence_skiplength(queryseq),
Sequence_trim_start(queryseq),Sequence_trim_end(queryseq),
Pair_nexons(this->pairarray,this->npairs),this->matches,this->unknowns,this->mismatches,
- this->qopens,this->qindels,this->topens,this->tindels,this->goodness,
+ this->qopens,this->qindels,this->topens,this->tindels,
this->watsonp,this->cdna_direction,
this->translation_start,this->translation_end,this->translation_length,
- /*relaastart*/0,/*relaaend*/0,this->stage2_source,this->stage2_indexsize);
- Translation_print_comparison(fp,this->pairarray,this->npairs,NULL,0,this->cdna_direction,
- this->relaastart,this->relaaend,maxmutations);
+ /*relaastart*/0,/*relaaend*/0);
+ Translation_print_comparison(fp,this->pairarray,this->npairs,this->relaastart,this->relaaend);
FPRINTF(fp,"\n");
return;
@@ -5487,8 +5550,8 @@ Stage3_print_gff3 (Filestring_T fp, T this, int pathnum, Univ_IIT_T chromosome_i
#ifndef PMAP
/* Only for GMAP program */
void
-Stage3_print_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths,
- int absmq_score, int first_absmq, int second_absmq, int mapq_score,
+Stage3_print_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths_primary, int npaths_altloc,
+ int absmq_score, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Sequence_T usersegment,
Sequence_T queryseq, int chimera_part, Chimera_T chimera,
int quality_shift, bool sam_paired_p, char *sam_read_group_id) {
@@ -5509,31 +5572,31 @@ Stage3_print_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths
Pair_print_sam(fp,abbrev,this->pairarray,this->npairs,this->cigar_tokens,this->intronp,
Sequence_accession(queryseq),/*acc2*/NULL,this->chrnum,chromosome_iit,usersegment,
Sequence_fullpointer(queryseq),Sequence_quality_string(queryseq),
- /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/querylength-this->circularpos,querylength,
+ /*hardclip5*/0,/*hardclip3*/querylength-this->circularpos,querylength,
this->watsonp,this->sensedir,chimera_part,chimera,
quality_shift,Sequence_firstp(queryseq),
- pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,this->chrlength,
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,this->chrlength,
mapq_score,sam_paired_p,sam_read_group_id,/*invertp*/false,
- /*circularp*/true,/*merged_overlap_p*/false,/*sarrayp*/false);
+ /*merged_overlap_p*/false,/*sarrayp*/false);
Pair_print_sam(fp,abbrev,this->pairarray,this->npairs,this->cigar_tokens,this->intronp,
Sequence_accession(queryseq),/*acc2*/NULL,this->chrnum,chromosome_iit,usersegment,
Sequence_fullpointer(queryseq),Sequence_quality_string(queryseq),
- /*clipdir*/0,/*hardclip5*/this->circularpos,/*hardclip3*/0,querylength,
+ /*hardclip5*/this->circularpos,/*hardclip3*/0,querylength,
this->watsonp,this->sensedir,chimera_part,chimera,
quality_shift,Sequence_firstp(queryseq),
- pathnum,npaths,absmq_score,first_absmq,second_absmq,/*chrpos*/1,this->chrlength,
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,/*chrpos*/1,this->chrlength,
mapq_score,sam_paired_p,sam_read_group_id,/*invertp*/false,
- /*circularp*/true,/*merged_overlap_p*/false,/*sarrayp*/false);
+ /*merged_overlap_p*/false,/*sarrayp*/false);
} else {
Pair_print_sam(fp,abbrev,this->pairarray,this->npairs,this->cigar_tokens,this->intronp,
Sequence_accession(queryseq),/*acc2*/NULL,this->chrnum,chromosome_iit,usersegment,
Sequence_fullpointer(queryseq),Sequence_quality_string(queryseq),
- /*clipdir*/0,/*hardclip5*/0,/*hardclip3*/0,querylength,
+ /*hardclip5*/0,/*hardclip3*/0,querylength,
this->watsonp,this->sensedir,chimera_part,chimera,
quality_shift,Sequence_firstp(queryseq),
- pathnum,npaths,absmq_score,first_absmq,second_absmq,chrpos,this->chrlength,
+ pathnum,npaths_primary,npaths_altloc,absmq_score,second_absmq,chrpos,this->chrlength,
mapq_score,sam_paired_p,sam_read_group_id,/*invertp*/false,
- /*circularp*/false,/*merged_overlap_p*/false,/*sarrayp*/false);
+ /*merged_overlap_p*/false,/*sarrayp*/false);
}
return;
@@ -5603,11 +5666,9 @@ Stage3_print_mutations (Filestring_T fp, T this, T reference, Univ_IIT_T chromos
dbversion,Sequence_fulllength_given(queryseq),Sequence_skiplength(queryseq),
Sequence_trim_start(queryseq),Sequence_trim_end(queryseq),
Pair_nexons(this->pairarray,this->npairs),this->matches,this->unknowns,this->mismatches,
- this->qopens,this->qindels,this->topens,this->tindels,this->goodness,
- this->watsonp,this->cdna_direction,0,0,0,this->relaastart,this->relaaend,
- this->stage2_source,this->stage2_indexsize);
- Translation_print_comparison(fp,this->pairarray,this->npairs,reference->pairarray,reference->npairs,
- this->cdna_direction,this->relaastart,this->relaaend,maxmutations);
+ this->qopens,this->qindels,this->topens,this->tindels,
+ this->watsonp,this->cdna_direction,0,0,0,this->relaastart,this->relaaend);
+ Translation_print_comparison(fp,this->pairarray,this->npairs,this->relaastart,this->relaaend);
FPRINTF(fp,"\n");
if (showalignp == true) {
@@ -5666,15 +5727,15 @@ print_map (Filestring_T fp, T this, IIT_T map_iit, int *map_divint_crosstable,
FPRINTF(fp," Map hits for path %d (%d):\n",pathnum,nmatches);
}
if (nflanking > 0) {
- IIT_print_header(fp,map_iit,leftflanks,nleftflanks,/*bothstrandsp*/true,chr,
+ IIT_print_header(fp,map_iit,leftflanks,nleftflanks,chr,
/*reversep*/true,/*relativep*/false,/*left*/0U,print_comment_p);
FPRINTF(fp," ====================\n");
}
- IIT_print_header(fp,map_iit,iit_matches,nmatches,/*bothstrandsp*/true,chr,
+ IIT_print_header(fp,map_iit,iit_matches,nmatches,chr,
/*reversep*/false,/*relativep*/false,/*left*/0U,print_comment_p);
if (nflanking > 0) {
FPRINTF(fp," ====================\n");
- IIT_print_header(fp,map_iit,rightflanks,nrightflanks,/*bothstrandsp*/true,chr,
+ IIT_print_header(fp,map_iit,rightflanks,nrightflanks,chr,
/*reversep*/false,/*relativep*/false,/*left*/0U,print_comment_p);
}
@@ -5690,15 +5751,15 @@ print_map (Filestring_T fp, T this, IIT_T map_iit, int *map_divint_crosstable,
FPRINTF(fp," Map hits for path %d (%d):\n",pathnum,nmatches);
}
if (nflanking > 0) {
- IIT_print_header(fp,map_iit,leftflanks,nleftflanks,/*bothstrandsp*/false,chr,
+ IIT_print_header(fp,map_iit,leftflanks,nleftflanks,chr,
/*reversep*/true,/*relativep*/false,/*left*/0U,print_comment_p);
FPRINTF(fp," ====================\n");
}
- IIT_print_header(fp,map_iit,iit_matches,nmatches,/*bothstrandsp*/false,chr,
+ IIT_print_header(fp,map_iit,iit_matches,nmatches,chr,
/*reversep*/false,/*relativep*/false,/*left*/0U,print_comment_p);
if (nflanking > 0) {
FPRINTF(fp," ====================\n");
- IIT_print_header(fp,map_iit,rightflanks,nrightflanks,/*bothstrandsp*/false,chr,
+ IIT_print_header(fp,map_iit,rightflanks,nrightflanks,chr,
/*reversep*/false,/*relativep*/false,/*left*/0U,print_comment_p);
}
}
@@ -5745,7 +5806,7 @@ print_exon_map (Filestring_T fp, T this, IIT_T map_iit, int *map_divint_crosstab
iit_matches = IIT_get(&nmatches,map_iit,chr,position2,position1,/*sortp*/true);
}
FPRINTF(fp," Map hits for path %d, exon %d (%d):\n",pathnum,++exonno,nmatches);
- IIT_print_header(fp,map_iit,iit_matches,nmatches,/*bothstrandsp*/true,chr,
+ IIT_print_header(fp,map_iit,iit_matches,nmatches,chr,
/*reversep*/false,/*relativep*/false,/*left*/0U,print_comment_p);
} else {
@@ -5757,7 +5818,7 @@ print_exon_map (Filestring_T fp, T this, IIT_T map_iit, int *map_divint_crosstab
/*sortp*/true,/*sign*/-1);
}
FPRINTF(fp," Map hits for path %d, exon %d (%d):\n",pathnum,++exonno,nmatches);
- IIT_print_header(fp,map_iit,iit_matches,nmatches,/*bothstrandsp*/false,chr,
+ IIT_print_header(fp,map_iit,iit_matches,nmatches,chr,
/*reversep*/false,/*relativep*/false,/*left*/0U,print_comment_p);
}
FPRINTF(fp,"\n");
@@ -6903,7 +6964,7 @@ traverse_single_gap (bool *filledp, int *dynprogindex, List_T pairs, List_T *pat
if (querydp3 >= querylength) {
querydp3 = querylength - 1;
}
- if (finalp == false && genomedp5 == last_genomedp5[querydp5] && genomedp3 == last_genomedp3[querydp3]) {
+ if (0 && finalp == false && genomedp5 == last_genomedp5[querydp5] && genomedp3 == last_genomedp3[querydp3]) {
debug(printf("Already solved for %u..%u at %d..%d\n",genomedp5,genomedp3,querydp5,querydp3));
pairs = Pairpool_transfer(pairs,peeled_pairs);
@@ -6989,7 +7050,11 @@ traverse_single_gap (bool *filledp, int *dynprogindex, List_T pairs, List_T *pat
debug(printf("Minor difference in queryjump and genomejump, so accepting this solution\n"));
pairs = Pairpool_transfer(pairs,gappairs);
*filledp = true;
+#ifdef PMAP
+ } else if (finalscore < 0 || finalscore < 2*origscore/3) { /* Allow for wobble */
+#else
} else if (finalscore < 0 || finalscore < origscore) {
+#endif
/* Put back peeled pairs */
debug(printf("Bad alignment, so undoing this solution\n"));
pairs = Pairpool_transfer(pairs,peeled_pairs);
@@ -7018,7 +7083,7 @@ traverse_cdna_gap (bool *filledp, bool *incompletep, int *dynprogindex_minor, in
List_T pairs, List_T *path, Pair_T leftpair, Pair_T rightpair,
Univcoord_T chroffset, Univcoord_T chrhigh,
char *queryseq_ptr, char *queryuc_ptr, int querylength,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
Chrpos_T *last_genomedp5, Chrpos_T *last_genomedp3,
int maxpeelback, double defect_rate, bool finalp) {
@@ -7062,7 +7127,7 @@ traverse_cdna_gap (bool *filledp, bool *incompletep, int *dynprogindex_minor, in
if (querydp3 >= querylength) {
querydp3 = querylength - 1;
}
- if (finalp == false && genomedp5 == last_genomedp5[querydp5] && genomedp3 == last_genomedp3[querydp3]) {
+ if (0 && finalp == false && genomedp5 == last_genomedp5[querydp5] && genomedp3 == last_genomedp3[querydp3]) {
debug(printf("Already solved for %u..%u at %d..%d\n",genomedp5,genomedp3,querydp5,querydp3));
pairs = Pairpool_transfer(pairs,peeled_pairs);
@@ -7116,7 +7181,7 @@ traverse_cdna_gap (bool *filledp, bool *incompletep, int *dynprogindex_minor, in
#endif
/*length1L*/queryjump,/*length1R*/queryjump,/*length2*/genomejump,
/*offset1L*/querydp5,/*revoffset1R*/querydp3,/*offset2*/genomedp5,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_paired,defect_rate);
debug(Pair_dump_list(gappairs,true));
*filledp = true;
@@ -7261,7 +7326,7 @@ traverse_genome_gap (bool *filledp, bool *shiftp, int *dynprogindex_minor, int *
if (querydp3 >= querylength) {
querydp3 = querylength - 1;
}
- if (finalp == false && genomedp5 == last_genomedp5[querydp5] && genomedp3 == last_genomedp3[querydp3]) {
+ if (0 && finalp == false && genomedp5 == last_genomedp5[querydp5] && genomedp3 == last_genomedp3[querydp3]) {
debug(printf("Already solved for %u..%u at %d..%d\n",genomedp5,genomedp3,querydp5,querydp3));
pairs = Pairpool_transfer(pairs,peeled_pairs);
@@ -7309,7 +7374,7 @@ traverse_genome_gap (bool *filledp, bool *shiftp, int *dynprogindex_minor, int *
&left_prob,&right_prob,&nmatches,&nmismatches,&nopens,&nindels,
&exonhead,&introntype,dynprogL,dynprogR,
&(queryseq_ptr[querydp5]),&(queryuc_ptr[querydp5]),
- queryjump,genomejump,genomejump,querydp5,genomedp5,genomedp3,
+ queryjump,genomejump,genomejump,querydp5,/*goffsetL*/genomedp5,/*rev_goffsetR*/genomedp3,
chrnum,chroffset,chrhigh,
cdna_direction,watsonp,jump_late_p,pairpool,
extraband_paired + n_peeled_indels_leftward + n_peeled_indels_rightward,
@@ -7451,7 +7516,7 @@ traverse_genome_gap (bool *filledp, bool *shiftp, int *dynprogindex_minor, int *
/*length1*/queryjump,/*length2L*/genomejump,/*length2R*/genomejump,
/*offset1*/querydp5,/*offset2L*/genomedp5,/*revoffset2R*/genomedp3,
cdna_direction,queryseq_ptr,queryuc_ptr,chroffset,chrhigh,watsonp,
- pairpool,defect_rate);
+ pairpool);
if (micropairs == NULL) {
debug(printf("No microexon found\n"));
@@ -7943,7 +8008,7 @@ distalmedial_ending5 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
List_T *pairs, int leftquerypos, Pair_T rightpair,
Univcoord_T chroffset, Univcoord_T chrhigh,
char *queryseq_ptr, char *queryuc_ptr,
- int cdna_direction, bool watsonp, bool jump_late_p, Pairpool_T pairpool,
+ bool watsonp, bool jump_late_p, Pairpool_T pairpool,
Dynprog_T dynprog, int maxpeelback, double defect_rate) {
List_T peeled_pairs, continuous_gappairs_medialgap = NULL;
int queryjump, genomejump;
@@ -7970,8 +8035,8 @@ distalmedial_ending5 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
*pairs = peel_rightward(&n_peeled_indels,&protectedp,&peeled_pairs,*pairs,&querydp3_distalgap,&genomedp3_distalgap,
maxpeelback,/*stop_at_indels_p*/true);
- continuous_goodness_distalgap = Pair_fracidentity_score(peeled_pairs,cdna_direction);
- /* continuous_goodness_distalgap += Pair_fracidentity_score(endgappairs,cdna_direction); */
+ continuous_goodness_distalgap = Pair_fracidentity_score(peeled_pairs);
+ /* continuous_goodness_distalgap += Pair_fracidentity_score(endgappairs); */
debug(printf("continuous_goodness_distalgap (%d pairs) is %d\n",
List_length(peeled_pairs),continuous_goodness_distalgap));
@@ -8000,14 +8065,14 @@ distalmedial_ending5 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
}
#endif
- debug(printf("Stage 3 (dir %d): traverse_ending5: Dynamic programming at 5' end (medial to gap): querydp5 = %d, querydp3 = %d, genomedp3 = %d\n",
- cdna_direction,querydp5,querydp3_medialgap,genomedp3_medialgap));
+ debug(printf("Stage 3: traverse_ending5: Dynamic programming at 5' end (medial to gap): querydp5 = %d, querydp3 = %d, genomedp3 = %d\n",
+ querydp5,querydp3_medialgap,genomedp3_medialgap));
continuous_gappairs_medialgap = Dynprog_end5_gap(&(*dynprogindex_minor),&(*finalscore),
&nmatches,&nmismatches,&nopens,&nindels,dynprog,
&(queryseq_ptr[querydp3_medialgap]),&(queryuc_ptr[querydp3_medialgap]),
queryjump,genomejump,querydp3_medialgap,genomedp3_medialgap,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,/*endalign*/QUERYEND_INDELS);
*ambig_end_length = 0;
*ambig_prob = 0.0;
@@ -8118,7 +8183,7 @@ extend_ending5 (bool *knownsplicep, int *dynprogindex_minor,
&nmatches,&nmismatches,&nopens,&nindels,dynprog,
&(queryseq_ptr[querydp3_distalgap]),&(queryuc_ptr[querydp3_distalgap]),
queryjump,genomejump,querydp3_distalgap,genomedp3_distalgap,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,endalign);
*ambig_end_length = 0;
*ambig_prob = 0.0;
@@ -8156,7 +8221,7 @@ distalmedial_ending3 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
List_T *path, Pair_T leftpair, int rightquerypos,
Univcoord_T chroffset, Univcoord_T chrhigh,
char *queryseq_ptr, char *queryuc_ptr,
- int cdna_direction, bool watsonp, bool jump_late_p,
+ bool watsonp, bool jump_late_p,
Pairpool_T pairpool, Dynprog_T dynprog, int maxpeelback, double defect_rate) {
List_T peeled_path, continuous_gappairs_medialgap = NULL;
int queryjump, genomejump;
@@ -8186,8 +8251,8 @@ distalmedial_ending3 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
*path = peel_leftward(&n_peeled_indels,&protectedp,&peeled_path,*path,&querydp5_distalgap,&genomedp5_distalgap,
maxpeelback,/*stop_at_indels_p*/true);
- continuous_goodness_distalgap = Pair_fracidentity_score(peeled_path,cdna_direction);
- /* continuous_goodness_distalgap += Pair_fracidentity_score(endgappairs,cdna_direction); */
+ continuous_goodness_distalgap = Pair_fracidentity_score(peeled_path);
+ /* continuous_goodness_distalgap += Pair_fracidentity_score(endgappairs); */
debug(printf("continuous_goodness_distalgap (%d pairs) is %d\n",
List_length(peeled_path),continuous_goodness_distalgap));
@@ -8216,8 +8281,8 @@ distalmedial_ending3 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
}
#endif
- debug(printf("Stage 3 (dir %d): distalmedial_ending3: Dynamic programming at 3' end (medial to gap): querydp5 = %d, querydp3 = %d, genomedp5 = %u\n",
- cdna_direction,querydp5_medialgap,querydp3,genomedp5_medialgap));
+ debug(printf("Stage 3: distalmedial_ending3: Dynamic programming at 3' end (medial to gap): querydp5 = %d, querydp3 = %d, genomedp5 = %u\n",
+ querydp5_medialgap,querydp3,genomedp5_medialgap));
debug(printf("Before solving the 3' end, here is the path:\n"));
debug(Pair_dump_list(*path,true));
@@ -8227,7 +8292,7 @@ distalmedial_ending3 (bool *knownsplicep, bool *chop_exon_p, int *dynprogindex_m
&nmatches,&nmismatches,&nopens,&nindels,dynprog,
&(queryseq_ptr[querydp5_medialgap]),&(queryuc_ptr[querydp5_medialgap]),
queryjump,genomejump,querydp5_medialgap,genomedp5_medialgap,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,/*endalign*/QUERYEND_INDELS);
*ambig_end_length = 0;
*ambig_prob = 0.0;
@@ -8334,7 +8399,7 @@ extend_ending3 (bool *knownsplicep, int *dynprogindex_minor, int *finalscore,
&nmatches,&nmismatches,&nopens,&nindels,dynprog,
&(queryseq_ptr[querydp5_distalgap]),&(queryuc_ptr[querydp5_distalgap]),
queryjump,genomejump,querydp5_distalgap,genomedp5_distalgap,
- chroffset,chrhigh,cdna_direction,watsonp,jump_late_p,pairpool,
+ chroffset,chrhigh,watsonp,jump_late_p,pairpool,
extraband_end,defect_rate,endalign);
*ambig_end_length = 0;
*ambig_prob = 0.0;
@@ -8380,7 +8445,7 @@ traverse_dual_break (List_T pairs, List_T *path, Pair_T leftpair, Pair_T rightpa
Oligoindex_array_T oligoindices_minor,
Diagpool_T diagpool, Cellpool_T cellpool) {
List_T gappairs, peeled_pairs = NULL, peeled_path = NULL;
- int querydp5, querydp3, source, indexsize;
+ int querydp5, querydp3;
Chrpos_T genomedp5, genomedp3;
bool protectedp;
int n_peeled_indels;
@@ -8442,7 +8507,7 @@ traverse_dual_break (List_T pairs, List_T *path, Pair_T leftpair, Pair_T rightpa
debug14(printf("Starting stage2 with chrstart %u, chrend %u, watsonp %d\n",
chrstart,chrend,watsonp));
- gappairs = Stage2_compute_one(&source,&indexsize,
+ gappairs = Stage2_compute_one(
#ifdef PMAP
&(queryaaseq_ptr[querydp5]),&(queryaaseq_ptr[querydp5]),
/*querylength*/querydp3-querydp5+1,/*query_offset*/querydp5*3,
@@ -8452,11 +8517,9 @@ traverse_dual_break (List_T pairs, List_T *path, Pair_T leftpair, Pair_T rightpa
#endif
chrstart,chrend,chroffset,chrhigh,/*plusp*/watsonp,genestrand,
- oligoindices_minor,/*proceed_pctcoverage*/0.80,
- pairpool,diagpool,cellpool,
+ oligoindices_minor,pairpool,diagpool,cellpool,
/*localp should be false*/true,/*skip_repetitive_p*/false,
- /*use_shifted_canonical_p*/true,/*favor_right_p*/false,
- /*debug_graphic_p*/false);
+ /*favor_right_p*/false,/*debug_graphic_p*/false);
debug14(printf("Internal stage2 result:\n"));
debug14(Pair_dump_list(gappairs,true));
@@ -8718,7 +8781,7 @@ build_path_end3 (bool *knownsplicep, int *ambig_end_length_3, Splicetype_T *ambi
&finalscore,&(*ambig_end_length_3),&(*ambig_prob_3),
&path,leftpair,rightquerypos,chroffset,chrhigh,
queryseq_ptr,queryuc_ptr,
- cdna_direction,watsonp,jump_late_p,pairpool,dynprogL,
+ watsonp,jump_late_p,pairpool,dynprogL,
maxpeelback,defect_rate);
}
@@ -8823,7 +8886,7 @@ build_pairs_end5 (bool *knownsplicep, int *ambig_end_length_5, Splicetype_T *amb
&finalscore,&(*ambig_end_length_5),&(*ambig_prob_5),
&pairs,leftquerypos,rightpair,chroffset,chrhigh,
queryseq_ptr,queryuc_ptr,
- cdna_direction,watsonp,jump_late_p,pairpool,dynprogR,
+ watsonp,jump_late_p,pairpool,dynprogR,
maxpeelback,defect_rate);
}
@@ -9155,7 +9218,7 @@ build_pairs_introns (bool *shiftp, bool *incompletep,
cdna_direction,leftpair->querypos,rightpair->querypos,leftpair->genomepos,rightpair->genomepos,pair->queryjump,pair->genomejump));
pairs = traverse_cdna_gap(&filledp,&(*incompletep),&(*dynprogindex_minor),&(*dynprogindex_major),
pairs,&path,leftpair,rightpair,
- chroffset,chrhigh,queryseq_ptr,queryuc_ptr,querylength,cdna_direction,watsonp,
+ chroffset,chrhigh,queryseq_ptr,queryuc_ptr,querylength,watsonp,
jump_late_p,pairpool,dynprogL,dynprogM,dynprogR,
last_genomedp5,last_genomedp3,maxpeelback,defect_rate,/*finalp*/true);
@@ -9202,7 +9265,7 @@ build_pairs_introns (bool *shiftp, bool *incompletep,
cdna_direction,leftpair->querypos,rightpair->querypos,leftpair->genomepos,rightpair->genomepos,pair->queryjump,pair->genomejump));
pairs = traverse_cdna_gap(&filledp,&(*incompletep),&(*dynprogindex_minor),&(*dynprogindex_major),
pairs,&path,leftpair,rightpair,
- chroffset,chrhigh,queryseq_ptr,queryuc_ptr,querylength,cdna_direction,watsonp,
+ chroffset,chrhigh,queryseq_ptr,queryuc_ptr,querylength,watsonp,
jump_late_p,pairpool,dynprogL,dynprogM,dynprogR,
last_genomedp5,last_genomedp3,maxpeelback,defect_rate,/*finalp*/true);
@@ -9347,7 +9410,7 @@ score_alignment (int *nmatches, int *nmismatches, int *nindels,
static List_T
score_introns (double *max_intron_score, double *avg_donor_score, double *avg_acceptor_score,
- int *ncanonical, int *nbadintrons, List_T path, int cdna_direction, bool watsonp,
+ int *nknown, int *ncanonical, int *nbadintrons, List_T path, int cdna_direction, bool watsonp,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh
#ifdef WASTE
, Pairpool_T pairpool
@@ -9371,7 +9434,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
minintronlen = MININTRONLEN_FINAL;
*max_intron_score = *avg_donor_score = *avg_acceptor_score = 0.0;
- *ncanonical = *nbadintrons = 0;
+ *nknown = *ncanonical = *nbadintrons = 0;
total_matches = total_denominator = 0;
for (p = path; p != NULL; p = p->rest) {
@@ -9475,6 +9538,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/+1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
donor_score = 1.0;
} else {
donor_score = Maxent_hr_donor_prob(chroffset + splicesitepos,chroffset);
@@ -9485,6 +9549,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,acceptor_typeint,/*sign*/+1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
acceptor_score = 1.0;
} else {
acceptor_score = Maxent_hr_acceptor_prob(chroffset + splicesitepos,chroffset);
@@ -9496,6 +9561,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/-1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
donor_score = 1.0;
} else {
donor_score = Maxent_hr_antidonor_prob(chroffset + splicesitepos,chroffset);
@@ -9506,6 +9572,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,acceptor_typeint,/*sign*/-1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
acceptor_score = 1.0;
} else {
acceptor_score = Maxent_hr_antiacceptor_prob(chroffset + splicesitepos,chroffset);
@@ -9517,7 +9584,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
rightpair->genomepos,acceptor_score,watsonp,cdna_direction,pair->comp));
nintrons += 1;
if (pair->knowngapp == true) {
- /* Skip */
+ *nknown += 1;
*ncanonical += 1;
} else if (pair->comp == FWD_CANONICAL_INTRON_COMP) {
*ncanonical += 1;
@@ -9547,6 +9614,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,acceptor_typeint,/*sign*/-1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
acceptor_score = 1.0;
} else {
acceptor_score = Maxent_hr_antiacceptor_prob(chroffset + splicesitepos,chroffset);
@@ -9558,6 +9626,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/-1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
donor_score = 1.0;
} else {
donor_score = Maxent_hr_antidonor_prob(chroffset + splicesitepos,chroffset);
@@ -9569,6 +9638,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,acceptor_typeint,/*sign*/+1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
acceptor_score = 1.0;
} else {
acceptor_score = Maxent_hr_acceptor_prob(chroffset + splicesitepos,chroffset);
@@ -9579,6 +9649,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
if (splicesites_iit && IIT_exists_with_divno_typed_signed(splicesites_iit,splicesites_divint_crosstable[chrnum],
splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/+1)) {
debug11(printf(" => known\n"));
+ pair->knowngapp = true;
donor_score = 1.0;
} else {
donor_score = Maxent_hr_donor_prob(chroffset + splicesitepos,chroffset);
@@ -9590,7 +9661,7 @@ score_introns (double *max_intron_score, double *avg_donor_score, double *avg_ac
rightpair->genomepos,acceptor_score,watsonp,cdna_direction,pair->comp));
nintrons += 1;
if (pair->knowngapp == true) {
- /* Skip */
+ *nknown += 1;
*ncanonical += 1;
} else if (pair->comp == REV_CANONICAL_INTRON_COMP) {
*ncanonical += 1;
@@ -9656,8 +9727,8 @@ end_compare (List_T x, List_T y, int cdna_direction, bool watsonp,
List_T pairs1, pairs2, path1, path2;
double max_intron_score;
- int ncanonical_1, nsemicanonical_1, nnoncanonical_1, nbadintrons_1;
- int ncanonical_2, nsemicanonical_2, nnoncanonical_2, nbadintrons_2;
+ int nknown_1, ncanonical_1, nsemicanonical_1, nnoncanonical_1, nbadintrons_1;
+ int nknown_2, ncanonical_2, nsemicanonical_2, nnoncanonical_2, nbadintrons_2;
double avg_donor_score_1, avg_acceptor_score_1;
double avg_donor_score_2, avg_acceptor_score_2;
int alignment_score_1, alignment_score_2;
@@ -9673,7 +9744,7 @@ end_compare (List_T x, List_T y, int cdna_direction, bool watsonp,
path1 = List_reverse(pairs1);
debug11(printf("Calling score_introns for end_compare on path1\n"));
- pairs1 = score_introns(&max_intron_score,&avg_donor_score_1,&avg_acceptor_score_1,&ncanonical_1,
+ pairs1 = score_introns(&max_intron_score,&avg_donor_score_1,&avg_acceptor_score_1,&nknown_1,&ncanonical_1,
&nbadintrons_1,path1,cdna_direction,watsonp,chrnum,chroffset,chrhigh);
alignment_score_1 = score_alignment(&nmatches_1,&nmismatches_1,&nindels_1,
#ifdef COMPLEX_DIRECTION
@@ -9683,7 +9754,7 @@ end_compare (List_T x, List_T y, int cdna_direction, bool watsonp,
path2 = List_reverse(pairs2);
debug11(printf("Calling score_introns for end_compare on path2\n"));
- pairs2 = score_introns(&max_intron_score,&avg_donor_score_2,&avg_acceptor_score_2,&ncanonical_2,
+ pairs2 = score_introns(&max_intron_score,&avg_donor_score_2,&avg_acceptor_score_2,&nknown_2,&ncanonical_2,
&nbadintrons_2,path2,cdna_direction,watsonp,chrnum,chroffset,chrhigh);
alignment_score_2 = score_alignment(&nmatches_2,&nmismatches_2,&nindels_2,
#ifdef COMPLEX_DIRECTION
@@ -9696,7 +9767,7 @@ end_compare (List_T x, List_T y, int cdna_direction, bool watsonp,
path2 = y;
debug11(printf("Calling score_introns for end_compare on path1\n"));
- pairs1 = score_introns(&max_intron_score,&avg_donor_score_1,&avg_acceptor_score_1,&ncanonical_1,
+ pairs1 = score_introns(&max_intron_score,&avg_donor_score_1,&avg_acceptor_score_1,&nknown_1,&ncanonical_1,
&nbadintrons_1,path1,cdna_direction,watsonp,chrnum,chroffset,chrhigh);
alignment_score_1 = score_alignment(&nmatches_1,&nmismatches_1,&nindels_1,
#ifdef COMPLEX_DIRECTION
@@ -9706,7 +9777,7 @@ end_compare (List_T x, List_T y, int cdna_direction, bool watsonp,
path1 = List_reverse(pairs1);
debug11(printf("Calling score_introns for end_compare on path2\n"));
- pairs2 = score_introns(&max_intron_score,&avg_donor_score_2,&avg_acceptor_score_2,&ncanonical_2,
+ pairs2 = score_introns(&max_intron_score,&avg_donor_score_2,&avg_acceptor_score_2,&nknown_2,&ncanonical_2,
&nbadintrons_2,path2,cdna_direction,watsonp,chrnum,chroffset,chrhigh);
alignment_score_2 = score_alignment(&nmatches_2,&nmismatches_2,&nindels_2,
#ifdef COMPLEX_DIRECTION
@@ -11231,47 +11302,70 @@ trim_novel_spliceends (List_T pairs,
int i;
Pair_T pair;
- Univcoord_T genomicpos, start_genomicpos, end_genomicpos, splice_genomepos_5, splice_genomepos_3;
- Univcoord_T start, end;
- double donor_prob, acceptor_prob, max_prob_5 = 0.0, max_prob_3 = 0.0,
+ int trim5, trim3;
+ Univcoord_T genomicpos, start_genomicpos, middle_genomicpos, end_genomicpos;
+ Univcoord_T splice_genomepos_5, splice_genomepos_3, splice_genomepos_5_mm, splice_genomepos_3_mm;
+ Univcoord_T start, middle, end; /* start to middle has mismatches, while middle to end has none */
+ double donor_prob, acceptor_prob;
+ double max_prob_5 = 0.0, max_prob_3 = 0.0,
max_prob_sense_forward_5 = 0.0, max_prob_sense_anti_5 = 0.0,
max_prob_sense_forward_3 = 0.0, max_prob_sense_anti_3 = 0.0;
- Splicetype_T splicetype5, splicetype3;
+ double max_prob_5_mm = 0.0, max_prob_3_mm = 0.0,
+ max_prob_sense_forward_5_mm = 0.0, max_prob_sense_anti_5_mm = 0.0,
+ max_prob_sense_forward_3_mm = 0.0, max_prob_sense_anti_3_mm = 0.0;
+ Splicetype_T splicetype5, splicetype3, splicetype5_mm, splicetype3_mm;
int splice_cdna_direction_5, splice_sensedir_5, splice_cdna_direction_3, splice_sensedir_3;
+ int splice_cdna_direction_5_mm, splice_sensedir_5_mm, splice_cdna_direction_3_mm, splice_sensedir_3_mm;
bool mismatchp;
- debug13(printf("\nEntered trim_novel_spliceends with cdna_direction %d and sensedir %d\n",
- *cdna_direction,*sensedir));
+ debug13(printf("\nEntered gmap_trim_novel_spliceends with cdna_direction %d and sensedir %d, ambig_end_lengths %d and %d\n",
+ *cdna_direction,*sensedir,*ambig_end_length_5,*ambig_end_length_3));
+
+ Pair_trim_distances(&trim5,&trim3,pairs);
+ debug13(printf("Trim distances are %d and %d\n",trim5,trim3));
path = List_reverse(pairs);
- if (path != NULL && knownsplice3p == false && *ambig_end_length_3 == 0 &&
- exon_length_3(path) >= END_SPLICESITE_EXON_LENGTH) {
+ if (path != NULL && knownsplice3p == false && *ambig_end_length_3 == 0
+ /* && exon_length_3(path) >= END_SPLICESITE_EXON_LENGTH */) {
/* See if there is a good splice site at the 3' end */
debug13(Pair_dump_list(path,true));
pair = (Pair_T) List_head(p = path);
- start = end = pair->genomepos;
+ start = middle = end = pair->genomepos;
+ debug13(printf("Initializing start and end to be %u\n",start));
i = 0;
mismatchp = false;
- while (i <= END_SPLICESITE_SEARCH) {
+ while (i < trim3) {
if ((p = List_next(p)) == NULL) {
break;
+ } else if (pair->gapp == true) {
+ break;
+ } else if (pair->comp == MATCH_COMP || pair->comp == DYNPROG_MATCH_COMP || pair->comp == AMBIGUOUS_COMP) {
+ middle = pair->genomepos;
+ debug13(printf("Resetting middle to be %u\n",middle));
} else {
- pair = (Pair_T) List_head(p);
- if (pair->gapp == true) {
- break;
- } else if (pair->comp == MATCH_COMP || pair->comp == DYNPROG_MATCH_COMP || pair->comp == AMBIGUOUS_COMP) {
- end = pair->genomepos;
- i++;
- } else {
- mismatchp = true;
- i = 0;
- }
+ middle = pair->genomepos;
+ mismatchp = true;
+ debug13(printf("Resetting middle to be %u\n",middle));
}
+ pair = (Pair_T) List_head(p);
+ i++;
}
+ while (i < trim3 + END_SPLICESITE_SEARCH) {
+ if ((p = List_next(p)) == NULL) {
+ break;
+ } else if (pair->gapp == true) {
+ break;
+ } else {
+ end = pair->genomepos;
+ debug13(printf("Resetting end to be %u\n",end));
+ }
+ pair = (Pair_T) List_head(p);
+ i++;
+ }
if (mismatchp == false) {
/* Allow perfect overhangs into intron */
@@ -11279,82 +11373,162 @@ trim_novel_spliceends (List_T pairs,
} else if (*sensedir == SENSE_FORWARD) {
if (watsonp) {
- splicetype3 = DONOR;
+ splicetype3 = splicetype3_mm = DONOR;
start_genomicpos = start + 1;
+ middle_genomicpos = middle + 1;
end_genomicpos = end + 1;
assert(start_genomicpos >= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos >= end_genomicpos; genomicpos--) {
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 1 */
+ debug13(printf("3', watson, sense anti %u %u %f mm\n",chroffset+genomicpos,genomicpos,donor_prob));
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = genomicpos - 1;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 1 */
- debug13(printf("3', watson, sense anti %u %f\n",genomicpos,donor_prob));
+ debug13(printf("3', watson, sense anti %u %u %f\n",chroffset+genomicpos,genomicpos,donor_prob));
if (donor_prob > max_prob_3) {
max_prob_3 = donor_prob;
splice_genomepos_3 = genomicpos - 1;
}
+ genomicpos--;
}
+ debug13(printf("\n"));
} else {
- splicetype3 = ANTIDONOR;
+ splicetype3 = splicetype3_mm = ANTIDONOR;
start_genomicpos = (chrhigh - chroffset) - start;
+ middle_genomicpos = (chrhigh - chroffset) - middle;
end_genomicpos = (chrhigh - chroffset) - end;
assert(start_genomicpos <= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos <= end_genomicpos; genomicpos++) {
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 3 */
- debug13(printf("3', crick, sense forward %u %f\n",genomicpos,donor_prob));
+ debug13(printf("3', crick, sense forward %u %u %f mm\n",chroffset+genomicpos,genomicpos,donor_prob));
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = (chrhigh - chroffset) - genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 3 */
+ debug13(printf("3', crick, sense forward %u %u %f\n",chroffset+genomicpos,genomicpos,donor_prob));
if (donor_prob > max_prob_3) {
max_prob_3 = donor_prob;
splice_genomepos_3 = (chrhigh - chroffset) - genomicpos;
}
+ genomicpos++;
}
+ debug13(printf("\n"));
}
} else if (*sensedir == SENSE_ANTI) {
if (watsonp) {
- splicetype3 = ANTIACCEPTOR;
+ splicetype3 = splicetype3_mm = ANTIACCEPTOR;
start_genomicpos = start + 1;
+ middle_genomicpos = middle + 1;
end_genomicpos = end + 1;
assert(start_genomicpos >= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos >= end_genomicpos; genomicpos--) {
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 5 */
- debug13(printf("3', watson, sense forward %u %f\n",genomicpos,acceptor_prob));
+ debug13(printf("3', watson, sense forward %u %u %f mm\n",chroffset+genomicpos,genomicpos,acceptor_prob));
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = genomicpos - 1;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 5 */
+ debug13(printf("3', watson, sense forward %u %u %f\n",chroffset+genomicpos,genomicpos,acceptor_prob));
if (acceptor_prob > max_prob_3) {
max_prob_3 = acceptor_prob;
splice_genomepos_3 = genomicpos - 1;
}
+ genomicpos--;
}
+ debug13(printf("\n"));
} else {
- splicetype3 = ACCEPTOR;
+ splicetype3 = splicetype3_mm = ACCEPTOR;
start_genomicpos = (chrhigh - chroffset) - start;
+ middle_genomicpos = (chrhigh - chroffset) - middle;
end_genomicpos = (chrhigh - chroffset) - end;
assert(start_genomicpos <= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos <= end_genomicpos; genomicpos++) {
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 7 */
+ debug13(printf("3', crick, sense anti %u %u %f mm\n",chroffset+genomicpos,genomicpos,acceptor_prob));
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = (chrhigh - chroffset) - genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 7 */
- debug13(printf("3', crick, sense anti %u %f\n",genomicpos,acceptor_prob));
+ debug13(printf("3', crick, sense anti %u %u %f\n",chroffset+genomicpos,genomicpos,acceptor_prob));
if (acceptor_prob > max_prob_3) {
max_prob_3 = acceptor_prob;
splice_genomepos_3 = (chrhigh - chroffset) - genomicpos;
}
+ genomicpos++;
}
+ debug13(printf("\n"));
}
} else {
if (watsonp) {
start_genomicpos = start + 1;
+ middle_genomicpos = middle + 1;
end_genomicpos = end + 1;
assert(start_genomicpos >= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos >= end_genomicpos; genomicpos--) {
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 1 */
acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 5 */
- debug13(printf("3', watson, sense null %u %f %f\n",genomicpos,donor_prob,acceptor_prob));
+ debug13(printf("3', watson, sense null %u %u %f %f mm\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
+ if (donor_prob > max_prob_sense_forward_3_mm) {
+ max_prob_sense_forward_3_mm = donor_prob;
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = genomicpos - 1;
+ splice_cdna_direction_3_mm = +1;
+ splice_sensedir_3_mm = SENSE_FORWARD;
+ splicetype3_mm = DONOR;
+ }
+ }
+ if (acceptor_prob > max_prob_sense_anti_3_mm) {
+ max_prob_sense_anti_3_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = genomicpos - 1;
+ splice_cdna_direction_3_mm = -1;
+ splice_sensedir_3_mm = SENSE_ANTI;
+ splicetype3_mm = ANTIACCEPTOR;
+ }
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 1 */
+ acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 5 */
+ debug13(printf("3', watson, sense null %u %u %f %f\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
if (donor_prob > max_prob_sense_forward_3) {
max_prob_sense_forward_3 = donor_prob;
if (donor_prob > max_prob_3) {
@@ -11375,17 +11549,47 @@ trim_novel_spliceends (List_T pairs,
splicetype3 = ANTIACCEPTOR;
}
}
+ genomicpos--;
}
+ debug13(printf("\n"));
} else {
start_genomicpos = (chrhigh - chroffset) - start;
+ middle_genomicpos = (chrhigh - chroffset) - middle;
end_genomicpos = (chrhigh - chroffset) - end;
assert(start_genomicpos <= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos <= end_genomicpos; genomicpos++) {
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 3 */
+ acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 7 */
+ debug13(printf("3', crick, sense null %u %u %f %f mm\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
+ if (donor_prob > max_prob_sense_forward_3_mm) {
+ max_prob_sense_forward_3_mm = donor_prob;
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = (chrhigh - chroffset) - genomicpos;
+ splice_cdna_direction_3_mm = +1;
+ splice_sensedir_3_mm = SENSE_FORWARD;
+ splicetype3_mm = ANTIDONOR;
+ }
+ }
+ if (acceptor_prob > max_prob_sense_anti_3_mm) {
+ max_prob_sense_anti_3_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = (chrhigh - chroffset) - genomicpos;
+ splice_cdna_direction_3_mm = -1;
+ splice_sensedir_3_mm = SENSE_ANTI;
+ splicetype3_mm = ACCEPTOR;
+ }
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 3 */
acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 7 */
- debug13(printf("3', crick, sense null %u %f %f\n",genomicpos,donor_prob,acceptor_prob));
+ debug13(printf("3', crick, sense null %u %u %f %f\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
if (donor_prob > max_prob_sense_forward_3) {
max_prob_sense_forward_3 = donor_prob;
if (donor_prob > max_prob_3) {
@@ -11406,12 +11610,14 @@ trim_novel_spliceends (List_T pairs,
splicetype3 = ACCEPTOR;
}
}
+ genomicpos++;
}
+ debug13(printf("\n"));
}
}
if (*sensedir != SENSE_NULL) {
- if (max_prob_3 > END_SPLICESITE_PROB) {
+ if (max_prob_3 > END_SPLICESITE_PROB_MATCH) {
debug13(printf("Found good splice %s on 3' end at %u with probability %f\n",
Splicetype_string(splicetype3),splice_genomepos_3,max_prob_3));
while (path != NULL && ((Pair_T) path->first)->genomepos > splice_genomepos_3) {
@@ -11424,36 +11630,64 @@ trim_novel_spliceends (List_T pairs,
*ambig_prob_3 = max_prob_3;
debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
}
+
+ } else if (max_prob_3_mm > END_SPLICESITE_PROB_MISMATCH) {
+ debug13(printf("Found good mismatch splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3_mm),splice_genomepos_3_mm,max_prob_3_mm));
+ while (path != NULL && ((Pair_T) path->first)->genomepos > splice_genomepos_3_mm) {
+ path = Pairpool_pop(path,&pair);
+ }
+ /* path = clean_path_end3(path); -- Gives wrong end */
+ if (path != NULL) {
+ *ambig_end_length_3 = (querylength - 1) - ((Pair_T) path->first)->querypos;
+ *ambig_splicetype_3 = splicetype3_mm;
+ *ambig_prob_3 = max_prob_3_mm;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ }
}
}
}
pairs = List_reverse(path);
- if (pairs != NULL && knownsplice5p == false && *ambig_end_length_5 == 0 &&
- exon_length_5(pairs) >= END_SPLICESITE_EXON_LENGTH) {
+ if (pairs != NULL && knownsplice5p == false && *ambig_end_length_5 == 0
+ /* && exon_length_5(pairs) >= END_SPLICESITE_EXON_LENGTH */) {
/* See if there is a good splice site at the 5' end */
debug13(Pair_dump_list(pairs,true));
pair = (Pair_T) List_head(p = pairs);
- start = end = pair->genomepos;
+ start = middle = end = pair->genomepos;
+ debug13(printf("Initializing start and end to be %u\n",start));
i = 0;
mismatchp = false;
- while (i <= END_SPLICESITE_SEARCH) {
+ while (i < trim5) {
if ((p = List_next(p)) == NULL) {
break;
+ } else if (pair->gapp == true) {
+ break;
+ } else if (pair->comp == MATCH_COMP || pair->comp == DYNPROG_MATCH_COMP || pair->comp == AMBIGUOUS_COMP) {
+ middle = pair->genomepos;
+ debug13(printf("Resetting middle to be %u\n",middle));
} else {
- pair = (Pair_T) List_head(p);
- if (pair->gapp == true) {
- break;
- } else if (pair->comp == MATCH_COMP || pair->comp == DYNPROG_MATCH_COMP || pair->comp == AMBIGUOUS_COMP) {
- end = pair->genomepos;
- i++;
- } else {
- mismatchp = true;
- i = 0;
- }
+ middle = pair->genomepos;
+ mismatchp = true;
+ debug13(printf("Resetting middle to be %u\n",middle));
}
+ pair = (Pair_T) List_head(p);
+ i++;
+ }
+
+ while (i < trim5 + END_SPLICESITE_SEARCH) {
+ if ((p = List_next(p)) == NULL) {
+ break;
+ } else if (pair->gapp == true) {
+ break;
+ } else {
+ end = pair->genomepos;
+ debug13(printf("Resetting end to be %u\n",end));
+ }
+ pair = (Pair_T) List_head(p);
+ i++;
}
if (mismatchp == false) {
@@ -11462,82 +11696,162 @@ trim_novel_spliceends (List_T pairs,
} else if (*sensedir == SENSE_FORWARD) {
if (watsonp) {
- splicetype5 = ACCEPTOR;
+ splicetype5 = splicetype5_mm = ACCEPTOR;
start_genomicpos = start;
+ middle_genomicpos = middle;
end_genomicpos = end;
assert(start_genomicpos <= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos <= end_genomicpos; genomicpos++) {
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 2 */
+ debug13(printf("5', watson, sense forward %u %u %f mm\n",chroffset+genomicpos,genomicpos,acceptor_prob));
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 2 */
- debug13(printf("5', watson, sense forward %u %f\n",genomicpos,acceptor_prob));
+ debug13(printf("5', watson, sense forward %u %u %f\n",chroffset+genomicpos,genomicpos,acceptor_prob));
if (acceptor_prob > max_prob_5) {
max_prob_5 = acceptor_prob;
splice_genomepos_5 = genomicpos;
}
+ genomicpos++;
}
+ debug13(printf("\n"));
} else {
- splicetype5 = ANTIACCEPTOR;
+ splicetype5 = splicetype5_mm = ANTIACCEPTOR;
start_genomicpos = (chrhigh - chroffset) - start + 1;
+ middle_genomicpos = (chrhigh - chroffset) - middle + 1;
end_genomicpos = (chrhigh - chroffset) - end + 1;
assert(start_genomicpos >= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos >= end_genomicpos; genomicpos--) {
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 4 */
+ debug13(printf("5', crick, sense anti %u %u %f mm\n",chroffset+genomicpos,genomicpos,acceptor_prob));
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = (chrhigh - chroffset) - genomicpos + 1;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 4 */
- debug13(printf("5', crick, sense anti %u %f\n",genomicpos,acceptor_prob));
+ debug13(printf("5', crick, sense anti %u %u %f\n",chroffset+genomicpos,genomicpos,acceptor_prob));
if (acceptor_prob > max_prob_5) {
max_prob_5 = acceptor_prob;
splice_genomepos_5 = (chrhigh - chroffset) - genomicpos + 1;
}
+ genomicpos--;
}
+ debug13(printf("\n"));
}
} else if (*sensedir == SENSE_ANTI) {
if (watsonp) {
- splicetype5 = ANTIDONOR;
+ splicetype5 = splicetype5_mm = ANTIDONOR;
start_genomicpos = start;
+ middle_genomicpos = middle;
end_genomicpos = end;
assert(start_genomicpos <= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos <= end_genomicpos; genomicpos++) {
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 6 */
+ debug13(printf("5', watson, sense anti %u %u %f mm\n",chroffset+genomicpos,genomicpos,donor_prob));
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 6 */
- debug13(printf("5', watson, sense anti %u %f\n",genomicpos,donor_prob));
+ debug13(printf("5', watson, sense anti %u %u %f\n",chroffset+genomicpos,genomicpos,donor_prob));
if (donor_prob > max_prob_5) {
max_prob_5 = donor_prob;
splice_genomepos_5 = genomicpos;
}
+ genomicpos++;
}
+ debug13(printf("\n"));
} else {
- splicetype5 = DONOR;
+ splicetype5 = splicetype5_mm = DONOR;
start_genomicpos = (chrhigh - chroffset) - start + 1;
+ middle_genomicpos = (chrhigh - chroffset) - middle + 1;
end_genomicpos = (chrhigh - chroffset) - end + 1;
assert(start_genomicpos >= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos >= end_genomicpos; genomicpos--) {
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 8 */
- debug13(printf("5', crick, sense forward %u %f\n",genomicpos,donor_prob));
+ debug13(printf("5', crick, sense forward %u %u %f mm\n",chroffset+genomicpos,genomicpos,donor_prob));
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = (chrhigh - chroffset) - genomicpos + 1;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 8 */
+ debug13(printf("5', crick, sense forward %u %u %f\n",chroffset+genomicpos,genomicpos,donor_prob));
if (donor_prob > max_prob_5) {
max_prob_5 = donor_prob;
splice_genomepos_5 = (chrhigh - chroffset) - genomicpos + 1;
}
+ genomicpos--;
}
+ debug13(printf("\n"));
}
} else {
if (watsonp) {
start_genomicpos = start;
+ middle_genomicpos = middle;
end_genomicpos = end;
assert(start_genomicpos <= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos <= end_genomicpos; genomicpos++) {
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 2 */
+ donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 6 */
+ debug13(printf("5', watson, sense null %u %u %f %f mm\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
+ if (acceptor_prob > max_prob_sense_forward_5_mm) {
+ max_prob_sense_forward_5_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ splice_cdna_direction_5_mm = +1;
+ splice_sensedir_5_mm = SENSE_FORWARD;
+ splicetype5_mm = ACCEPTOR;
+ }
+ }
+ if (donor_prob > max_prob_sense_anti_5_mm) {
+ max_prob_sense_anti_5_mm = donor_prob;
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ splice_cdna_direction_5_mm = -1;
+ splice_sensedir_5_mm = SENSE_ANTI;
+ splicetype5_mm = ANTIDONOR;
+ }
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
acceptor_prob = Maxent_hr_acceptor_prob(chroffset+genomicpos,chroffset); /* Case 2 */
donor_prob = Maxent_hr_antidonor_prob(chroffset+genomicpos,chroffset); /* Case 6 */
- debug13(printf("5', watson, sense null %u %f %f\n",genomicpos,donor_prob,acceptor_prob));
+ debug13(printf("5', watson, sense null %u %u %f %f\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
if (acceptor_prob > max_prob_sense_forward_5) {
max_prob_sense_forward_5 = acceptor_prob;
if (acceptor_prob > max_prob_5) {
@@ -11558,17 +11872,47 @@ trim_novel_spliceends (List_T pairs,
splicetype5 = ANTIDONOR;
}
}
+ genomicpos++;
}
+ debug13(printf("\n"));
} else {
start_genomicpos = (chrhigh - chroffset) - start + 1;
+ middle_genomicpos = (chrhigh - chroffset) - middle + 1;
end_genomicpos = (chrhigh - chroffset) - end + 1;
assert(start_genomicpos >= end_genomicpos);
- for (genomicpos = start_genomicpos; genomicpos >= end_genomicpos; genomicpos--) {
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 4 */
+ donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 8 */
+ debug13(printf("5', crick, sense null %u %u %f %f mm\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
+ if (acceptor_prob > max_prob_sense_forward_5_mm) {
+ max_prob_sense_forward_5_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = (chrhigh - chroffset) - genomicpos + 1;
+ splice_cdna_direction_5_mm = +1;
+ splice_sensedir_5_mm = SENSE_FORWARD;
+ splicetype5_mm = ANTIACCEPTOR;
+ }
+ }
+ if (donor_prob > max_prob_sense_anti_5_mm) {
+ max_prob_sense_anti_5_mm = donor_prob;
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = (chrhigh - chroffset) - genomicpos + 1;
+ splice_cdna_direction_5_mm = -1;
+ splice_sensedir_5_mm = SENSE_ANTI;
+ splicetype5_mm = DONOR;
+ }
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
acceptor_prob = Maxent_hr_antiacceptor_prob(chroffset+genomicpos,chroffset); /* Case 4 */
donor_prob = Maxent_hr_donor_prob(chroffset+genomicpos,chroffset); /* Case 8 */
- debug13(printf("5', crick, sense null %u %f %f\n",genomicpos,donor_prob,acceptor_prob));
+ debug13(printf("5', crick, sense null %u %u %f %f\n",chroffset+genomicpos,genomicpos,donor_prob,acceptor_prob));
if (acceptor_prob > max_prob_sense_forward_5) {
max_prob_sense_forward_5 = acceptor_prob;
if (acceptor_prob > max_prob_5) {
@@ -11589,12 +11933,14 @@ trim_novel_spliceends (List_T pairs,
splicetype5 = DONOR;
}
}
+ genomicpos--;
}
+ debug13(printf("\n"));
}
}
if (*sensedir != SENSE_NULL) {
- if (max_prob_5 > END_SPLICESITE_PROB) {
+ if (max_prob_5 > END_SPLICESITE_PROB_MATCH) {
debug13(printf("Found good splice %s on 5' end at %u with probability %f\n",
Splicetype_string(splicetype5),splice_genomepos_5,max_prob_5));
while (pairs != NULL && ((Pair_T) pairs->first)->genomepos < splice_genomepos_5) {
@@ -11607,13 +11953,99 @@ trim_novel_spliceends (List_T pairs,
*ambig_prob_5 = max_prob_5;
debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
}
+ } else if (max_prob_5_mm > END_SPLICESITE_PROB_MISMATCH) {
+ debug13(printf("Found good mismatch splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5_mm),splice_genomepos_5_mm,max_prob_5_mm));
+ while (pairs != NULL && ((Pair_T) pairs->first)->genomepos < splice_genomepos_5_mm) {
+ pairs = Pairpool_pop(pairs,&pair);
+ }
+ /* pairs = clean_pairs_end5(pairs); -- gives wrong end */
+ if (pairs != NULL) {
+ *ambig_end_length_5 = ((Pair_T) pairs->first)->querypos;
+ *ambig_splicetype_5 = splicetype5_mm;
+ *ambig_prob_5 = max_prob_5_mm;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ }
}
}
}
if (*sensedir == SENSE_NULL) {
- if (max_prob_3 > max_prob_5) {
- if (max_prob_3 >= END_SPLICESITE_PROB) {
+ if (max_prob_3 >= END_SPLICESITE_PROB_MATCH || max_prob_5 >= END_SPLICESITE_PROB_MATCH) {
+ if (max_prob_3 >= END_SPLICESITE_PROB_MATCH && max_prob_5 >= END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_5 < END_SPLICESITE_PROB_MATCH) {
+ /* Forward sense wins on both sides */
+
+ debug13(printf("Found good splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5),splice_genomepos_5,max_prob_5));
+ while (pairs != NULL && ((Pair_T) pairs->first)->genomepos < splice_genomepos_5) {
+ pairs = Pairpool_pop(pairs,&pair);
+ }
+ /* pairs = clean_pairs_end5(pairs); -- gives wrong end */
+ if (pairs != NULL) {
+ *ambig_end_length_5 = ((Pair_T) pairs->first)->querypos;
+ *ambig_splicetype_5 = splicetype5;
+ *ambig_prob_5 = max_prob_5;
+ *cdna_direction = splice_cdna_direction_5;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ }
+
+ debug13(printf("Found good splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3),splice_genomepos_3,max_prob_3));
+ path = List_reverse(pairs);
+ while (path != NULL && ((Pair_T) path->first)->genomepos > splice_genomepos_3) {
+ path = Pairpool_pop(path,&pair);
+ }
+ /* path = clean_path_end3(path); -- gives wrong end */
+ if (path != NULL) {
+ *ambig_end_length_3 = (querylength - 1) - ((Pair_T) path->first)->querypos;
+ *ambig_splicetype_3 = splicetype3;
+ *ambig_prob_3 = max_prob_3;
+ *cdna_direction = splice_cdna_direction_3;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ }
+ *sensedir = SENSE_FORWARD;
+ pairs = List_reverse(path);
+
+ } else if (max_prob_3 >= END_SPLICESITE_PROB_MATCH && max_prob_5 >= END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_5 < END_SPLICESITE_PROB_MATCH) {
+
+ /* Anti sense wins on both sides */
+ debug13(printf("Found good splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5),splice_genomepos_5,max_prob_5));
+ while (pairs != NULL && ((Pair_T) pairs->first)->genomepos < splice_genomepos_5) {
+ pairs = Pairpool_pop(pairs,&pair);
+ }
+ /* pairs = clean_pairs_end5(pairs); -- gives wrong end */
+ if (pairs != NULL) {
+ *ambig_end_length_5 = ((Pair_T) pairs->first)->querypos;
+ *ambig_splicetype_5 = splicetype5;
+ *ambig_prob_5 = max_prob_5;
+ *cdna_direction = splice_cdna_direction_5;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ }
+
+ debug13(printf("Found good splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3),splice_genomepos_3,max_prob_3));
+ path = List_reverse(pairs);
+ while (path != NULL && ((Pair_T) path->first)->genomepos > splice_genomepos_3) {
+ path = Pairpool_pop(path,&pair);
+ }
+ /* path = clean_path_end3(path); -- gives wrong end */
+ if (path != NULL) {
+ *ambig_end_length_3 = (querylength - 1) - ((Pair_T) path->first)->querypos;
+ *ambig_splicetype_3 = splicetype3;
+ *ambig_prob_3 = max_prob_3;
+ *cdna_direction = splice_cdna_direction_3;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ }
+ *sensedir = SENSE_ANTI;
+ pairs = List_reverse(path);
+
+ } else if (max_prob_3 > max_prob_5) {
+ /* Consider just 3' end */
debug13(printf("Found good splice %s on 3' end at %u with probability %f\n",
Splicetype_string(splicetype3),splice_genomepos_3,max_prob_3));
path = List_reverse(pairs);
@@ -11627,20 +12059,20 @@ trim_novel_spliceends (List_T pairs,
*ambig_prob_3 = max_prob_3;
*cdna_direction = splice_cdna_direction_3;
debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
- if (max_prob_sense_forward_3 >= END_SPLICESITE_PROB && max_prob_sense_anti_3 < END_SPLICESITE_PROB
- && max_prob_sense_anti_5 < END_SPLICESITE_PROB) {
+ if (max_prob_sense_forward_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_5 < END_SPLICESITE_PROB_MATCH) {
*sensedir = splice_sensedir_3;
- } else if (max_prob_sense_anti_3 >= END_SPLICESITE_PROB && max_prob_sense_forward_3 < END_SPLICESITE_PROB
- && max_prob_sense_forward_5 < END_SPLICESITE_PROB) {
+ } else if (max_prob_sense_anti_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_5 < END_SPLICESITE_PROB_MATCH) {
*sensedir = splice_sensedir_3;
} else {
/* Not enough evidence to set sensedir */
}
}
pairs = List_reverse(path);
- }
- } else {
- if (max_prob_5 >= END_SPLICESITE_PROB) {
+
+ } else {
+ /* Consider just 5' end */
debug13(printf("Found good splice %s on 5' end at %u with probability %f\n",
Splicetype_string(splicetype5),splice_genomepos_5,max_prob_5));
while (pairs != NULL && ((Pair_T) pairs->first)->genomepos < splice_genomepos_5) {
@@ -11653,17 +12085,68 @@ trim_novel_spliceends (List_T pairs,
*ambig_prob_5 = max_prob_5;
*cdna_direction = splice_cdna_direction_5;
debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
- if (max_prob_sense_forward_5 >= END_SPLICESITE_PROB && max_prob_sense_anti_5 < END_SPLICESITE_PROB
- && max_prob_sense_anti_3 < END_SPLICESITE_PROB) {
+ if (max_prob_sense_forward_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_5 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_3 < END_SPLICESITE_PROB_MATCH) {
*sensedir = splice_sensedir_5;
- } else if (max_prob_sense_anti_5 >= END_SPLICESITE_PROB && max_prob_sense_forward_5 < END_SPLICESITE_PROB
- && max_prob_sense_forward_3 < END_SPLICESITE_PROB) {
+ } else if (max_prob_sense_anti_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_5 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_3 < END_SPLICESITE_PROB_MATCH) {
*sensedir = splice_sensedir_5;
} else {
/* Not enough evidence to set sensedir */
}
}
}
+
+ } else if (max_prob_3_mm >= END_SPLICESITE_PROB_MISMATCH || max_prob_5_mm >= END_SPLICESITE_PROB_MISMATCH) {
+ if (max_prob_3_mm > max_prob_5_mm) {
+ debug13(printf("Found good mismatch splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3_mm),splice_genomepos_3_mm,max_prob_3_mm));
+ path = List_reverse(pairs);
+ while (path != NULL && ((Pair_T) path->first)->genomepos > splice_genomepos_3_mm) {
+ path = Pairpool_pop(path,&pair);
+ }
+ /* path = clean_path_end3(path); -- gives wrong end */
+ if (path != NULL) {
+ *ambig_end_length_3 = (querylength - 1) - ((Pair_T) path->first)->querypos;
+ *ambig_splicetype_3 = splicetype3_mm;
+ *ambig_prob_3 = max_prob_3_mm;
+ *cdna_direction = splice_cdna_direction_3_mm;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ if (max_prob_sense_forward_3_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_anti_3_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_anti_5_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_3_mm;
+ } else if (max_prob_sense_anti_3_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_forward_3_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_forward_5_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_3_mm;
+ } else {
+ /* Not enough evidence to set sensedir */
+ }
+ }
+ pairs = List_reverse(path);
+ } else {
+ debug13(printf("Found good mismatch splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5_mm),splice_genomepos_5_mm,max_prob_5_mm));
+ while (pairs != NULL && ((Pair_T) pairs->first)->genomepos < splice_genomepos_5_mm) {
+ pairs = Pairpool_pop(pairs,&pair);
+ }
+ /* pairs = clean_pairs_end5(pairs); -- gives wrong end */
+ if (pairs != NULL) {
+ *ambig_end_length_5 = ((Pair_T) pairs->first)->querypos;
+ *ambig_splicetype_5 = splicetype5_mm;
+ *ambig_prob_5 = max_prob_5_mm;
+ *cdna_direction = splice_cdna_direction_5_mm;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ if (max_prob_sense_forward_5_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_anti_5_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_anti_3_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_5_mm;
+ } else if (max_prob_sense_anti_5_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_forward_5_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_forward_3_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_5_mm;
+ } else {
+ /* Not enough evidence to set sensedir */
+ }
+ }
+ }
}
}
@@ -11673,6 +12156,9 @@ trim_novel_spliceends (List_T pairs,
+
+
+
static List_T
path_trim (double defect_rate, int *ambig_end_length_5, int *ambig_end_length_3,
Splicetype_T *ambig_splicetype_5, Splicetype_T *ambig_splicetype_3,
@@ -11820,8 +12306,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
List_T pairs_pretrim, pairs_fwd, pairs_rev, best_pairs, temp_pairs, path_fwd, path_rev, best_path, temp_path;
List_T copy;
List_T joined_ends, joined_starts;
- int ncanonical_fwd, nsemicanonical_fwd, nnoncanonical_fwd,
- ncanonical_rev, nsemicanonical_rev, nnoncanonical_rev;
+ int nknown_fwd, ncanonical_fwd, nsemicanonical_fwd, nnoncanonical_fwd,
+ nknown_rev, ncanonical_rev, nsemicanonical_rev, nnoncanonical_rev;
int nbadintrons_fwd, nbadintrons_rev;
double max_intron_score_fwd = 0.0, max_intron_score_rev = 0.0,
avg_donor_score_fwd = 0.0, avg_acceptor_score_fwd = 0.0,
@@ -11838,12 +12324,30 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
/* stage2pairs = Stage2_middle(stage2); */
- debug0(printf("Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u)\n",
- chrnum,((Pair_T) stage2pairs->first)->genomepos));
- debug(printf("Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u)\n",
- chrnum,((Pair_T) stage2pairs->first)->genomepos));
- debug(fprintf(stderr,"Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u)\n",
- chrnum,((Pair_T) stage2pairs->first)->genomepos));
+#ifdef DEBUG0
+ if (watsonp == true) {
+ printf("Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u, chrend %u, query_subseq_offset %d)\n",
+ chrnum,((Pair_T) stage2pairs->first)->genomepos,
+ ((Pair_T) List_last_value(stage2pairs))->genomepos,query_subseq_offset);
+ } else {
+ printf("Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u, chrend %u, query_subseq_offset %d)\n",
+ chrnum,(chrhigh - chroffset) - ((Pair_T) stage2pairs->first)->genomepos,
+ (chrhigh - chroffset) - ((Pair_T) List_last_value(stage2pairs))->genomepos,query_subseq_offset);
+ }
+#endif
+
+#ifdef DEBUG
+ if (watsonp == true) {
+ printf("Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u, chrend %u, query_subseq_offset %d)\n",
+ chrnum,((Pair_T) stage2pairs->first)->genomepos,
+ ((Pair_T) List_last_value(stage2pairs))->genomepos,query_subseq_offset);
+ } else {
+ printf("Stage 3: *** Starting stage 3 at chrnum #%d, chrstart %u, chrend %u, query_subseq_offset %d)\n",
+ chrnum,(chrhigh - chroffset) - ((Pair_T) stage2pairs->first)->genomepos,
+ (chrhigh - chroffset) - ((Pair_T) List_last_value(stage2pairs))->genomepos,query_subseq_offset);
+ }
+#endif
+
#ifdef PMAP
pairs_fwd = stage2pairs;
@@ -11919,7 +12423,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
path_fwd = List_reverse(pairs_fwd);
debug11(printf("Calling score_introns for path_fwd after path_compute_dir\n"));
pairs_fwd = score_introns(&max_intron_score_fwd,&avg_donor_score_fwd,&avg_acceptor_score_fwd,
- &ncanonical_fwd,&nbadintrons_fwd,path_fwd,/*cdna_direction*/+1,watsonp,
+ &nknown_fwd,&ncanonical_fwd,&nbadintrons_fwd,path_fwd,/*cdna_direction*/+1,watsonp,
chrnum,chroffset,chrhigh
#ifdef WASTE
,pairpool
@@ -11931,7 +12435,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
path_rev = List_reverse(pairs_rev);
debug11(printf("Calling score_introns for path_rev after path_compute_dir\n"));
pairs_rev = score_introns(&max_intron_score_rev,&avg_donor_score_rev,&avg_acceptor_score_rev,
- &ncanonical_rev,&nbadintrons_rev,path_rev,/*cdna_direction*/-1,watsonp,
+ &nknown_rev,&ncanonical_rev,&nbadintrons_rev,path_rev,/*cdna_direction*/-1,watsonp,
chrnum,chroffset,chrhigh
#ifdef WASTE
,pairpool
@@ -12269,7 +12773,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
path_fwd = List_reverse(pairs_fwd);
debug11(printf("Calling score_introns for path_fwd before path_trim\n"));
pairs_fwd = score_introns(&max_intron_score_fwd,&avg_donor_score_fwd,&avg_acceptor_score_fwd,
- &ncanonical_fwd,&nbadintrons_fwd,path_fwd,/*cdna_direction*/+1,watsonp,
+ &nknown_fwd,&ncanonical_fwd,&nbadintrons_fwd,path_fwd,/*cdna_direction*/+1,watsonp,
chrnum,chroffset,chrhigh
#ifdef WASTE
,pairpool
@@ -12285,7 +12789,7 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
path_rev = List_reverse(pairs_rev);
debug11(printf("Calling score_introns for path_rev before path_trim\n"));
pairs_rev = score_introns(&max_intron_score_rev,&avg_donor_score_rev,&avg_acceptor_score_rev,
- &ncanonical_rev,&nbadintrons_rev,path_rev,/*cdna_direction*/-1,watsonp,
+ &nknown_rev,&ncanonical_rev,&nbadintrons_rev,path_rev,/*cdna_direction*/-1,watsonp,
chrnum,chroffset,chrhigh
#ifdef WASTE
,pairpool
@@ -12300,8 +12804,8 @@ Stage3_compute (List_T *finalpairs, int *npairs, int *goodness, int *cdna_direct
pairs_pretrim = pick_cdna_direction(&(*cdna_direction),&(*sensedir),pairs_fwd,pairs_rev,
defect_rate_fwd,defect_rate_rev,
- ncanonical_fwd,nsemicanonical_fwd,nnoncanonical_fwd,nbadintrons_fwd,
- ncanonical_rev,nsemicanonical_rev,nnoncanonical_rev,nbadintrons_rev,
+ nknown_fwd,ncanonical_fwd,nsemicanonical_fwd,nnoncanonical_fwd,nbadintrons_fwd,
+ nknown_rev,ncanonical_rev,nsemicanonical_rev,nnoncanonical_rev,nbadintrons_rev,
max_intron_score_fwd,avg_donor_score_fwd,avg_acceptor_score_fwd,
max_intron_score_rev,avg_donor_score_rev,avg_acceptor_score_rev,
#ifdef COMPLEX_DIRECTION
@@ -13180,6 +13684,9 @@ merge_local_single (T this_left, T this_right,
static List_T
recompute_for_cdna_direction (int *cdna_direction, List_T pairs, int genestrand, bool watsonp,
+#ifdef PMAP
+ char *queryaaseq_ptr,
+#endif
char *queryseq_ptr, char *queryuc_ptr,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
@@ -13189,8 +13696,10 @@ recompute_for_cdna_direction (int *cdna_direction, List_T pairs, int genestrand,
double max_intron_score_fwd = 0.0, max_intron_score_rev = 0.0,
avg_donor_score_fwd = 0.0, avg_acceptor_score_fwd = 0.0,
avg_donor_score_rev = 0.0, avg_acceptor_score_rev = 0.0;
- int nmatches_fwd, nmismatches_fwd, nindels_fwd, ncanonical_fwd, nsemicanonical_fwd, nnoncanonical_fwd, nbadintrons_fwd,
- nmatches_rev, nmismatches_rev, nindels_rev, ncanonical_rev, nsemicanonical_rev, nnoncanonical_rev, nbadintrons_rev;
+ int nmatches_fwd, nmismatches_fwd, nindels_fwd,
+ nknown_fwd, ncanonical_fwd, nsemicanonical_fwd, nnoncanonical_fwd, nbadintrons_fwd,
+ nmatches_rev, nmismatches_rev, nindels_rev,
+ nknown_rev, ncanonical_rev, nsemicanonical_rev, nnoncanonical_rev, nbadintrons_rev;
int sensedir;
double defect_rate_fwd, defect_rate_rev;
@@ -13207,7 +13716,7 @@ recompute_for_cdna_direction (int *cdna_direction, List_T pairs, int genestrand,
maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,/*last_genomedp5*/NULL,/*last_genomedp3*/NULL,
oligoindices_minor,diagpool,cellpool);
pairs_fwd = score_introns(&max_intron_score_fwd,&avg_donor_score_fwd,&avg_acceptor_score_fwd,
- &ncanonical_fwd,&nbadintrons_fwd,path_fwd,/*cdna_direction*/+1,watsonp,
+ &nknown_fwd,&ncanonical_fwd,&nbadintrons_fwd,path_fwd,/*cdna_direction*/+1,watsonp,
chrnum,chroffset,chrhigh
#ifdef WASTE
,pairpool
@@ -13231,7 +13740,7 @@ recompute_for_cdna_direction (int *cdna_direction, List_T pairs, int genestrand,
maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,/*last_genomedp5*/NULL,/*last_genomedp3*/NULL,
oligoindices_minor,diagpool,cellpool);
pairs_rev = score_introns(&max_intron_score_rev,&avg_donor_score_rev,&avg_acceptor_score_rev,
- &ncanonical_rev,&nbadintrons_rev,path_rev,/*cdna_direction*/-1,watsonp,
+ &nknown_rev,&ncanonical_rev,&nbadintrons_rev,path_rev,/*cdna_direction*/-1,watsonp,
chrnum,chroffset,chrhigh
#ifdef WASTE
,pairpool
@@ -13246,8 +13755,8 @@ recompute_for_cdna_direction (int *cdna_direction, List_T pairs, int genestrand,
pairs = pick_cdna_direction(&(*cdna_direction),&sensedir,pairs_fwd,pairs_rev,
defect_rate_fwd,defect_rate_rev,
- ncanonical_fwd,nsemicanonical_fwd,nnoncanonical_fwd,nbadintrons_fwd,
- ncanonical_rev,nsemicanonical_rev,nnoncanonical_rev,nbadintrons_rev,
+ nknown_fwd,ncanonical_fwd,nsemicanonical_fwd,nnoncanonical_fwd,nbadintrons_fwd,
+ nknown_rev,ncanonical_rev,nsemicanonical_rev,nnoncanonical_rev,nbadintrons_rev,
max_intron_score_fwd,avg_donor_score_fwd,avg_acceptor_score_fwd,
max_intron_score_rev,avg_donor_score_rev,avg_acceptor_score_rev,
#ifdef COMPLEX_DIRECTION
@@ -13397,6 +13906,9 @@ Stage3_merge_local (T this_left, T this_right,
this_left->pairs =
recompute_for_cdna_direction(&cdna_direction,this_left->pairs,genestrand,watsonp,
+#ifdef PMAP
+ queryaaseq_ptr,
+#endif
queryseq_ptr,queryuc_ptr,
this_left->chrnum,this_left->chroffset,this_left->chrhigh,
pairpool,dynprogL,dynprogM,dynprogR,maxpeelback,
@@ -13448,6 +13960,9 @@ Stage3_merge_local (T this_left, T this_right,
this_left->pairs =
recompute_for_cdna_direction(&cdna_direction,this_left->pairs,genestrand,watsonp,
+#ifdef PMAP
+ queryaaseq_ptr,
+#endif
queryseq_ptr,queryuc_ptr,
this_left->chrnum,this_left->chroffset,this_left->chrhigh,
pairpool,dynprogL,dynprogM,dynprogR,maxpeelback,
@@ -13458,7 +13973,7 @@ Stage3_merge_local (T this_left, T this_right,
this_right->pairs = traverse_cdna_gap(&filledp,&incompletep,&dynprogindex_minor,&dynprogindex_major,
this_right->pairs,&path,leftpair,rightpair,
this_left->chroffset,this_left->chrhigh,
- queryseq_ptr,queryuc_ptr,/*querylength*/0,cdna_direction,watsonp,
+ queryseq_ptr,queryuc_ptr,/*querylength*/0,watsonp,
/*jump_late_p*/watsonp ? false : true,pairpool,
dynprogL,dynprogM,dynprogR,/*last_genomedp5*/NULL,/*last_genomedp3*/NULL,
maxpeelback,/*defect_rate*/0,/*finalp*/true);
@@ -13502,6 +14017,9 @@ Stage3_merge_local (T this_left, T this_right,
debug10(printf("Need to make dir consistent\n"));
this_left->pairs =
recompute_for_cdna_direction(&cdna_direction,this_left->pairs,genestrand,watsonp,
+#ifdef PMAP
+ queryaaseq_ptr,
+#endif
queryseq_ptr,queryuc_ptr,
this_left->chrnum,this_left->chroffset,this_left->chrhigh,
pairpool,dynprogL,dynprogM,dynprogR,maxpeelback,
diff --git a/src/stage3.h b/src/stage3.h
index 6287f0c..099a5eb 100644
--- a/src/stage3.h
+++ b/src/stage3.h
@@ -1,4 +1,4 @@
-/* $Id: stage3.h 166641 2015-05-29 21:13:04Z twu $ */
+/* $Id: stage3.h 184470 2016-02-18 00:11:42Z twu $ */
#ifndef STAGE3_INCLUDED
#define STAGE3_INCLUDED
@@ -56,7 +56,7 @@ extern void
Stage3_setup (bool splicingp_in, bool novelsplicingp_in, bool require_splicedir_p_in,
IIT_T splicesites_iit_in, int *splicesites_divint_crosstable_in,
int donor_typeint_in, int acceptor_typeint_in,
- Univcoord_T *splicesites_in,
+ Univcoord_T *splicesites_in, bool *altlocp_in, Univcoord_T *alias_starts_in, Univcoord_T *alias_ends_in,
int min_intronlength_in, int max_deletionlength_in, int min_indel_end_matches_in,
int maxpeelback_distalmedial_in, int nullgap_in,
int extramaterial_end_in, int extramaterial_paired_in,
@@ -115,6 +115,8 @@ extern void
Stage3_print_ends (T this);
extern Chrnum_T
Stage3_chrnum (T this);
+extern bool
+Stage3_altloc_chr (Univcoord_T *alias_start, Univcoord_T *alias_end, T this);
extern Chrpos_T
Stage3_chrstart (T this);
extern Chrpos_T
@@ -166,6 +168,10 @@ Stage3_overlap (T x, T y);
extern void
Stage3_compute_mapq (List_T stage3list);
extern void
+Stage3_count_paths (int *npaths_primary, int *npaths_altloc, List_T stage3list);
+extern void
+Stage3_recompute_goodness (List_T stage3list);
+extern void
Stage3_recompute_coverage (List_T stage3list, Sequence_T queryseq);
extern void
Stage3_free (T *old);
@@ -215,8 +221,8 @@ Stage3_print_gff3 (Filestring_T fp, T this, int pathnum, Univ_IIT_T chromosome_i
Sequence_T queryseq, int querylength, Printtype_T printtype, char *sourcename);
#ifndef PMAP
extern void
-Stage3_print_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths,
- int absmq_score, int first_absmq, int second_absmq, int mapq_score,
+Stage3_print_sam (Filestring_T fp, char *abbrev, T this, int pathnum, int npaths_primary, int npaths_altloc,
+ int absmq_score, int second_absmq, int mapq_score,
Univ_IIT_T chromosome_iit, Sequence_T usersegment,
Sequence_T queryseq, int chimera_part, Chimera_T chimera,
int quality_shift, bool sam_paired_p, char *sam_read_group_id);
@@ -258,11 +264,11 @@ Stage3_print_compressed (Filestring_T fp, T this, Sequence_T queryseq, Univ_IIT_
double donor_prob, double acceptor_prob, int chimera_cdna_direction);
extern T
Stage3_new (struct Pair_T *pairarray, List_T pairs, int npairs, int goodness,
- int cdna_direction, int sensedir, int stage2_source, int stage2_indexsize,
+ int cdna_direction, int sensedir,
int matches, int unknowns, int mismatches, int qopens, int qindels,
int topens, int tindels, int ncanonical, int nsemicanonical, int nnoncanonical,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
- bool watsonp, int querylength, int skiplength, int trimlength, double stage3_runtime,
+ bool watsonp, int querylength, int skiplength, int trimlength,
int straintype, char *strain, IIT_T altstrain_iit);
extern bool
diff --git a/src/stage3hr.c b/src/stage3hr.c
index 03a1e21..e9563bd 100644
--- a/src/stage3hr.c
+++ b/src/stage3hr.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: stage3hr.c 184529 2016-02-18 19:28:56Z twu $";
+static char rcsid[] = "$Id: stage3hr.c 186731 2016-03-30 23:19:01Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -21,6 +21,7 @@ static char rcsid[] = "$Id: stage3hr.c 184529 2016-02-18 19:28:56Z twu $";
#include "genome128_hr.h"
#include "mapq.h"
#include "pair.h" /* For Pair_print_gsnap and Pair_compute_mapq */
+#include "pairdef.h"
#include "comp.h" /* For Stage3end_run_gmap */
#include "maxent_hr.h"
#include "fastlog.h"
@@ -39,10 +40,14 @@ static char rcsid[] = "$Id: stage3hr.c 184529 2016-02-18 19:28:56Z twu $";
errors if first chromosome is circular. Now checking in samprint.c
whether the CIGAR string is bad. But now needed again because we
are allowing alignments that are out of bounds. However, can cause
- left to be negative, so cannot use. */
-/* #define SOFT_CLIPS_AVOID_CIRCULARIZATION 1 -- Turn off here, but on in pair.c */
+ left to be negative, so cannot use. Alignments to circular
+ chromosomes should not extend beyond the ends, because we have the
+ option of aligning across the origin. */
-#define TRANSLOC_SPECIAL 1 /* Eliminates translocations if non-translocations are found */
+#define SOFT_CLIPS_AVOID_CIRCULARIZATION 1
+
+/* Eliminates distant splices if short splices are found */
+/* #define DISTANT_SPLICE_SPECIAL 1 */
#define MAX_HITS 100000
@@ -200,6 +205,10 @@ static char rcsid[] = "$Id: stage3hr.c 184529 2016-02-18 19:28:56Z twu $";
#define MAPQ_MAXIMUM_SCORE 40
+/* Controlled by --end-detail. high (2): true/true, medium (1): false/true, low (0): false/false */
+static bool high_resolution_substring_ends_p = false; /* major performance hit, about 3x, for 5% of cases */
+static bool high_resolution_gmap_ends_p = true; /* minor performance hit */
+
static bool want_random_p;
static bool invert_first_p;
static bool invert_second_p;
@@ -216,7 +225,8 @@ static int *tally_divint_crosstable;
static IIT_T runlength_iit;
static int *runlength_divint_crosstable;
-static int pairmax;
+static int pairmax_linear;
+static int pairmax_circular;
#if 0
static int expected_pairlength;
@@ -237,9 +247,14 @@ static int gmap_min_nconsecutive;
static int ambig_end_interval; /* For penalizing large ambiguous ends
in GMAP alignments, since such ends
should have been found */
+static int subopt_levels;
static bool novelsplicingp;
+static Chrpos_T shortsplicedist;
static bool merge_samechr_p;
static bool *circularp;
+static bool *altlocp;
+static Univcoord_T *alias_starts;
+static Univcoord_T *alias_ends;
static char *failedinput_root;
static bool print_m8_p;
@@ -257,14 +272,15 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in, Genome_T genome
IIT_T genes_iit_in, int *genes_divint_crosstable_in,
IIT_T tally_iit_in, int *tally_divint_crosstable_in,
IIT_T runlength_iit_in, int *runlength_divint_crosstable_in,
- bool distances_observed_p, int pairmax_in,
+ bool distances_observed_p, int pairmax_linear_in, int pairmax_circular_in,
Chrpos_T expected_pairlength, Chrpos_T pairlength_deviation,
int localsplicing_penalty_in, int indel_penalty_middle_in,
int antistranded_penalty_in, bool favor_multiexon_p_in,
- int gmap_min_nconsecutive_in, int index1part,
- int index1interval, bool novelsplicingp_in, bool merge_samechr_p_in,
- bool *circularp_in, char *failedinput_root_in,
- bool print_m8_p_in, bool want_random_p_in) {
+ int gmap_min_nconsecutive_in, int end_detail, int subopt_levels_in,
+ bool novelsplicingp_in, Chrpos_T shortsplicedist_in, bool merge_samechr_p_in,
+ bool *circularp_in, bool *altlocp_in, Univcoord_T *alias_starts_in, Univcoord_T *alias_ends_in,
+ char *failedinput_root_in, bool print_m8_p_in, bool want_random_p_in) {
+
invert_first_p = invert_first_p_in;
invert_second_p = invert_second_p_in;
genome = genome_in;
@@ -284,7 +300,8 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in, Genome_T genome
favor_multiexon_p = favor_multiexon_p_in;
gmap_min_nconsecutive = gmap_min_nconsecutive_in;
- pairmax = pairmax_in;
+ pairmax_linear = pairmax_linear_in;
+ pairmax_circular = pairmax_circular_in;
if (pairlength_deviation > expected_pairlength) {
expected_pairlength_low = 0;
} else {
@@ -299,15 +316,34 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in, Genome_T genome
favor_ambiguous_p = true;
}
+ if (end_detail == 2) {
+ high_resolution_substring_ends_p = true;
+ high_resolution_gmap_ends_p = true;
+ } else if (end_detail == 1) {
+ high_resolution_substring_ends_p = false;
+ high_resolution_gmap_ends_p = true;
+ } else if (end_detail == 0) {
+ high_resolution_substring_ends_p = false;
+ high_resolution_gmap_ends_p = false;
+ } else {
+ fprintf(stderr,"Unexpected value %d for end_detail\n",end_detail);
+ abort();
+ }
+
#if 0
ambig_end_interval = index1part + (index1interval - 1);
#else
ambig_end_interval = 8; /* Since GMAP uses 8-mers */
#endif
+ subopt_levels = subopt_levels_in;
novelsplicingp = novelsplicingp_in;
+ shortsplicedist = shortsplicedist_in;
merge_samechr_p = merge_samechr_p_in;
circularp = circularp_in;
+ altlocp = altlocp_in;
+ alias_starts = alias_starts_in;
+ alias_ends = alias_ends_in;
failedinput_root = failedinput_root_in;
@@ -318,7 +354,7 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in, Genome_T genome
}
-
+#ifdef DEBUG0
static char *
print_sense (int sense) {
if (sense == SENSE_NULL) {
@@ -331,7 +367,7 @@ print_sense (int sense) {
abort();
}
}
-
+#endif
/* Note: Substring_T has genomiclength, but not Stage3end_T */
@@ -343,7 +379,18 @@ struct T {
GMAP_source_T gmap_source;
bool improved_by_gmap_p; /* true if GMAP alignment based on this hit is better */
- Chrnum_T chrnum; /* Needed for printing paired-end results. A chrnum of 0 indicates a distant splice. */
+ bool distant_splice_p; /* Indicates a distant splice (same
+ chromosome or different ones).
+ Used for filtering (e.g., by
+ DISTANT_SPLICE_SPECIAL) */
+
+ Chrnum_T chrnum; /* Needed for printing paired-end results. A
+ chrnum of 0 indicates a translocation (two
+ different chromosomes), or an alignment that
+ needs to be printed as a translocation
+ (samechr_splice unless --merge_samechr is
+ selected). Used for printing. */
+
Chrnum_T effective_chrnum; /* For determining concordance */
Chrnum_T other_chrnum; /* 0 for non-translocations, and other chrnum besides effective_chrnum for translocations */
Univcoord_T chroffset;
@@ -359,6 +406,7 @@ struct T {
Univcoord_T low;
Univcoord_T high;
+
Chrpos_T genomiclength;
Chrpos_T guided_insertlength; /* Used only by Stage3end_eval_and_sort_guided */
@@ -464,9 +512,11 @@ struct T {
bool paired_seenp; /* for paired-end. set to true by Stage3_pair_up(). */
bool concordantp; /* for paired-end. set to true by Stage3_pair_up(). */
- int alias; /* -1 if all below chrlength, 0 if straddles or NA (e.g., transloc), and +1 if above */
+ int circularalias; /* -1 if all below chrlength, 0 if straddles or NA (e.g., transloc), and +1 if above */
/* -2 if extends below beginning of circular chromosome, +2 if extends beyond end of second copy */
- int circularpos; /* if alias == 0, then amount of queryseq below chrlength */
+ int circularpos; /* if circularalias == 0, then amount of queryseq below chrlength */
+
+ bool altlocp;
};
@@ -520,12 +570,6 @@ struct Stage3pair_T {
-char *
-Stage3end_deletion_string (T this) {
- abort();
-}
-
-
Hittype_T
Stage3end_hittype (T this) {
return this->hittype;
@@ -586,9 +630,7 @@ Stage3end_set_improved_by_gmap (T this) {
bool
Stage3end_anomalous_splice_p (T this) {
- if (this->chrnum == 0) {
- return true;
- } else if (this->hittype == SAMECHR_SPLICE) {
+ if (this->distant_splice_p == true) {
return true;
} else {
return false;
@@ -929,7 +971,7 @@ Stage3end_substring1 (T this) {
/* Called only by samprint currently */
Substring_T
-Stage3end_substring2 (T this) {
+Stage3end_substringN (T this) {
return (Substring_T) List_head(this->substrings_Nto1);
}
@@ -1509,6 +1551,26 @@ Stage3end_trimlength (T this) {
}
+void
+Stage3end_count_hits (int *npaths_primary, int *npaths_altloc, List_T hits) {
+ T hit;
+
+ *npaths_primary = *npaths_altloc = 0;
+
+ while (hits != NULL) {
+ hit = (T) List_head(hits);
+ if (altlocp[hit->chrnum] == true) {
+ *npaths_altloc += 1;
+ } else {
+ *npaths_primary += 1;
+ }
+ hits = List_next(hits);
+ }
+
+ return;
+}
+
+
static Overlap_T
Stage3end_gene_overlap (T this) {
Overlap_T overlap;
@@ -1751,9 +1813,9 @@ Stage3end_list_free (List_T *values) {
bool
Stage3pair_anomalous_splice_p (Stage3pair_T this) {
- if (this->hit5 != NULL && (this->hit5->chrnum == 0 || this->hit5->hittype == SAMECHR_SPLICE)) {
+ if (this->hit5 != NULL && this->hit5->distant_splice_p == true) {
return true;
- } else if (this->hit3 != NULL && (this->hit3->chrnum == 0 || this->hit3->hittype == SAMECHR_SPLICE)) {
+ } else if (this->hit3 != NULL && this->hit3->distant_splice_p == true) {
return true;
} else {
return false;
@@ -1813,6 +1875,27 @@ Stage3pair_concordantp (List_T hitpairs) {
return false;
}
+void
+Stage3pair_count_hits (int *npaths_primary, int *npaths_altloc, List_T hitpairs) {
+ Stage3pair_T hitpair;
+
+ *npaths_primary = *npaths_altloc = 0;
+
+ while (hitpairs != NULL) {
+ hitpair = (Stage3pair_T) List_head(hitpairs);
+ if (altlocp[hitpair->hit5->chrnum] == true) {
+ *npaths_altloc += 1;
+ } else if (altlocp[hitpair->hit3->chrnum] == true) {
+ *npaths_altloc += 1;
+ } else {
+ *npaths_primary += 1;
+ }
+ hitpairs = List_next(hitpairs);
+ }
+
+ return;
+}
+
List_T
Stage3pair_filter_nonconcordant (List_T hitpairs) {
List_T filtered = NULL, p;
@@ -3827,12 +3910,14 @@ adjust_hardclips_left (int *shift, int hardclip_low, Stage3end_T hit_low,
int
Stage3pair_overlap (int *hardclip5_low, int *hardclip5_high, int *hardclip3_low, int *hardclip3_high, Stage3pair_T this) {
Stage3end_T hit5, hit3;
- int overlap;
int clipdir;
int ilength53, ilength35, ilength5_low, ilength5_high, ilength3_low, ilength3_high;
int common_shift, common_left, common_right;
Univcoord_T common_genomicpos, common_genomicpos_right, common_genomicpos_left;
int shift_right, shift_left;
+#ifdef DEBUG15
+ int overlap;
+#endif
*hardclip5_low = *hardclip5_high = *hardclip3_low = *hardclip3_high = 0;
@@ -4388,6 +4473,7 @@ Stage3pair_tally (Stage3pair_T this) {
#endif
+#if 0
static char complCode[128] = COMPLEMENT_LC;
static char *
@@ -4401,7 +4487,7 @@ make_complement_buffered (char *complement, char *sequence, unsigned int length)
complement[length] = '\0';
return complement;
}
-
+#endif
const Except_T Copy_Substring = { "Substring invalid during copy" };
@@ -4421,6 +4507,7 @@ Stage3end_copy (T old) {
new->gmap_source = old->gmap_source;
new->improved_by_gmap_p = old->improved_by_gmap_p;
+ new->distant_splice_p = old->distant_splice_p;
new->chrnum = old->chrnum;
new->effective_chrnum = old->effective_chrnum;
new->other_chrnum = old->other_chrnum;
@@ -4552,15 +4639,17 @@ Stage3end_copy (T old) {
new->paired_seenp = old->paired_seenp;
new->concordantp = old->concordantp;
- new->alias = old->alias;
+ new->circularalias = old->circularalias;
new->circularpos = old->circularpos;
+ new->altlocp = old->altlocp;
+
return new;
}
static int
-compute_circularpos (int *alias, T hit) {
+compute_circularpos (int *circularalias, T hit) {
int circularpos;
List_T p;
Substring_T substring;
@@ -4572,44 +4661,50 @@ compute_circularpos (int *alias, T hit) {
if (circularp[hit->chrnum] == false) {
debug12(printf("Chromosome #%d is not circular\n",hit->chrnum));
/* This also handles hit->chrnum == 0, where translocation cannot be circular */
- *alias = 0;
+ *circularalias = 0;
return -1;
} else if (hit->hittype == GMAP) {
- debug12(printf("Pair circularpos is %d\n",Pair_circularpos(&(*alias),hit->pairarray,hit->npairs,hit->chrlength,
+ debug12(printf("Pair circularpos is %d\n",Pair_circularpos(&(*circularalias),hit->pairarray,hit->npairs,hit->chrlength,
hit->plusp,hit->querylength)));
- return Pair_circularpos(&(*alias),hit->pairarray,hit->npairs,hit->chrlength,
+ return Pair_circularpos(&(*circularalias),hit->pairarray,hit->npairs,hit->chrlength,
hit->plusp,hit->querylength);
} else if (hit->plusp == true) {
- if (hit->low >= hit->chroffset + hit->chrlength) {
- /* hit->low + hit->trim_left >= hit->chroffset + hit->chrlength (SOFT_CLIPS_AVOID_CIRCULARIZATION) */
- /* hit->low >= hit->chroffset + hit->chrlength */
+ debug12(printf("plus: Comparing low %u with chroffset %u + chrlength %u\n",hit->low,hit->chroffset,hit->chrlength));
+ debug12(printf("plus: Comparing high %u with chroffset %u + chrlength %u\n",hit->high,hit->chroffset,hit->chrlength));
+ if (hit->low
+#ifdef SOFT_CLIPS_AVOID_CIRCULARIZATION
+ + hit->trim_left
+#endif
+ >= hit->chroffset + hit->chrlength) {
- /* All of read after trimming is in circular alias */
+ /* All of read after trimming is in one copy */
debug12(printf("Soft clip of %d on left avoids circularization\n",hit->trim_left));
if (hit->high >= hit->chrhigh) {
- *alias = +2;
+ *circularalias = +2; /* Extends beyond end of second copy */
} else {
- *alias = +1;
+ *circularalias = +1; /* All of read is in second copy */
}
return -1;
- } else if (hit->high < hit->chroffset + hit->chrlength) {
- /* hit->high - hit->trim_right <= hit->chroffset + hit->chrlength (SOFT_CLIPS_AVOID_CIRCULARIZATION) */
- /* hit->high <= hit->chroffset + hit->chrlength */
+ } else if (hit->high
+#ifdef SOFT_CLIPS_AVOID_CIRCULARIZATION
+ - hit->trim_right
+#endif
+ < hit->chroffset + hit->chrlength) {
- /* All of read after trimming is in circular proper */
+ /* All of read after trimming is in one copy */
debug12(printf("Soft clip of %d on right avoids circularization\n",hit->trim_right));
if (hit->low < hit->chroffset) {
- *alias = -2;
+ *circularalias = -2; /* Extends beyond beginning of first copy */
} else {
- *alias = -1;
+ *circularalias = -1; /* All of read is in first copy */
}
return -1;
} else {
- *alias = 0;
+ *circularalias = 0;
for (p = hit->substrings_1toN; p != NULL; p = List_next(p)) {
substring = (Substring_T) List_head(p);
if ((circularpos = Substring_circularpos(substring)) > 0) {
@@ -4622,36 +4717,40 @@ compute_circularpos (int *alias, T hit) {
} else {
/* Without SOFT_CLIPS_AVOID_CIRCULARIZATION, the branches are similar for plus/minus hits */
- if (hit->low >= hit->chroffset + hit->chrlength) {
- /* hit->low + hit->trim_right >= hit->chroffset + hit->chrlength (SOFT_CLIPS_AVOID_CIRCULARIZATION) */
- /* hit->low >= hit->chroffset + hit->chrlength */
+ if (hit->low
+#ifdef SOFT_CLIPS_AVOID_CIRCULARIZATION
+ + hit->trim_right
+#endif
+ >= hit->chroffset + hit->chrlength) {
/* All of read after trimming is in circular alias */
debug12(printf("Soft clip of %d on right avoids circularization\n",hit->trim_right));
debug12(printf("All of read after trimming is in circular alias\n"));
if (hit->high >= hit->chrhigh) {
- *alias = +2;
+ *circularalias = +2; /* Extends beyond end of second copy */
} else {
- *alias = +1;
+ *circularalias = +1; /* All of read is in second copy */
}
return -1;
- } else if (hit->high < hit->chroffset + hit->chrlength) {
- /* hit->high - hit->trim_left <= hit->chroffset + hit->chrlength (SOFT_CLIPS_AVOID_CIRCULARIZATION) */
- /* hit->high <= hit->chroffset + hit->chrlength */
+ } else if (hit->high
+#ifdef SOFT_CLIPS_AVOID_CIRCULARIZATION
+ - hit->trim_left
+#endif
+ < hit->chroffset + hit->chrlength) {
/* All of read after trimming is in circular proper */
debug12(printf("Soft clip of %d on left avoids circularization\n",hit->trim_left));
debug12(printf("All of read after trimming is in circular proper\n"));
if (hit->low < hit->chroffset) {
- *alias = -2;
+ *circularalias = -2; /* Extends beyond beginning of first copy */
} else {
- *alias = -1;
+ *circularalias = -1; /* All of read is in first copy */
}
return -1;
} else {
- *alias = 0;
+ *circularalias = 0;
for (p = hit->substrings_Nto1; p != NULL; p = List_next(p)) {
substring = (Substring_T) List_head(p);
if ((circularpos = Substring_circularpos(substring)) > 0) {
@@ -4675,13 +4774,13 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
Intlist_T nmismatches_list, List_T junctions, int querylength,
Compress_T query_compress,
Substring_T right_ambig, Substring_T left_ambig,
- bool plusp, int genestrand, int sensedir, bool first_read_p,
+ bool plusp, int genestrand, int sensedir,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Chrpos_T chrlength, bool sarrayp) {
T new;
- Univcoord_T genomicstart, genomicend, genomicstart_adj, genomicend_adj,
- alignstart, alignend, alignstart_trim, alignend_trim;
+ Univcoord_T genomicstart, genomicend, alignstart, alignend;
+ /* Univcoord_T genomicstart_adj, genomicend_adj; */
int querylength_trimmed = 0;
int querystart, queryend;
Univcoord_T left;
@@ -4692,18 +4791,17 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
Uintlist_T q;
#endif
Substring_T substring, substring1, substringN;
- Junction_T junction, junction_ambig = NULL;
- Junctiontype_T type;
+ Junction_T junction;
List_T substrings = NULL, p, j;
- bool trim_left_p = false, trim_right_p = false;
+ Trimaction_T trim_left_action = NO_TRIM, trim_right_action = NO_TRIM;
int outofbounds_start = 0, outofbounds_end = 0;
int adj = 0, adj0; /* deletions - insertions */
int nmismatches_whole = 0, nmismatches, indel_score = 0, nindels = 0;
int nmismatches_bothdiff = 0;
- debug0(printf("%s read: Entered Stage3end_new_substrings at left %u, with plusp %d, sensedir %d, and endpoints %s\n",
- first_read_p ? "First" : "Second",Uintlist_head(lefts),plusp,sensedir,Intlist_to_string(endpoints)));
+ debug0(printf("Entered Stage3end_new_substrings at left %u, with plusp %d, sensedir %d, and endpoints %s\n",
+ Uintlist_head(lefts),plusp,sensedir,Intlist_to_string(endpoints)));
debug0(printf("There are %d endpoints, %d lefts, %d nmismatches, and %d junctions\n",
Intlist_length(endpoints),Uintlist_length(lefts),Intlist_length(nmismatches_list),List_length(junctions)));
debug0(printf("Ambig left %p, right %p\n",left_ambig,right_ambig));
@@ -4711,7 +4809,11 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
debug0(printf("Lefts: %s\n",Uintlist_to_string(lefts)));
debug0(printf("Mismatches: %s\n",Intlist_to_string(nmismatches_list)));
+#ifdef LARGE_GENOMES
+ assert(Uint8list_length(lefts) == Intlist_length(endpoints) - 1);
+#else
assert(Uintlist_length(lefts) == Intlist_length(endpoints) - 1);
+#endif
assert(Intlist_length(nmismatches_list) == Intlist_length(endpoints) - 1);
assert(List_length(junctions) == Intlist_length(endpoints) - 2);
@@ -4732,7 +4834,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
Substring_amb_donor_prob(left_ambig),
Substring_amb_acceptor_prob(left_ambig)));
} else {
- trim_left_p = true;
+ trim_left_action = COMPUTE_TRIM;
}
/* Add querypos to get alignstart/alignend */
@@ -4753,8 +4855,8 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
genomicstart = left;
genomicend = left + querylength;
- genomicstart_adj = genomicstart + adj;
- genomicend_adj = genomicend + adj;
+ /* genomicstart_adj = genomicstart + adj; */
+ /* genomicend_adj = genomicend + adj; */
alignstart = genomicstart + querystart;
alignend = genomicstart + queryend;
@@ -4808,27 +4910,26 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
if ((nmismatches = Intlist_head(x)) < 0) {
nmismatches = Genome_count_mismatches_substring(query_compress,left,/*pos5*/querystart,/*pos3*/queryend,
- /*plusp*/true,genestrand,first_read_p);
+ /*plusp*/true,genestrand);
debug0(printf("nmismatches %d from genome\n",nmismatches));
}
nmismatches_whole += nmismatches;
debug0(printf("nmismatches %d from sarray\n",nmismatches));
#ifdef LARGE_GENOMES
if (Uint8list_next(q) == NULL && right_ambig == NULL) {
- trim_right_p = true;
+ trim_right_action = COMPUTE_TRIM;
}
#else
if (Uintlist_next(q) == NULL && right_ambig == NULL) {
- trim_right_p = true;
+ trim_right_action = COMPUTE_TRIM;
}
#endif
if ((substring = Substring_new(/*nmismatches_whole*/nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,/*start_endtype*/END,/*end_endtype*/END,
querystart,queryend,querylength,alignstart,alignend,
- /*genomiclength*/querylength,
- /*exactp*/Intlist_head(x) == 0 ? true : false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,outofbounds_start,outofbounds_end,
- /*minlength*/0)) == NULL) {
+ /*exactp*/Intlist_head(x) == 0 ? true : false,plusp,genestrand,
+ trim_left_action,trim_right_action,outofbounds_start,outofbounds_end,
+ /*minlength*/0,sensedir)) == NULL) {
/* Don't know how to fix the junctions */
debug0(printf("Don't know how to fix the junctions, so returning NULL from Stage3end_new_substrings\n"));
for (p = substrings; p != NULL; p = List_next(p)) {
@@ -4847,7 +4948,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
} else {
substrings = List_push(substrings,(void *) substring);
nmismatches_bothdiff += Substring_nmismatches_bothdiff(substring);
- querylength_trimmed += Substring_querylength(substring);
+ querylength_trimmed += Substring_match_length(substring);
}
/* Prepare for next iteration */
@@ -4863,7 +4964,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
}
}
}
- trim_left_p = false;
+ trim_left_action = NO_TRIM;
}
} else {
@@ -4874,7 +4975,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
Substring_amb_donor_prob(left_ambig),
Substring_amb_acceptor_prob(left_ambig)));
} else {
- trim_right_p = true;
+ trim_right_action = COMPUTE_TRIM;
}
/* Subtract querypos to get alignstart/alignend */
@@ -4895,8 +4996,8 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
genomicend = left;
genomicstart = left + querylength;
- genomicend_adj = genomicend - adj;
- genomicstart_adj = genomicend - adj;
+ /* genomicend_adj = genomicend - adj; */
+ /* genomicstart_adj = genomicend - adj; */
alignstart = genomicstart - (querylength - queryend);
alignend = genomicstart - (querylength - querystart);
@@ -4949,27 +5050,27 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
if ((nmismatches = Intlist_head(x)) < 0) {
nmismatches = Genome_count_mismatches_substring(query_compress,left,/*pos5*/querystart,/*pos3*/queryend,
- /*plusp*/false,genestrand,first_read_p);
+ /*plusp*/false,genestrand);
debug0(printf("nmismatches %d from genome\n",nmismatches));
}
nmismatches_whole += nmismatches;
debug0(printf("nmismatches %d from sarray\n",nmismatches));
#ifdef LARGE_GENOMES
if (Uint8list_next(q) == NULL && right_ambig == NULL) {
- trim_left_p = true;
+ trim_left_action = COMPUTE_TRIM;
}
#else
if (Uintlist_next(q) == NULL && right_ambig == NULL) {
- trim_left_p = true;
+ trim_left_action = COMPUTE_TRIM;
}
#endif
if ((substring = Substring_new(/*nmismatches_whole*/nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,/*start_endtype*/END,/*end_endtype*/END,
/*querystart*/querylength - queryend,/*queryend*/querylength - querystart,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/Intlist_head(x) == 0 ? true : false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,outofbounds_start,outofbounds_end,
- /*minlength*/0)) == NULL) {
+ alignstart,alignend,
+ /*exactp*/Intlist_head(x) == 0 ? true : false,plusp,genestrand,
+ trim_left_action,trim_right_action,outofbounds_start,outofbounds_end,
+ /*minlength*/0,sensedir)) == NULL) {
/* Don't know how to fix the junctions */
debug0(printf("Don't know how to fix the junctions, so returning NULL from Stage3end_new_substrings\n"));
for (p = substrings; p != NULL; p = List_next(p)) {
@@ -4988,7 +5089,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
} else {
substrings = List_push(substrings,(void *) substring);
nmismatches_bothdiff += Substring_nmismatches_bothdiff(substring);
- querylength_trimmed += Substring_querylength(substring);
+ querylength_trimmed += Substring_match_length(substring);
}
/* Prepare for next iteration */
@@ -5004,7 +5105,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
}
}
}
- trim_right_p = false;
+ trim_right_action = NO_TRIM;
}
}
@@ -5073,7 +5174,8 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
printf("NEW SUBSTRINGS\n");
for (p = new->substrings_1toN; p != NULL; p = List_next(p)) {
substring = List_head(p);
- printf("%d..%d\n",Substring_querystart(substring),Substring_queryend(substring));
+ printf("%d..%d\t%u..%u\n",Substring_querystart(substring),Substring_queryend(substring),
+ Substring_alignstart_trim_chr(substring),Substring_alignend_trim_chr(substring));
}
printf("\n");
#endif
@@ -5102,6 +5204,7 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -5131,7 +5234,9 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
/* new->gene_overlap = NO_KNOWN_GENE; -- initialized later when resolving multimappers */
new->tally = -1L;
- *found_score = new->score;
+ if (new->score < *found_score) {
+ *found_score = new->score;
+ }
new->nsplices = 0;
for (p = junctions; p != NULL; p = List_next(p)) {
@@ -5148,14 +5253,24 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
- debug0(printf("Returning NULL from Stage3end_new_substrings because of alias of %d\n",new->alias));
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
+ debug0(printf("Returning NULL from Stage3end_new_substrings because of circularalias of %d\n",new->circularalias));
Stage3end_free(&new);
/* Junction_gc(&junctions); -- Done by Stage3end_free */
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ debug0(printf("Returning circular %p from Stage3end_new_substrings with found_score %d\n",new,*found_score));
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ debug0(printf("Returning primary %p from Stage3end_new_substrings with found_score %d\n",new,*found_score));
+ return new;
+
} else {
- debug0(printf("Returning %p from Stage3end_new_substrings with found_score %d\n",new,*found_score));
+ debug0(printf("Returning altloc %p from Stage3end_new_substrings with found_score %d\n",new,*found_score));
return new;
}
}
@@ -5166,11 +5281,12 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
/* Modified from run_gmap_plus in sarray-read.c */
+/* extend_ends_p is an expensive operation, slowing down speed by 5x */
T
-Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
- int genestrand, bool first_read_p,
+Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength, int genestrand,
int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool) {
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool extend_ends_p) {
T hit;
List_T stage2pairs, all_stage2_starts, all_stage2_ends;
List_T p, startp;
@@ -5199,6 +5315,7 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
int nsegments, nmismatches_whole, nindels, nintrons, nindelbreaks;
char *gsequence_orig, *gsequence_alt;
+ Chrpos_T chrstart, chrend;
debug13(printf("Entered Stage3hr_substrings_run_gmap_plus\n"));
@@ -5227,7 +5344,6 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
/* D. Make all_stage2_starts (paths) */
- all_stage2_starts = (List_T) NULL;
if (first_ambig != NULL) {
debug13(printf("Handling first ambig\n"));
querystart = Substring_querystart(first_ambig);
@@ -5235,6 +5351,7 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
seglength = queryend - querystart;
ambcoords = Substring_ambcoords(first_ambig);
+ all_stage2_starts = (List_T) NULL;
for (k = 0; k < Substring_nambcoords(first_ambig); k++) {
debug13(printf("START, PLUS\n"));
stage2pairs = (List_T) NULL;
@@ -5261,11 +5378,45 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
debug13(Pair_dump_list(stage2pairs,true));
all_stage2_starts = List_push(all_stage2_starts,(void *) stage2pairs);
}
+
+ } else if (extend_ends_p == false) {
+ all_stage2_starts = (List_T) NULL;
+
+ } else {
+ substring = (Substring_T) List_head(this->substrings_1toN);
+ if (high_resolution_substring_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_starts = (List_T) NULL;
+ } else if ((querypos = Substring_querystart(substring)) < 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ debug13(printf("No starts, since querystart %d < 15\n",querypos));
+ all_stage2_starts = (List_T) NULL;
+ } else {
+ chrend = Substring_alignstart_trim_chr(substring);
+ if (chrend < shortsplicedist) {
+ chrstart = 0;
+ } else {
+ chrstart = chrend - shortsplicedist;
+ }
+ all_stage2_starts = Stage2_compute_starts(
+#ifdef PMAP
+ &(queryaaseq_ptr[0]),&(queryaaseq_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0*3,
+#else
+ &(queryuc_ptr[0]),&(queryuc_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/true,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d starts\n",List_length(all_stage2_starts)));
+ }
}
/* E. Make all_stage2_ends (pairs) */
- all_stage2_ends = (List_T) NULL;
if (last_ambig != NULL) {
debug13(printf("Handling last ambig\n"));
querystart = Substring_querystart(last_ambig);
@@ -5273,6 +5424,7 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
seglength = queryend - querystart;
ambcoords = Substring_ambcoords(last_ambig);
+ all_stage2_ends = (List_T) NULL;
for (k = 0; k < Substring_nambcoords(last_ambig); k++) {
debug13(printf("END, PLUS\n"));
stage2pairs = (List_T) NULL;
@@ -5300,97 +5452,141 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
debug13(Pair_dump_list(stage2pairs,true));
all_stage2_ends = List_push(all_stage2_ends,(void *) List_reverse(stage2pairs));
}
- }
- /* F. Make stage2pairs */
- stage2pairs = (List_T) NULL;
- for (p = startp; p != NULL; p = List_next(p)) {
- substring = (Substring_T) List_head(p);
- if (Substring_ambiguous_p(substring) == true) {
- /* Skip */
- } else {
- debug13(printf("Handling substring for %d..%d, %u..%u, chrlength %u\n",
- Substring_querystart(substring),Substring_queryend(substring),
- Substring_alignstart_trim_chr(substring),Substring_alignend_trim_chr(substring),
- this->chrlength));
- querypos = Substring_querystart(substring);
- seglength = Substring_queryend(substring) - querypos;
-
- genomepos = Substring_alignstart_trim_chr(substring);
- Genome_get_segment_blocks_right(gsequence_orig,gsequence_alt,/*left*/Substring_alignstart_trim(substring),
- seglength,this->chrhigh,/*revcomp*/false);
+ } else if (extend_ends_p == false) {
+ all_stage2_ends = (List_T) NULL;
- for (i = 0; i < seglength; i++) {
- c = queryuc_ptr[querypos];
- g = gsequence_orig[i];
- g_alt = gsequence_alt[i];
- if (g == c || g_alt == c) {
- comp = MATCH_COMP;
- } else {
- comp = MISMATCH_COMP;
- }
- debug13(printf("Pushing %c %c %c at %d,%u\n",c,comp,g,querypos,genomepos));
- stage2pairs = Pairpool_push(stage2pairs,pairpool,querypos,genomepos,
- /*cdna*/c,comp,/*genome*/g,/*genomealt*/g_alt,
- /*dynprogindex*/0);
- querypos++;
- genomepos++;
+ } else {
+ substring = (Substring_T) List_head(this->substrings_Nto1);
+ if (high_resolution_substring_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_ends = (List_T) NULL;
+ } else if ((querypos = Substring_queryend(substring)) > querylength - 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ debug13(printf("No ends, since queryend %d > querylength %d - 15\n",querypos,querylength));
+ all_stage2_ends = (List_T) NULL;
+ } else {
+ chrstart = Substring_alignend_trim_chr(substring);
+ if (chrstart + shortsplicedist > (this->chrhigh - this->chroffset)) {
+ chrend = this->chrhigh - this->chroffset;
+ } else {
+ chrend = chrstart + shortsplicedist;
}
- debug13(Pair_dump_list(stage2pairs,true));
- debug13(printf("\n"));
+ all_stage2_ends = Stage2_compute_ends(
+#ifdef PMAP
+ &(queryaaseq_ptr[querypos]),&(queryaaseq_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos*3,
+#else
+ &(queryuc_ptr[querypos]),&(queryuc_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/true,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d ends\n",List_length(all_stage2_ends)));
}
}
- if (stage2pairs == NULL) {
+
+ /* Get better results if we turn off this branch, because GMAP finds
+ indels at ends, so do re-run GMAP in all cases */
+ if (high_resolution_substring_ends_p == false && extend_ends_p == true && all_stage2_starts == NULL && all_stage2_ends == NULL) {
+ /* Don't run re-run GMAP on central portion. Just rely on substrings. */
hit = (T) NULL;
+
} else {
- knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
- stage2pairs = List_reverse(stage2pairs);
- knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
-
- if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
- &matches,&nmatches_posttrim,&max_match_length,
- &ambig_end_length_5,&ambig_end_length_3,
- &ambig_splicetype_5,&ambig_splicetype_3,
- &ambig_prob_5,&ambig_prob_3,
- &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
- &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
- stage2pairs,all_stage2_starts,all_stage2_ends,
+ /* F. Make stage2pairs */
+ stage2pairs = (List_T) NULL;
+ for (p = startp; p != NULL; p = List_next(p)) {
+ substring = (Substring_T) List_head(p);
+ if (Substring_ambiguous_p(substring) == true) {
+ /* Skip */
+ } else {
+ debug13(printf("Handling substring for %d..%d, %u..%u, chrlength %u\n",
+ Substring_querystart(substring),Substring_queryend(substring),
+ Substring_alignstart_trim_chr(substring),Substring_alignend_trim_chr(substring),
+ this->chrlength));
+ querypos = Substring_querystart(substring);
+ seglength = Substring_queryend(substring) - querypos;
+
+ genomepos = Substring_alignstart_trim_chr(substring);
+ Genome_get_segment_blocks_right(gsequence_orig,gsequence_alt,/*left*/Substring_alignstart_trim(substring),
+ seglength,this->chrhigh,/*revcomp*/false);
+
+ for (i = 0; i < seglength; i++) {
+ c = queryuc_ptr[querypos];
+ g = gsequence_orig[i];
+ g_alt = gsequence_alt[i];
+ if (g == c || g_alt == c) {
+ comp = MATCH_COMP;
+ } else {
+ comp = MISMATCH_COMP;
+ }
+ debug13(printf("Pushing %c %c %c at %d,%u\n",c,comp,g,querypos,genomepos));
+ stage2pairs = Pairpool_push(stage2pairs,pairpool,querypos,genomepos,
+ /*cdna*/c,comp,/*genome*/g,/*genomealt*/g_alt,
+ /*dynprogindex*/0);
+ querypos++;
+ genomepos++;
+ }
+ debug13(Pair_dump_list(stage2pairs,true));
+ debug13(printf("\n"));
+ }
+ }
+
+ if (stage2pairs == NULL) {
+ hit = (T) NULL;
+ } else {
+ knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ stage2pairs = List_reverse(stage2pairs);
+ knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+
+ if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
+ &matches,&nmatches_posttrim,&max_match_length,
+ &ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,
+ &ambig_prob_5,&ambig_prob_3,
+ &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
+ &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
+ stage2pairs,all_stage2_starts,all_stage2_ends,
#ifdef END_KNOWNSPLICING_SHORTCUT
- cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
- watsonp ? query_compress_fwd : query_compress_rev,
+ cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
+ watsonp ? query_compress_fwd : query_compress_rev,
#endif
- /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
+ /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
#ifdef EXTRACT_GENOMICSEG
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#else
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#endif
- this->chrnum,this->chroffset,this->chrhigh,
- knownsplice_limit_low,knownsplice_limit_high,/*plusp*/true,genestrand,
- /*jump_late_p*/false,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
- /*sense_try*/0,/*sense_filter*/0,
- oligoindices_minor,diagpool,cellpool)) == NULL) {
- hit = (T) NULL;
-
- } else {
- nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
- pairarray,npairs);
- start = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
- /*minusterm*/Pair_querypos(&(pairarray[0])),this->chroffset);
- end = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
- /*plusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chrhigh);
+ this->chrnum,this->chroffset,this->chrhigh,
+ knownsplice_limit_low,knownsplice_limit_high,/*plusp*/true,genestrand,
+ /*jump_late_p*/false,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ /*sense_try*/0,/*sense_filter*/0,
+ oligoindices_minor,diagpool,cellpool)) == NULL) {
+ hit = (T) NULL;
- if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
- ambig_end_length_5,ambig_end_length_3,
- ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
- pairarray,npairs,nsegments,nintrons,nindelbreaks,
- /*left*/start,/*genomiclength*/end - start + 1,
- /*plusp*/true,genestrand,first_read_p,
- /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
- cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
- FREE_OUT(pairarray);
+ } else {
+ nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
+ pairarray,npairs);
+ start = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
+ /*minusterm*/Pair_querypos(&(pairarray[0])),this->chroffset);
+ end = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
+ /*plusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chrhigh);
+
+ if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
+ ambig_end_length_5,ambig_end_length_3,
+ ambig_splicetype_5,ambig_splicetype_3,
+ min_splice_prob,
+ pairarray,npairs,nsegments,nintrons,nindelbreaks,
+ /*left*/start,/*genomiclength*/end - start + 1,
+ /*plusp*/true,genestrand,
+ /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
+ cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
+ FREE_OUT(pairarray);
+ }
}
}
}
@@ -5411,11 +5607,12 @@ Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
/* Modified from run_gmap_minus in sarray-read.c */
+/* extend_ends_p is an expensive operation, slowing down speed by 5x */
T
-Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
- int genestrand, bool first_read_p,
+Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength, int genestrand,
int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool) {
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool extend_ends_p) {
T hit;
List_T stage2pairs, all_stage2_starts, all_stage2_ends;
List_T p, startp;
@@ -5442,9 +5639,10 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
Univcoord_T knownsplice_limit_low, knownsplice_limit_high;
Univcoord_T start, end;
int nsegments, nmismatches_whole, nindels, nintrons, nindelbreaks;
-
char *gsequence_orig, *gsequence_alt;
+ Chrpos_T chrstart, chrend;
+
debug13(printf("Entered Stage3hr_substrings_run_gmap_minus\n"));
#ifdef HAVE_ALLOCA
@@ -5472,7 +5670,6 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
/* D. Make all_stage2_starts (paths) */
- all_stage2_starts = (List_T) NULL;
if (first_ambig != NULL) {
debug13(printf("Handling first ambig\n"));
querystart = Substring_querystart(first_ambig);
@@ -5480,6 +5677,7 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
seglength = queryend - querystart;
ambcoords = Substring_ambcoords(first_ambig);
+ all_stage2_starts = (List_T) NULL;
for (k = 0; k < Substring_nambcoords(first_ambig); k++) {
debug13(printf("START, MINUS\n"));
stage2pairs = (List_T) NULL;
@@ -5507,11 +5705,45 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
debug13(Pair_dump_list(stage2pairs,true));
all_stage2_starts = List_push(all_stage2_starts,(void *) stage2pairs);
}
+
+ } else if (extend_ends_p == false) {
+ all_stage2_starts = (List_T) NULL;
+
+ } else {
+ substring = (Substring_T) List_head(this->substrings_1toN);
+ if (high_resolution_substring_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_starts = (List_T) NULL;
+ } else if ((querypos = Substring_querystart(substring)) < 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ debug13(printf("No starts, since querystart %d < 15\n",querypos));
+ all_stage2_starts = (List_T) NULL;
+ } else {
+ chrstart = Substring_alignstart_trim_chr(substring);
+ if (chrstart + shortsplicedist > (this->chrhigh - this->chroffset)) {
+ chrend = this->chrhigh - this->chroffset;
+ } else {
+ chrend = chrstart + shortsplicedist;
+ }
+ all_stage2_starts = Stage2_compute_starts(
+#ifdef PMAP
+ &(queryaaseq_ptr[0]),&(queryaaseq_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0*3,
+#else
+ &(queryuc_ptr[0]),&(queryuc_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/false,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d starts\n",List_length(all_stage2_starts)));
+ }
}
/* E. Make all_stage2_ends (pairs) */
- all_stage2_ends = (List_T) NULL;
if (last_ambig != NULL) {
debug13(printf("Handling last ambig\n"));
querystart = Substring_querystart(last_ambig);
@@ -5519,6 +5751,7 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
seglength = queryend - querystart;
ambcoords = Substring_ambcoords(last_ambig);
+ all_stage2_ends = (List_T) NULL;
for (k = 0; k < Substring_nambcoords(last_ambig); k++) {
debug13(printf("END, MINUS\n"));
stage2pairs = (List_T) NULL;
@@ -5546,100 +5779,144 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
debug13(Pair_dump_list(stage2pairs,true));
all_stage2_ends = List_push(all_stage2_ends,(void *) List_reverse(stage2pairs));
}
- }
- /* F. Make stage2pairs */
- stage2pairs = (List_T) NULL;
- for (p = startp; p != NULL; p = List_next(p)) {
- substring = (Substring_T) List_head(p);
- if (Substring_ambiguous_p(substring) == true) {
- /* Skip */
- } else {
- debug13(printf("Handling substring for %d..%d, %u..%u, chrlength %u\n",
- Substring_querystart(substring),Substring_queryend(substring),
- Substring_alignstart_trim_chr(substring),Substring_alignend_trim_chr(substring),
- this->chrlength));
- querypos = Substring_querystart(substring);
- seglength = Substring_queryend(substring) - querypos;
-
- /* Don't understand why it isn't this->chrhigh - 1, but it
- looks like the minus coordinates for substrings are +1 higher
- than they should be */
- genomepos = (this->chrhigh + 1) - Substring_alignstart_trim(substring);
- Genome_get_segment_blocks_right(gsequence_orig,gsequence_alt,/*left*/Substring_alignend_trim(substring),
- seglength,this->chrhigh,/*revcomp*/true);
+ } else if (extend_ends_p == false) {
+ all_stage2_ends = (List_T) NULL;
- for (i = 0; i < seglength; i++) {
- c = queryuc_ptr[querypos];
- g = gsequence_orig[i];
- g_alt = gsequence_alt[i];
- if (g == c || g_alt == c) {
- comp = MATCH_COMP;
- } else {
- comp = MISMATCH_COMP;
- }
- debug13(printf("Pushing %c %c %c at %d,%u\n",c,comp,g,querypos,genomepos));
- stage2pairs = Pairpool_push(stage2pairs,pairpool,querypos,genomepos,
- /*cdna*/c,comp,/*genome*/g,/*genomealt*/g_alt,
- /*dynprogindex*/0);
- querypos++;
- genomepos++;
+ } else {
+ substring = (Substring_T) List_head(this->substrings_Nto1);
+ if (high_resolution_substring_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_ends = (List_T) NULL;
+ } else if ((querypos = Substring_queryend(substring)) > querylength - 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ debug13(printf("No ends, since queryend %d > querylength %d - 15\n",querypos,querylength));
+ all_stage2_ends = (List_T) NULL;
+ } else {
+ chrend = Substring_alignend_trim_chr(substring);
+ if (chrend < shortsplicedist) {
+ chrstart = 0;
+ } else {
+ chrstart = chrend - shortsplicedist;
}
- debug13(Pair_dump_list(stage2pairs,true));
- debug13(printf("\n"));
+ all_stage2_ends = Stage2_compute_ends(
+#ifdef PMAP
+ &(queryaaseq_ptr[querypos]),&(queryaaseq_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos*3,
+#else
+ &(queryuc_ptr[querypos]),&(queryuc_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/false,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d ends\n",List_length(all_stage2_ends)));
}
}
- if (stage2pairs == NULL) {
+
+ /* Get better results if we turn off this branch, because GMAP finds
+ indels at ends, so do re-run GMAP in all cases */
+ if (high_resolution_substring_ends_p == false && extend_ends_p == true && all_stage2_starts == NULL && all_stage2_ends == NULL) {
+ /* Don't run re-run GMAP on central portion. Just rely on substrings. */
hit = (T) NULL;
+
} else {
- knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
- stage2pairs = List_reverse(stage2pairs);
- knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
-
+ /* F. Make stage2pairs */
+ stage2pairs = (List_T) NULL;
+ for (p = startp; p != NULL; p = List_next(p)) {
+ substring = (Substring_T) List_head(p);
+ if (Substring_ambiguous_p(substring) == true) {
+ /* Skip */
+ } else {
+ debug13(printf("Handling substring for %d..%d, %u..%u, chrlength %u\n",
+ Substring_querystart(substring),Substring_queryend(substring),
+ Substring_alignstart_trim_chr(substring),Substring_alignend_trim_chr(substring),
+ this->chrlength));
+ querypos = Substring_querystart(substring);
+ seglength = Substring_queryend(substring) - querypos;
+
+ /* Don't understand why it isn't this->chrhigh - 1, but it
+ looks like the minus coordinates for substrings are +1 higher
+ than they should be */
+ /* genomepos = (this->chrlength + 1) - Substring_alignstart_trim_chr(substring); -- fails for circular chromosomes */
+ genomepos = (this->chrhigh + 1) - Substring_alignstart_trim(substring);
+ Genome_get_segment_blocks_right(gsequence_orig,gsequence_alt,/*left*/Substring_alignend_trim(substring),
+ seglength,this->chrhigh,/*revcomp*/true);
+
+ for (i = 0; i < seglength; i++) {
+ c = queryuc_ptr[querypos];
+ g = gsequence_orig[i];
+ g_alt = gsequence_alt[i];
+ if (g == c || g_alt == c) {
+ comp = MATCH_COMP;
+ } else {
+ comp = MISMATCH_COMP;
+ }
+ debug13(printf("Pushing %c %c %c at %d,%u\n",c,comp,g,querypos,genomepos));
+ stage2pairs = Pairpool_push(stage2pairs,pairpool,querypos,genomepos,
+ /*cdna*/c,comp,/*genome*/g,/*genomealt*/g_alt,
+ /*dynprogindex*/0);
+ querypos++;
+ genomepos++;
+ }
+ debug13(Pair_dump_list(stage2pairs,true));
+ debug13(printf("\n"));
+ }
+ }
- if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
- &matches,&nmatches_posttrim,&max_match_length,
- &ambig_end_length_5,&ambig_end_length_3,
- &ambig_splicetype_5,&ambig_splicetype_3,
- &ambig_prob_5,&ambig_prob_3,
- &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
- &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
- stage2pairs,all_stage2_starts,all_stage2_ends,
+ if (stage2pairs == NULL) {
+ hit = (T) NULL;
+ } else {
+ knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ stage2pairs = List_reverse(stage2pairs);
+ knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+
+ if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
+ &matches,&nmatches_posttrim,&max_match_length,
+ &ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,
+ &ambig_prob_5,&ambig_prob_3,
+ &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
+ &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
+ stage2pairs,all_stage2_starts,all_stage2_ends,
#ifdef END_KNOWNSPLICING_SHORTCUT
- cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
- watsonp ? query_compress_fwd : query_compress_rev,
+ cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
+ watsonp ? query_compress_fwd : query_compress_rev,
#endif
- /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
+ /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
#ifdef EXTRACT_GENOMICSEG
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#else
- /*query_subseq_offset*/0,
+ /*query_subseq_offset*/0,
#endif
- this->chrnum,this->chroffset,this->chrhigh,
- knownsplice_limit_low,knownsplice_limit_high,/*plusp*/false,genestrand,
- /*jump_late_p*/true,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
- /*sense_try*/0,/*sense_filter*/0,
- oligoindices_minor,diagpool,cellpool)) == NULL) {
- hit = (T) NULL;
+ this->chrnum,this->chroffset,this->chrhigh,
+ knownsplice_limit_low,knownsplice_limit_high,/*plusp*/false,genestrand,
+ /*jump_late_p*/true,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ /*sense_try*/0,/*sense_filter*/0,
+ oligoindices_minor,diagpool,cellpool)) == NULL) {
+ hit = (T) NULL;
- } else {
- nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
- pairarray,npairs);
- start = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
- /*plusterm*/Pair_querypos(&(pairarray[0])),this->chrhigh);
- end = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
- /*minusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chroffset);
- if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
- ambig_end_length_5,ambig_end_length_3,
- ambig_splicetype_5,ambig_splicetype_3,
- ambig_prob_5,ambig_prob_3,min_splice_prob,
- pairarray,npairs,nsegments,nintrons,nindelbreaks,
- /*left*/end,/*genomiclength*/start - end + 1,
- /*plusp*/false,genestrand,first_read_p,
- /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
- cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
- FREE_OUT(pairarray);
+ } else {
+ nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
+ pairarray,npairs);
+ start = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
+ /*plusterm*/Pair_querypos(&(pairarray[0])),this->chrhigh);
+ end = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
+ /*minusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chroffset);
+ if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
+ ambig_end_length_5,ambig_end_length_3,
+ ambig_splicetype_5,ambig_splicetype_3,
+ min_splice_prob,
+ pairarray,npairs,nsegments,nintrons,nindelbreaks,
+ /*left*/end,/*genomiclength*/start - end + 1,
+ /*plusp*/false,genestrand,
+ /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
+ cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
+ FREE_OUT(pairarray);
+ }
}
}
}
@@ -5659,11 +5936,350 @@ Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
}
+/* Modified from Stage3end_substrings_run_gmap_plus */
+T
+Stage3end_gmap_run_gmap_plus (T this, char *queryuc_ptr, int querylength, int genestrand,
+ int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool) {
+ T hit;
+ List_T stage2pairs, all_stage2_starts, all_stage2_ends;
+
+ int i;
+
+ int sensedir;
+
+ struct Pair_T *pairarray;
+ List_T pairs;
+ int querypos;
+
+ int npairs, goodness, cdna_direction, matches, nmatches_posttrim,
+ max_match_length, ambig_end_length_5, ambig_end_length_3,
+ unknowns, mismatches, qopens, qindels, topens, tindels,
+ ncanonical, nsemicanonical, nnoncanonical;
+ double ambig_prob_5, ambig_prob_3, min_splice_prob;
+ Splicetype_T ambig_splicetype_5, ambig_splicetype_3;
+ Univcoord_T knownsplice_limit_low, knownsplice_limit_high;
+ Univcoord_T start, end;
+ int nsegments, nmismatches_whole, nindels, nintrons, nindelbreaks;
+
+ Chrpos_T chrstart, chrend;
+
+ debug13(printf("Entered Stage3hr_gmap_run_gmap_plus\n"));
+
+
+ /* D. Make all_stage2_starts (paths) */
+ if (high_resolution_gmap_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_starts = (List_T) NULL;
+ } else if ((querypos = Pair_querypos(&(this->pairarray[0]))) < 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ all_stage2_starts = (List_T) NULL;
+ } else {
+ chrend = Pair_genomepos(&(this->pairarray[0]));
+ if (chrend < shortsplicedist) {
+ chrstart = 0;
+ } else {
+ chrstart = chrend - shortsplicedist;
+ }
+ all_stage2_starts = Stage2_compute_starts(
+#ifdef PMAP
+ &(queryaaseq_ptr[0]),&(queryaaseq_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0*3,
+#else
+ &(queryuc_ptr[0]),&(queryuc_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/true,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d starts\n",List_length(all_stage2_starts)));
+ }
+
+
+ /* E. Make all_stage2_ends (pairs) */
+ if (high_resolution_gmap_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_ends = (List_T) NULL;
+ } else if ((querypos = Pair_querypos(&(this->pairarray[this->npairs - 1]))) > querylength - 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ all_stage2_ends = (List_T) NULL;
+ } else {
+ chrstart = Pair_genomepos(&(this->pairarray[this->npairs - 1]));
+ if (chrstart + shortsplicedist > (this->chrhigh - this->chroffset)) {
+ chrend = this->chrhigh - this->chroffset;
+ } else {
+ chrend = chrstart + shortsplicedist;
+ }
+ all_stage2_ends = Stage2_compute_ends(
+#ifdef PMAP
+ &(queryaaseq_ptr[querypos]),&(queryaaseq_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos*3,
+#else
+ &(queryuc_ptr[querypos]),&(queryuc_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/true,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d ends\n",List_length(all_stage2_ends)));
+ }
+
+
+ if (all_stage2_starts == NULL && all_stage2_ends == NULL) {
+ hit = (T) NULL;
+
+ } else {
+ /* F. Make stage2pairs */
+ stage2pairs = (List_T) NULL;
+ for (i = 0; i < this->npairs; i++) {
+ stage2pairs = Pairpool_push_copy(stage2pairs,pairpool,&(this->pairarray[i]));
+ }
+ debug13(Pair_dump_list(stage2pairs,true));
+ debug13(printf("\n"));
+
+ if (stage2pairs == NULL) {
+ hit = (T) NULL;
+ } else {
+ knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ stage2pairs = List_reverse(stage2pairs);
+ knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+
+ if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
+ &matches,&nmatches_posttrim,&max_match_length,
+ &ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,
+ &ambig_prob_5,&ambig_prob_3,
+ &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
+ &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
+ stage2pairs,all_stage2_starts,all_stage2_ends,
+#ifdef END_KNOWNSPLICING_SHORTCUT
+ cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
+ watsonp ? query_compress_fwd : query_compress_rev,
+#endif
+ /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
+#ifdef EXTRACT_GENOMICSEG
+ /*query_subseq_offset*/0,
+#else
+ /*query_subseq_offset*/0,
+#endif
+ this->chrnum,this->chroffset,this->chrhigh,
+ knownsplice_limit_low,knownsplice_limit_high,/*plusp*/true,genestrand,
+ /*jump_late_p*/false,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ /*sense_try*/0,/*sense_filter*/0,
+ oligoindices_minor,diagpool,cellpool)) == NULL) {
+ hit = (T) NULL;
+
+ } else {
+ nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
+ pairarray,npairs);
+ start = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
+ /*minusterm*/Pair_querypos(&(pairarray[0])),this->chroffset);
+ end = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
+ /*plusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chrhigh);
+
+ if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
+ ambig_end_length_5,ambig_end_length_3,
+ ambig_splicetype_5,ambig_splicetype_3,
+ min_splice_prob,
+ pairarray,npairs,nsegments,nintrons,nindelbreaks,
+ /*left*/start,/*genomiclength*/end - start + 1,
+ /*plusp*/true,genestrand,
+ /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
+ cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
+ FREE_OUT(pairarray);
+ }
+ }
+
+ List_free(&all_stage2_ends);
+ List_free(&all_stage2_starts);
+ }
+ }
+
+ return hit;
+}
+
+
+/* Modified from Stage3end_substrings_run_gmap_minus */
+T
+Stage3end_gmap_run_gmap_minus (T this, char *queryuc_ptr, int querylength, int genestrand,
+ int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool) {
+ T hit;
+ List_T stage2pairs, all_stage2_starts, all_stage2_ends;
+
+ int i;
+
+ int sensedir;
+
+ Pair_T pair;
+ struct Pair_T *pairarray;
+ List_T pairs;
+ int querypos;
+
+ int npairs, goodness, cdna_direction, matches, nmatches_posttrim,
+ max_match_length, ambig_end_length_5, ambig_end_length_3,
+ unknowns, mismatches, qopens, qindels, topens, tindels,
+ ncanonical, nsemicanonical, nnoncanonical;
+ double ambig_prob_5, ambig_prob_3, min_splice_prob;
+ Splicetype_T ambig_splicetype_5, ambig_splicetype_3;
+ Univcoord_T knownsplice_limit_low, knownsplice_limit_high;
+ Univcoord_T start, end;
+ int nsegments, nmismatches_whole, nindels, nintrons, nindelbreaks;
+
+ Chrpos_T chrstart, chrend;
+
+ debug13(printf("Entered Stage3hr_gmap_run_gmap_minus with %u..%u in chr %d of length %u\n",
+ this->genomicstart - this->chroffset,this->genomicend - this->chroffset,
+ this->chrnum,this->chrlength));
+
+ /* D. Make all_stage2_starts (paths) */
+ if (high_resolution_gmap_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_starts = (List_T) NULL;
+ } else if ((querypos = Pair_querypos(&(this->pairarray[0]))) < 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ all_stage2_starts = (List_T) NULL;
+ } else {
+ chrstart = Pair_genomepos(&(this->pairarray[0]));
+ if (chrstart + shortsplicedist > (this->chrhigh - this->chroffset)) {
+ chrend = this->chrhigh - this->chroffset;
+ } else {
+ chrend = chrstart + shortsplicedist;
+ }
+ debug13(printf("For starts, chrstart %u, chrend %u\n",chrstart,chrend));
+ all_stage2_starts = Stage2_compute_starts(
+#ifdef PMAP
+ &(queryaaseq_ptr[0]),&(queryaaseq_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0*3,
+#else
+ &(queryuc_ptr[0]),&(queryuc_ptr[0]),
+ /*querylength*/querypos,/*query_offset*/0,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/false,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d starts\n",List_length(all_stage2_starts)));
+ }
+
+
+ /* E. Make all_stage2_ends (pairs) */
+ if (high_resolution_gmap_ends_p == false) {
+ /* Don't try to solve ends, as requested by user */
+ all_stage2_ends = (List_T) NULL;
+ } else if ((querypos = Pair_querypos(&(this->pairarray[this->npairs - 1]))) > querylength - 15) {
+ /* Don't try to solve short ends, for sake of efficiency */
+ all_stage2_ends = (List_T) NULL;
+ } else {
+ chrend = Pair_genomepos(&(this->pairarray[this->npairs - 1]));
+ if (chrend < shortsplicedist) {
+ chrstart = 0;
+ } else {
+ chrstart = chrend - shortsplicedist;
+ }
+ debug13(printf("For ends, chrstart %u, chrend %u\n",chrstart,chrend));
+ all_stage2_ends = Stage2_compute_ends(
+#ifdef PMAP
+ &(queryaaseq_ptr[querypos]),&(queryaaseq_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos*3,
+#else
+ &(queryuc_ptr[querypos]),&(queryuc_ptr[querypos]),
+ /*querylength*/querylength - querypos,/*query_offset*/querypos,
+#endif
+ chrstart,chrend,this->chroffset,this->chrhigh,/*plusp*/false,genestrand,
+
+ oligoindices_minor,pairpool,diagpool,cellpool,
+ /*localp should be false*/true,/*skip_repetitive_p*/false,
+ /*favor_right_p*/false,/*max_nalignments*/5,/*debug_graphic_p*/false);
+ debug13(printf("Got %d ends\n",List_length(all_stage2_ends)));
+ }
+
+
+ if (all_stage2_starts == NULL && all_stage2_ends == NULL) {
+ hit = (T) NULL;
+
+ } else {
+ /* F. Make stage2pairs */
+ stage2pairs = (List_T) NULL;
+ for (i = 0; i < this->npairs; i++) {
+ stage2pairs = Pairpool_push_copy(stage2pairs,pairpool,&(this->pairarray[i]));
+ pair = (Pair_T) stage2pairs->first;
+ pair->genomepos = (this->chrhigh - this->chroffset /*+ 1*/) - pair->genomepos;
+ }
+ debug13(Pair_dump_list(stage2pairs,true));
+ debug13(printf("\n"));
+
+ if (stage2pairs == NULL) {
+ hit = (T) NULL;
+ } else {
+ knownsplice_limit_low = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+ stage2pairs = List_reverse(stage2pairs);
+ knownsplice_limit_high = ((Pair_T) stage2pairs->first)->genomepos + this->chroffset;
+
+ if ((pairarray = Stage3_compute(&pairs,&npairs,&goodness,&cdna_direction,&sensedir,
+ &matches,&nmatches_posttrim,&max_match_length,
+ &ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,
+ &ambig_prob_5,&ambig_prob_3,
+ &unknowns,&mismatches,&qopens,&qindels,&topens,&tindels,
+ &ncanonical,&nsemicanonical,&nnoncanonical,&min_splice_prob,
+ stage2pairs,all_stage2_starts,all_stage2_ends,
+#ifdef END_KNOWNSPLICING_SHORTCUT
+ cutoff_level,/*queryptr*/watsonp ? queryuc_ptr : queryrc,
+ watsonp ? query_compress_fwd : query_compress_rev,
+#endif
+ /*queryseq_ptr*/queryuc_ptr,queryuc_ptr,querylength,/*skiplength*/0,
+#ifdef EXTRACT_GENOMICSEG
+ /*query_subseq_offset*/0,
+#else
+ /*query_subseq_offset*/0,
+#endif
+ this->chrnum,this->chroffset,this->chrhigh,
+ knownsplice_limit_low,knownsplice_limit_high,/*plusp*/false,genestrand,
+ /*jump_late_p*/true,maxpeelback,pairpool,dynprogL,dynprogM,dynprogR,
+ /*sense_try*/0,/*sense_filter*/0,
+ oligoindices_minor,diagpool,cellpool)) == NULL) {
+ hit = (T) NULL;
+
+ } else {
+ nsegments = Pair_gsnap_nsegments(&nmismatches_whole,&nindels,&nintrons,&nindelbreaks,
+ pairarray,npairs);
+ start = add_bounded(this->chroffset + Pair_genomepos(&(pairarray[0])),
+ /*plusterm*/Pair_querypos(&(pairarray[0])),this->chrhigh);
+ end = subtract_bounded(this->chroffset + Pair_genomepos(&(pairarray[npairs-1])),
+ /*minusterm*/querylength - 1 - Pair_querypos(&(pairarray[npairs-1])),this->chroffset);
+ if ((hit = Stage3end_new_gmap(nmismatches_whole,nmatches_posttrim,max_match_length,
+ ambig_end_length_5,ambig_end_length_3,
+ ambig_splicetype_5,ambig_splicetype_3,
+ min_splice_prob,
+ pairarray,npairs,nsegments,nintrons,nindelbreaks,
+ /*left*/end,/*genomiclength*/start - end + 1,
+ /*plusp*/false,genestrand,
+ /*accession*/NULL,querylength,this->chrnum,this->chroffset,this->chrhigh,this->chrlength,
+ cdna_direction,sensedir,/*gmap_source*/GMAP_VIA_SUBSTRINGS)) == NULL) {
+ FREE_OUT(pairarray);
+ }
+ }
+
+ List_free(&all_stage2_ends);
+ List_free(&all_stage2_starts);
+ }
+ }
+
+ return hit;
+}
+
+
T
Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Compress_T query_compress,
- bool plusp, int genestrand, bool first_read_p,
+ bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Chrpos_T chrlength, bool sarrayp) {
T new;
@@ -5754,8 +6370,9 @@ Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Comp
query_compress,/*start_endtype*/END,/*end_endtype*/END,
/*querystart*/0,/*queryend*/genomiclength,/*querylength*/genomiclength,
/*alignstart*/genomicstart,/*alignend*/genomicend,
- genomiclength,exactp,plusp,genestrand,first_read_p,/*trim_left_p*/false,/*trim_right_p*/false,
- outofbounds_start,outofbounds_end,/*minlength*/0)) == NULL) {
+ exactp,plusp,genestrand,/*trim_left_action*/NO_TRIM,/*trim_right_action*/NO_TRIM,
+ outofbounds_start,outofbounds_end,/*minlength*/0,
+ /*sensedir*/SENSE_NULL)) == NULL) {
return (T) NULL;
} else {
@@ -5800,6 +6417,7 @@ Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Comp
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -5844,10 +6462,18 @@ Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Comp
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ return new;
+
} else {
return new;
}
@@ -5858,7 +6484,7 @@ Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Comp
T
Stage3end_new_substitution (int *found_score, int nmismatches_whole, Univcoord_T left,
int genomiclength, Compress_T query_compress,
- bool plusp, int genestrand, bool first_read_p,
+ bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Chrpos_T chrlength, bool sarrayp) {
T new;
@@ -5946,8 +6572,9 @@ Stage3end_new_substitution (int *found_score, int nmismatches_whole, Univcoord_T
query_compress,/*start_endtype*/END,/*end_endtype*/END,
/*querystart*/0,/*queryend*/genomiclength,/*querylength*/genomiclength,
/*alignstart*/genomicstart,/*alignend*/genomicend,
- genomiclength,/*exactp*/false,plusp,genestrand,first_read_p,/*trim_left_p*/true,/*trim_right_p*/true,
- outofbounds_start,outofbounds_end,/*minlength*/genomiclength/2)) == NULL) {
+ /*exactp*/false,plusp,genestrand,/*trim_left_action*/COMPUTE_TRIM,/*trim_right_action*/COMPUTE_TRIM,
+ outofbounds_start,outofbounds_end,/*minlength*/genomiclength/2,
+ /*sensedir*/SENSE_NULL)) == NULL) {
debug0(printf("Returning NULL\n"));
return (T) NULL;
@@ -5993,6 +6620,7 @@ Stage3end_new_substitution (int *found_score, int nmismatches_whole, Univcoord_T
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -6009,11 +6637,11 @@ Stage3end_new_substitution (int *found_score, int nmismatches_whole, Univcoord_T
new->nindels = 0;
new->nmismatches_whole = nmismatches_whole;
- new->ntscore = nmismatches_whole;
- new->score = nmismatches_whole;
+ new->nmismatches_bothdiff = Substring_nmismatches_bothdiff(substring);
+ new->ntscore = new->nmismatches_whole;
+ new->score = new->nmismatches_whole;
new->nsegments = 1;
- new->nmismatches_bothdiff = Substring_nmismatches_bothdiff(substring);
/* new->nmismatches_refdiff = Substring_nmismatches_refdiff(new->substring1); */
#if 0
@@ -6048,12 +6676,19 @@ Stage3end_new_substitution (int *found_score, int nmismatches_whole, Univcoord_T
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ return new;
+
} else {
- debug(printf("Returning substitution %p\n",new));
return new;
}
}
@@ -6063,16 +6698,15 @@ Stage3end_new_substitution (int *found_score, int nmismatches_whole, Univcoord_T
T
Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmismatches1_whole, int nmismatches2_whole,
- Univcoord_T left, int genomiclength, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int indel_penalty, bool sarrayp) {
T new;
Substring_T substring1, substring2;
Junction_T junction;
int querystart1, queryend1, querystart2, queryend2;
- Univcoord_T genomicstart1, genomicend1, genomicstart2, genomicend2;
- Univcoord_T genomicstart_adj_2, genomicend_adj_2;
+ Univcoord_T genomicstart1, genomicend2;
+ /* Univcoord_T genomicend1, genomicstart2; */
Univcoord_T alignstart1, alignend1, alignstart2, alignend2;
int outofbounds_start = 0, outofbounds_end = 0;
@@ -6097,8 +6731,8 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
alignend2 = (left - nindels) + /*queryend2*/querylength;
genomicstart1 = alignstart1;
- genomicend1 = alignend1;
- genomicstart2 = alignstart2;
+ /* genomicend1 = alignend1; */
+ /* genomicstart2 = alignstart2; */
genomicend2 = alignend2;
if (genomicstart1 < chroffset && genomicend2 > chrhigh) {
@@ -6156,8 +6790,8 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
alignend2 = left /* + (querylength - queryend)*/;
genomicstart1 = alignstart1;
- genomicend1 = alignend1;
- genomicstart2 = alignstart2;
+ /* genomicend1 = alignend1; */
+ /* genomicstart2 = alignstart2; */
genomicend2 = alignend2;
if (genomicend2 < chroffset && genomicstart1 > chrhigh) {
@@ -6212,18 +6846,19 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
if ((substring1 = Substring_new(nmismatches1_whole,chrnum,chroffset,chrhigh,chrlength,
query_compress,/*start_endtype*/END,/*end_endtype*/INS,
- querystart1,queryend1,querylength,alignstart1,alignend1,genomiclength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- /*trim_left_p (previously was end1_indel_p ? false : true)*/true,
- /*trim_right_p*/false,outofbounds_start,/*outofbounds_end*/0,/*minlength*/0)) == NULL) {
+ querystart1,queryend1,querylength,alignstart1,alignend1,
+ /*exactp*/false,plusp,genestrand,
+ /*trim_left_action (previously was end1_indel_p ? false : true)*/COMPUTE_TRIM,
+ /*trim_right_action*/NO_TRIM,outofbounds_start,/*outofbounds_end*/0,
+ /*minlength*/0,/*sensedir*/SENSE_NULL)) == NULL) {
return (T) NULL;
} else if ((substring2 = Substring_new(nmismatches2_whole,chrnum,chroffset,chrhigh,chrlength,
query_compress,/*start_endtype*/INS,/*end_endtype*/END,
- querystart2,queryend2,querylength,alignstart2,alignend2,genomiclength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- /*trim_left_p*/false,/*trim_right_p (previously was end2_indel_p ? false : true)*/true,
- /*outofbounds_start*/0,outofbounds_end,/*minlength*/0)) == NULL) {
+ querystart2,queryend2,querylength,alignstart2,alignend2,
+ /*exactp*/false,plusp,genestrand,
+ /*trim_left_action*/NO_TRIM,/*trim_right_action (previously was end2_indel_p ? false : true)*/COMPUTE_TRIM,
+ /*outofbounds_start*/0,outofbounds_end,/*minlength*/0,/*sensedir*/SENSE_NULL)) == NULL) {
Substring_free(&substring1);
return (T) NULL;
@@ -6275,6 +6910,7 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -6340,10 +6976,18 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ return new;
+
} else {
return new;
}
@@ -6353,16 +6997,15 @@ Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmism
T
Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmismatches1_whole, int nmismatches2_whole,
- Univcoord_T left, int genomiclength, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int indel_penalty, bool sarrayp) {
T new;
Substring_T substring1, substring2;
Junction_T junction;
int querystart1, queryend1, querystart2, queryend2;
- Univcoord_T genomicstart1, genomicend1, genomicstart2, genomicend2;
- Univcoord_T genomicstart_adj_2, genomicend_adj_2;
+ Univcoord_T genomicstart1, genomicend2;
+ /* Univcoord_T genomicend1, genomicstart2; */
Univcoord_T alignstart1, alignend1, alignstart2, alignend2;
int outofbounds_start = 0, outofbounds_end = 0;
@@ -6389,8 +7032,8 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
alignend2 = (left + nindels) + querylength;
genomicstart1 = alignstart1;
- genomicend1 = alignend1;
- genomicstart2 = alignstart2;
+ /* genomicend1 = alignend1; */
+ /* genomicstart2 = alignstart2; */
genomicend2 = alignend2;
debug3(printf("plusp is true. genomicstart %llu, genomicend %llu, alignstart1 %llu, alignend1 %llu, alignstart2 %llu, alignend2 %llu, left1 %llu\n",
@@ -6452,7 +7095,7 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
alignstart1 = left + (querylength /*- querystart (0)*/);
alignend1 = left + (querylength - indel_pos);
alignstart2 = (left - nindels) + (querylength - indel_pos);
- if (left < nindels) {
+ if (left < (Univcoord_T) nindels) {
/* Handles deletion at start of genome, and avoids left alignend2 becoming negative */
alignend2 = 0;
} else {
@@ -6460,8 +7103,8 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
}
genomicstart1 = alignstart1;
- genomicend1 = alignend1;
- genomicstart2 = alignstart2;
+ /* genomicend1 = alignend1; */
+ /* genomicstart2 = alignstart2; */
genomicend2 = alignend2;
debug3(printf("plusp is false. genomicstart %llu, genomicend %llu, alignstart1 %llu, alignend1 %llu, alignstart2 %llu, alignend2 %llu, left1 %llu\n",
@@ -6521,18 +7164,19 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
if ((substring1 = Substring_new(nmismatches1_whole,chrnum,chroffset,chrhigh,chrlength,
query_compress,/*start_endtype*/END,/*end_endtype*/DEL,
- querystart1,queryend1,querylength,alignstart1,alignend1,genomiclength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- /*trim_left_p (previously was end1_indel_p ? false : true)*/true,
- /*trim_right_p*/false,outofbounds_start,/*outofbounds_end*/0,/*minlength*/0)) == NULL) {
+ querystart1,queryend1,querylength,alignstart1,alignend1,
+ /*exactp*/false,plusp,genestrand,
+ /*trim_left_action (previously was end1_indel_p ? false : true)*/COMPUTE_TRIM,
+ /*trim_right_action*/NO_TRIM,outofbounds_start,/*outofbounds_end*/0,
+ /*minlength*/0,/*sensedir*/SENSE_NULL)) == NULL) {
return (T) NULL;
} else if ((substring2 = Substring_new(nmismatches2_whole,chrnum,chroffset,chrhigh,chrlength,
query_compress,/*start_endtype*/DEL,/*end_endtype*/END,
- querystart2,queryend2,querylength,alignstart2,alignend2,genomiclength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- /*trim_left_p*/false,/*trim_right_p (previously was end2_indel_p ? false : true) */true,
- /*outofbounds_start*/0,outofbounds_end,/*minlength*/0)) == NULL) {
+ querystart2,queryend2,querylength,alignstart2,alignend2,
+ /*exactp*/false,plusp,genestrand,
+ /*trim_left_action*/NO_TRIM,/*trim_right_action (previously was end2_indel_p ? false : true) */COMPUTE_TRIM,
+ /*outofbounds_start*/0,outofbounds_end,/*minlength*/0,/*sensedir*/SENSE_NULL)) == NULL) {
Substring_free(&substring1);
return (T) NULL;
@@ -6593,6 +7237,7 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -6656,10 +7301,18 @@ Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmisma
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ return new;
+
} else {
return new;
}
@@ -6673,7 +7326,7 @@ T
Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_acceptor,
Substring_T donor, Substring_T acceptor,
double donor_prob, double acceptor_prob, Chrpos_T distance,
- bool shortdistancep, int splicing_penalty, int querylength, int amb_length, double amb_prob,
+ bool shortdistancep, int splicing_penalty, int querylength,
#ifdef LARGE_GENOMES
Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
#else
@@ -6689,13 +7342,10 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
Substring_T substring_other; /* the outer substring */
Substring_T substring;
Junction_T junction;
-#ifdef DEBUG0
- int i;
-#endif
new = (T) MALLOC_OUT(sizeof(*new));
- debug0(printf("Stage3end_new_splice %p with sensedir %d, donor substring %p and acceptor substring %p, and amb_length %d, sarrayp %d\n",
- new,sensedir,donor,acceptor,amb_length,sarrayp));
+ debug0(printf("Stage3end_new_splice %p with sensedir %d, donor substring %p and acceptor substring %p, sarrayp %d\n",
+ new,sensedir,donor,acceptor,sarrayp));
#if 0
assert(Substring_match_length_orig(donor) + Substring_match_length_orig(acceptor) + amb_length == querylength);
@@ -6745,6 +7395,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
if (donor == NULL) {
new->hittype = SPLICE;
new->genestrand = Substring_genestrand(acceptor);
+ new->distant_splice_p = false;
new->chrnum = Substring_chrnum(acceptor);
new->chroffset = Substring_chroffset(acceptor);
new->chrhigh = Substring_chrhigh(acceptor);
@@ -6754,6 +7405,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
} else if (acceptor == NULL) {
new->hittype = SPLICE;
new->genestrand = Substring_genestrand(donor);
+ new->distant_splice_p = false;
new->chrnum = Substring_chrnum(donor);
new->chroffset = Substring_chroffset(donor);
new->chrhigh = Substring_chrhigh(donor);
@@ -6763,6 +7415,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
} else if (shortdistancep == true) {
new->hittype = SPLICE;
new->genestrand = Substring_genestrand(donor);
+ new->distant_splice_p = false;
new->chrnum = Substring_chrnum(donor);
new->chroffset = Substring_chroffset(donor);
new->chrhigh = Substring_chrhigh(donor);
@@ -6793,7 +7446,6 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
new->plusp = Substring_plusp(donor);
#endif
-
#if 0
} else if (merge_samechr_p == false) {
new->hittype = DISTANT_SPLICE;
@@ -6810,13 +7462,21 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
new->sarrayp = sarrayp;
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = true;
if (Substring_chrnum(donor) == Substring_chrnum(acceptor)) {
new->hittype = SAMECHR_SPLICE;
new->genestrand = Substring_genestrand(donor);
- new->chrnum = Substring_chrnum(donor);
- new->chroffset = Substring_chroffset(donor);
- new->chrhigh = Substring_chrhigh(donor);
- new->chrlength = Substring_chrlength(donor);
+ if (merge_samechr_p == true) {
+ new->chrnum = Substring_chrnum(donor);
+ new->chroffset = Substring_chroffset(donor);
+ new->chrhigh = Substring_chrhigh(donor);
+ new->chrlength = Substring_chrlength(donor);
+ } else {
+ new->chrnum = 0;
+ new->chroffset = 0;
+ new->chrhigh = 0;
+ new->chrlength = 0;
+ }
new->plusp = Substring_plusp(donor); /* default value, used if merge_samechr_p is true */
} else {
@@ -6856,7 +7516,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
donor = Substring_new_ambig(/*querystart*/0,/*queryend*/Substring_querystart(acceptor),
/*splice_pos*/Substring_querystart(acceptor),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_donor,amb_knowni_donor,amb_nmismatches_donor,amb_probs_donor,
/*amb_common_prob*/acceptor_prob,/*amb_donor_common_p*/false,
/*substring1p*/true);
@@ -6871,7 +7531,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
acceptor = Substring_new_ambig(/*querystart*/Substring_queryend(donor),/*queryend*/querylength,
/*splice_pos*/Substring_queryend(donor),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_acceptor,amb_knowni_acceptor,amb_nmismatches_acceptor,amb_probs_acceptor,
/*amb_common_prob*/donor_prob,/*amb_donor_common_p*/true,
/*substring1p*/false);
@@ -6893,7 +7553,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
donor = Substring_new_ambig(/*querystart*/Substring_queryend(acceptor),/*queryend*/querylength,
/*splice_pos*/Substring_queryend(acceptor),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_donor,amb_knowni_donor,amb_nmismatches_donor,amb_probs_donor,
/*amb_common_prob*/acceptor_prob,/*amb_donor_common_p*/false,
/*substring1p*/false);
@@ -6908,7 +7568,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
acceptor = Substring_new_ambig(/*querystart*/0,/*queryend*/Substring_querystart(donor),
/*splice_pos*/Substring_querystart(donor),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_acceptor,amb_knowni_acceptor,amb_nmismatches_acceptor,amb_probs_acceptor,
/*amb_common_prob*/donor_prob,/*amb_donor_common_p*/true,
/*substring1p*/true);
@@ -7129,17 +7789,24 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
} else {
- debug0(printf("Returning new splice %p at genomic %u..%u, donor %p (%u => %u), acceptor %p (%u => %u)\n",
+ if (new->circularalias >= 0) {
+ new->altlocp = false;
+ } else if ((new->altlocp = altlocp[new->chrnum]) == false) {
+ } else {
+ }
+
+ debug0(printf("Returning new splice %p at genomic %u..%u, donor %p (%u => %u), acceptor %p (%u => %u), score %d\n",
new,new->genomicstart - new->chroffset,new->genomicend - new->chroffset,donor,
donor == NULL ? 0 : Substring_left_genomicseg(donor),
donor == NULL ? 0 : Substring_splicecoord(donor),
acceptor,acceptor == NULL ? 0 : Substring_left_genomicseg(acceptor),
- acceptor == NULL ? 0 : Substring_splicecoord(acceptor)));
+ acceptor == NULL ? 0 : Substring_splicecoord(acceptor),new->score));
debug0(printf("sensedir %d\n",new->sensedir));
return new;
}
@@ -7152,7 +7819,7 @@ Stage3end_new_splice (int *found_score, int nmismatches_donor, int nmismatches_a
T
Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T acceptor, Substring_T shortexon,
double donor_prob, double shortexonA_prob, double shortexonD_prob, double acceptor_prob,
- int amb_length_donor, int amb_length_acceptor, double amb_prob_donor, double amb_prob_acceptor,
+ int amb_length_donor, int amb_length_acceptor,
#ifdef LARGE_GENOMES
Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
#else
@@ -7162,9 +7829,8 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
Intlist_T amb_nmismatches_donor, Intlist_T amb_nmismatches_acceptor,
Doublelist_T amb_probs_donor, Doublelist_T amb_probs_acceptor,
bool copy_donor_p, bool copy_acceptor_p, bool copy_shortexon_p,
- int splicing_penalty, int querylength, bool first_read_p, int sensedir, bool sarrayp) {
+ int splicing_penalty, int querylength, int sensedir, bool sarrayp) {
T new;
- int ignore;
Substring_T substring, substring0, substring1, substring2;
Chrpos_T distance;
Junction_T junction0, junction2;
@@ -7210,6 +7876,7 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
new->nindels = 0;
+ new->distant_splice_p = false;
new->chrnum = Substring_chrnum(shortexon);
new->chroffset = Substring_chroffset(shortexon);
new->chrhigh = Substring_chrhigh(shortexon);
@@ -7255,7 +7922,7 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
donor = substring0 = Substring_new_ambig(/*querystart*/0,/*queryend*/Substring_querystart(shortexon),
/*splice_pos*/Substring_querystart(shortexon),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_donor,amb_knowni_donor,amb_nmismatches_donor,amb_probs_donor,
/*amb_common_prob*/acceptor_prob,/*amb_donor_common_p*/false,
/*substring1p*/true);
@@ -7275,7 +7942,7 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
acceptor = substring2 = Substring_new_ambig(/*querystart*/Substring_queryend(shortexon),/*queryend*/querylength,
/*splice_pos*/Substring_queryend(shortexon),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_acceptor,amb_knowni_acceptor,amb_nmismatches_acceptor,amb_probs_acceptor,
/*amb_common_prob*/donor_prob,/*amb_donor_common_p*/true,
/*substring1p*/false);
@@ -7296,7 +7963,7 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
acceptor = substring0 = Substring_new_ambig(/*querystart*/0,/*queryend*/Substring_querystart(shortexon),
/*splice_pos*/Substring_querystart(shortexon),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_acceptor,amb_knowni_acceptor,amb_nmismatches_acceptor,amb_probs_acceptor,
/*amb_common_prob*/donor_prob,/*amb_donor_common_p*/true,
/*substring1p*/true);
@@ -7316,7 +7983,7 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
donor = substring2 = Substring_new_ambig(/*querystart*/Substring_queryend(shortexon),/*queryend*/querylength,
/*splice_pos*/Substring_queryend(shortexon),querylength,
new->chrnum,new->chroffset,new->chrhigh,new->chrlength,
- /*genomiclength*/querylength,new->plusp,new->genestrand,first_read_p,
+ new->plusp,new->genestrand,
ambcoords_donor,amb_knowni_donor,amb_nmismatches_donor,amb_probs_donor,
/*amb_common_prob*/acceptor_prob,/*amb_donor_common_p*/false,
/*substring1p*/false);
@@ -7468,10 +8135,18 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[new->chrnum]) == false) {
+ return new;
+
} else {
return new;
}
@@ -7480,7 +8155,7 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
T
Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ int querylength, bool plusp, int genestrand,
Endtype_T start_endtype, Endtype_T end_endtype,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int max_mismatches_allowed, bool sarrayp) {
@@ -7488,16 +8163,22 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
Substring_T substring;
Univcoord_T genomicstart, genomicend, alignstart, alignend, alignstart_trim, alignend_trim;
int nmismatches_whole, minlength;
- bool trim_left_p, trim_right_p;
+ Trimaction_T trim_left_action, trim_right_action;
int outofbounds_start = 0, outofbounds_end = 0;
- int *mismatch_positions_left, *mismatch_positions_right, nmismatches_left, nmismatches_right;
+#ifdef TRY_EXTENDING_TERMINALS
+ int *mismatch_positions_left, *mismatch_positions_right;
int length_left, length_right, pos5, pos3;
+#ifdef DEBUG0
int i;
+ int nmismatches_left, nmismatches_right;
+#endif
+#endif
- debug0(printf("\nStage3end_new_terminal possible: endtypes %s and %s, left %llu, querystart %d, queryend %d, sarrayp %d\n",
- Endtype_string(start_endtype),Endtype_string(end_endtype),(unsigned long long) left,querystart,queryend,sarrayp));
+ debug0(printf("\nStage3end_new_terminal possible: endtypes %s and %s, left %llu (%llu), querystart %d, queryend %d, sarrayp %d\n",
+ Endtype_string(start_endtype),Endtype_string(end_endtype),(unsigned long long) left,
+ (unsigned long long) left - chroffset,querystart,queryend,sarrayp));
if (plusp == true) {
genomicstart = left;
@@ -7581,15 +8262,15 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
}
if (start_endtype == TERM) {
- trim_left_p = true;
+ trim_left_action = COMPUTE_TRIM;
} else {
- trim_left_p = false;
+ trim_left_action = NO_TRIM;
}
if (end_endtype == TERM) {
- trim_right_p = true;
+ trim_right_action = COMPUTE_TRIM;
} else {
- trim_right_p = false;
+ trim_right_action = NO_TRIM;
}
/* Note: Changing querylength/3 to querylength/2 loses about 1% of concordant reads */
@@ -7600,9 +8281,9 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
if ((substring = Substring_new(/*nmismatches_whole*/0,chrnum,chroffset,chrhigh,chrlength,
query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,outofbounds_start,outofbounds_end,minlength)) == NULL) {
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ trim_left_action,trim_right_action,outofbounds_start,outofbounds_end,
+ minlength,/*sensedir*/SENSE_NULL)) == NULL) {
debug0(printf("returning NULL\n"));
return (T) NULL;
@@ -7627,21 +8308,95 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
alignstart_trim = Substring_alignstart_trim(substring);
alignend_trim = Substring_alignend_trim(substring);
- debug0(printf("alignstart_trim = %llu, alignend_trim = %llu\n",(unsigned long long) alignstart_trim,(unsigned long long) alignend_trim));
+ debug0(printf("alignstart_trim = %llu, alignend_trim = %llu\n",(unsigned long long) alignstart_trim - chroffset,(unsigned long long) alignend_trim - chroffset));
if (plusp == true) {
debug0(printf("plus: pos5 = %d, pos3 = %d\n",(int) (alignstart_trim-left),(int) (alignend_trim-left)));
nmismatches_whole =
Genome_count_mismatches_substring(query_compress,left,/*pos5*/alignstart_trim-left,
- /*pos3*/alignend_trim-left,/*plusp*/true,genestrand,first_read_p);
+ /*pos3*/alignend_trim-left,/*plusp*/true,genestrand);
debug0(printf("Recomputing nmismatches_whole as %d\n",nmismatches_whole));
if (nmismatches_whole <= max_mismatches_allowed) {
/* Code in substring.c suggests that nmismatches_bothdiff would be the same value as nmismatches_whole */
Substring_set_nmismatches_terminal(substring,nmismatches_whole,/*nmismatches_bothdiff*/nmismatches_whole);
+#ifdef TRY_EXTENDING_TERMINALS
} else {
- debug0(printf("returning NULL\n"));
+ /* Try finding a long string within the max_mismatches_allowed, but leads to bad partial alignments */
+#ifdef HAVE_ALLOCA
+ mismatch_positions_left = (int *) ALLOCA((max_mismatches_allowed+1)*sizeof(int));
+ mismatch_positions_right = (int *) ALLOCA((max_mismatches_allowed+1)*sizeof(int));
+#else
+ mismatch_positions_left = (int *) MALLOC((max_mismatches_allowed+1)*sizeof(int));
+ mismatch_positions_right = (int *) MALLOC((max_mismatches_allowed+1)*sizeof(int));
+#endif
+
+ pos5 = alignstart_trim-left;
+ pos3 = alignend_trim-left;
+
+ debug0(printf("Computing mismatches from pos5 %d to pos3 %d\n",pos5,pos3));
+#ifdef DEBUG0
+ nmismatches_left =
+#endif
+ Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,query_compress,
+ left,pos5,pos3,/*plusp*/true,genestrand);
+ length_left = mismatch_positions_left[max_mismatches_allowed] - pos5;
+#ifdef DEBUG0
+ nmismatches_right =
+#endif
+ Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,query_compress,
+ left,pos5,pos3,/*plusp*/true,genestrand);
+ length_right = pos3 - mismatch_positions_right[max_mismatches_allowed];
+
+#ifdef DEBUG0
+ printf("full read: %d (max %d) mismatches from left:",nmismatches_left,max_mismatches_allowed);
+ for (i = 0; i <= nmismatches_left; i++) {
+ printf(" %d",mismatch_positions_left[i]);
+ }
+ printf("\n");
+ printf("length %d = %d - %d\n",length_left,
+ mismatch_positions_left[max_mismatches_allowed],alignstart_trim-left);
+
+ printf("full read: %d (max %d) mismatches from right:",nmismatches_right,max_mismatches_allowed);
+ for (i = 0; i <= nmismatches_right; i++) {
+ printf(" %d",mismatch_positions_right[i]);
+ }
+ printf("\n");
+ printf("length %d = %d - %d\n",length_right,
+ alignend_trim-left,mismatch_positions_right[max_mismatches_allowed]);
+#endif
+
+ if (length_left >= length_right) {
+ querystart = pos5;
+ queryend = mismatch_positions_left[max_mismatches_allowed];
+ alignstart = genomicstart + querystart; /* really alignstart_trim */
+ alignend = genomicstart + queryend; /* really alignend_trim */
+ } else {
+ querystart = mismatch_positions_right[max_mismatches_allowed] + 1;
+ queryend = pos3;
+ alignstart = genomicstart + querystart; /* really alignstart_trim */
+ alignend = genomicstart + queryend; /* really alignend_trim */
+ }
+
+#ifdef HAVE_ALLOCA
+ FREEA(mismatch_positions_left);
+ FREEA(mismatch_positions_right);
+#else
+ FREE(mismatch_positions_left);
+ FREE(mismatch_positions_right);
+#endif
+
Substring_free(&substring);
- return (T) NULL;
+ if ((substring = Substring_new(/*nmismatches_whole*/0,chrnum,chroffset,chrhigh,chrlength,
+ query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ /*trim_left_action*/PRE_TRIMMED,/*trim_right_action*/PRE_TRIMMED,
+ outofbounds_start,outofbounds_end,minlength,/*sensedir*/SENSE_NULL)) == NULL) {
+ debug0(printf("returning NULL\n"));
+ return (T) NULL;
+ } else {
+ Substring_set_nmismatches_terminal(substring,max_mismatches_allowed,/*nmismatches_bothdiff*/max_mismatches_allowed);
+ }
+#endif
}
if (0) {
@@ -7655,23 +8410,102 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
debug0(printf("minus: pos5 = %d, pos3 = %d\n",(int) (alignend_trim-left),(int) (alignstart_trim-left)));
nmismatches_whole =
Genome_count_mismatches_substring(query_compress,left,/*pos5*/alignend_trim-left,
- /*pos3*/alignstart_trim-left,/*plusp*/false,genestrand,first_read_p);
+ /*pos3*/alignstart_trim-left,/*plusp*/false,genestrand);
debug0(printf("Recomputing nmismatches_whole as %d\n",nmismatches_whole));
if (nmismatches_whole <= max_mismatches_allowed) {
/* Code in substring.c suggests that nmismatches_bothdiff would be the same value as nmismatches_whole */
Substring_set_nmismatches_terminal(substring,nmismatches_whole,/*nmismatches_bothdiff*/nmismatches_whole);
+#ifdef TRY_EXTENDING_TERMINALS
} else {
- debug0(printf("returning NULL\n"));
+ /* Try finding a long string within the max_mismatches_allowed, but leads to bad partial alignments */
+#ifdef HAVE_ALLOCA
+ mismatch_positions_left = (int *) ALLOCA((max_mismatches_allowed+1)*sizeof(int));
+ mismatch_positions_right = (int *) ALLOCA((max_mismatches_allowed+1)*sizeof(int));
+#else
+ mismatch_positions_left = (int *) MALLOC((max_mismatches_allowed+1)*sizeof(int));
+ mismatch_positions_right = (int *) MALLOC((max_mismatches_allowed+1)*sizeof(int));
+#endif
+
+ pos5 = alignend_trim-left;
+ pos3 = alignstart_trim-left;
+
+ debug0(printf("Computing mismatches from pos5 %d to pos3 %d\n",pos5,pos3));
+#ifdef DEBUG0
+ nmismatches_left =
+#endif
+ Genome_mismatches_left(mismatch_positions_left,max_mismatches_allowed,query_compress,
+ left,pos5,pos3,/*plusp*/false,genestrand);
+ length_left = mismatch_positions_left[max_mismatches_allowed] - pos5;
+#ifdef DEBUG0
+ nmismatches_right =
+#endif
+ Genome_mismatches_right(mismatch_positions_right,max_mismatches_allowed,query_compress,
+ left,pos5,pos3,/*plusp*/false,genestrand);
+ length_right = pos3 - mismatch_positions_right[max_mismatches_allowed];
+
+#ifdef DEBUG0
+ printf("full read: %d (max %d) mismatches from left:",nmismatches_left,max_mismatches_allowed);
+ for (i = 0; i <= nmismatches_left; i++) {
+ printf(" %d",mismatch_positions_left[i]);
+ }
+ printf("\n");
+ printf("length %d = %d - %d\n",length_left,
+ mismatch_positions_left[max_mismatches_allowed],alignend_trim-left);
+
+ printf("full read: %d (max %d) mismatches from right:",nmismatches_right,max_mismatches_allowed);
+ for (i = 0; i <= nmismatches_right; i++) {
+ printf(" %d",mismatch_positions_right[i]);
+ }
+ printf("\n");
+ printf("length %d = %d - %d\n",length_right,
+ alignstart_trim-left,mismatch_positions_right[max_mismatches_allowed]);
+#endif
+
+ if (length_left >= length_right) {
+ /* querystart = querylength - mismatch_positions_left[max_mismatches_allowed]; -- wrong */
+ /* queryend = pos3; -- wrong */
+ querystart = pos5; /* same as for plus */
+ queryend = mismatch_positions_left[max_mismatches_allowed]; /* same as for plus */
+ alignstart = genomicstart - querystart; /* really alignstart_trim */
+ alignend = genomicstart - queryend; /* really alignend_trim */
+ } else {
+ /* querystart = pos5; -- wrong */
+ /* queryend = querylength - (mismatch_positions_right[max_mismatches_allowed] + 1); -- wrong */
+ querystart = mismatch_positions_right[max_mismatches_allowed] + 1; /* same as for plus */
+ queryend = pos3; /* same as for plus */
+ alignstart = genomicstart - querystart; /* really alignstart_trim */
+ alignend = genomicstart - queryend; /* really alignend_trim */
+ }
+
+#ifdef HAVE_ALLOCA
+ FREEA(mismatch_positions_left);
+ FREEA(mismatch_positions_right);
+#else
+ FREE(mismatch_positions_left);
+ FREE(mismatch_positions_right);
+#endif
+
Substring_free(&substring);
- return (T) NULL;
+ if ((substring = Substring_new(/*nmismatches_whole*/0,chrnum,chroffset,chrhigh,chrlength,
+ query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ /*trim_left_action*/PRE_TRIMMED,/*trim_right_action*/PRE_TRIMMED,
+ outofbounds_start,outofbounds_end,minlength,/*sensedir*/SENSE_NULL)) == NULL) {
+ debug0(printf("returning NULL\n"));
+ return (T) NULL;
+ } else {
+ Substring_set_nmismatches_terminal(substring,max_mismatches_allowed,/*nmismatches_bothdiff*/max_mismatches_allowed);
+ }
+#endif
+
}
}
new = (T) MALLOC_OUT(sizeof(*new));
debug0(printf("Stage3end_new_terminal %p: endtypes %s and %s, left %llu, genomicstart/end %llu..%llu, chrhigh %llu, chrnum %d, querystart %d, queryend %d\n",
new,Endtype_string(start_endtype),Endtype_string(end_endtype),
- (unsigned long long) left,(unsigned long long) genomicstart,(unsigned long long) genomicend,
+ (unsigned long long) left - chroffset,(unsigned long long) genomicstart - chroffset,(unsigned long long) genomicend - chroffset,
(unsigned long long) chrhigh,chrnum,querystart,queryend));
new->substrings_LtoH = List_push(NULL,(void *) substring);
@@ -7708,6 +8542,7 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
new->gmap_source = GMAP_NOT_APPLICABLE;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -7762,10 +8597,18 @@ Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
Stage3end_free(&new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ return new;
+
} else {
return new;
}
@@ -7776,9 +8619,9 @@ T
Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_length,
int ambig_end_length_5, int ambig_end_length_3,
Splicetype_T ambig_splicetype_5, Splicetype_T ambig_splicetype_3,
- double ambig_prob_5, double ambig_prob_3, double min_splice_prob,
+ double min_splice_prob,
struct Pair_T *pairarray, int npairs, int nsegments, int nintrons, int nindelbreaks,
- Univcoord_T left, int genomiclength, bool plusp, int genestrand, bool first_read_p,
+ Univcoord_T left, int genomiclength, bool plusp, int genestrand,
char *accession, int querylength, Chrnum_T chrnum,
Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int cdna_direction, int sensedir, GMAP_source_T gmap_source) {
@@ -7799,7 +8642,7 @@ Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_
*/
/* However, this leads to fatal bugs later, so restored these statements */
- debug0(printf("Entered Stage3end_new_gmap with first_read_p %d and sensedir %d\n",first_read_p,sensedir));
+ debug0(printf("Entered Stage3end_new_gmap with sensedir %d\n",sensedir));
start = &(pairarray[0]);
end = &(pairarray[npairs-1]);
@@ -7814,7 +8657,7 @@ Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_
Pair_dump_array_stderr(pairarray,npairs,/*zerobasedp*/true);
Pair_tokens_free(&cigar_tokens);
#ifdef CHECK_ASSERTIONS
- abort();
+ /* abort(); */
#endif
return (T) NULL;
@@ -7856,7 +8699,7 @@ Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_
debug0(printf("Stage3end_new_gmap %p: left %llu, genomicstart/end %u..%u, chrhigh %llu, chrnum %d, nmismatches %d, cdna_direction %d, sensedir %d, max_match_length %d, gmap_source %d\n",
new,(unsigned long long) left,(unsigned int) (genomicstart - chroffset),(unsigned int) (genomicend - chroffset),
(unsigned long long) chrhigh,chrnum,nmismatches_whole,cdna_direction,sensedir,max_match_length,gmap_source));
- debug0(printf(" ambig_end_length_5 %d (prob %f), ambig_end_length_3 %d (prob %f)\n",ambig_end_length_5,ambig_prob_5,ambig_end_length_3,ambig_prob_3));
+ debug0(printf(" ambig_end_length_5 %d, ambig_end_length_3 %d\n",ambig_end_length_5,ambig_end_length_3));
new->substrings_LtoH = (List_T) NULL;
new->substrings_1toN = (List_T) NULL;
@@ -7894,6 +8737,7 @@ Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_
new->gmap_source = gmap_source;
new->improved_by_gmap_p = false;
+ new->distant_splice_p = false;
new->chrnum = new->effective_chrnum = chrnum;
new->other_chrnum = 0;
new->chroffset = chroffset;
@@ -7913,7 +8757,7 @@ Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_
new->nindels = 0;
new->nmismatches_whole = nmismatches_whole;
- new->ntscore = nmismatches_whole;
+ new->ntscore = nmismatches_whole; /* equals nmismatches_bothdiff */
#if 1
/* This favors the trimmed results */
@@ -8072,13 +8916,21 @@ Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_
new->paired_seenp = false;
new->concordantp = false;
- new->circularpos = compute_circularpos(&new->alias,new);
- if (new->alias == +2 || new->alias == -2) {
+ new->circularpos = compute_circularpos(&new->circularalias,new);
+ if (new->circularalias == +2 || new->circularalias == -2) {
/* Stage3end_free(&new); -- Cannot use, because it frees pairarray */
Pair_tokens_free(&new->cigar_tokens);
/* No substrings or junctions */
FREE(new);
return (T) NULL;
+
+ } else if (new->circularalias >= 0) {
+ new->altlocp = false;
+ return new;
+
+ } else if ((new->altlocp = altlocp[chrnum]) == false) {
+ return new;
+
} else {
return new;
}
@@ -8098,6 +8950,10 @@ Stage3end_output_cmp (const void *a, const void *b) {
return -1;
} else if (y->mapq_loglik > x->mapq_loglik) {
return +1;
+ } else if (x->distant_splice_p == false && y->distant_splice_p == true) {
+ return -1;
+ } else if (y->distant_splice_p == false && x->distant_splice_p == true) {
+ return +1;
} else if (x->guided_insertlength > 0 && y->guided_insertlength == 0) {
return -1;
} else if (y->guided_insertlength > 0 && x->guided_insertlength == 0) {
@@ -8225,17 +9081,17 @@ Stage3end_compute_mapq (Stage3end_T this, Compress_T query_compress_fwd, Compres
static void
-Stage3end_display_prep (Stage3end_T this, char *queryuc_ptr, char *queryrc,
+Stage3end_display_prep (Stage3end_T this, char *queryuc_ptr,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
int amb_resolve, bool first_read_p) {
List_T p, q;
Substring_T substring, anchor;
Junction_T pre_junction, post_junction, junction;
- int extraleft, extraright, extralow, extrahigh;
+ int extraleft, extraright;
Univcoord_T left, ignore;
double donor_prob, acceptor_prob;
- int type;
-
+ /* int type; */
+ /* int extralow, extrahigh; */
if (this != NULL) {
debug0(printf("Doing a display prep of end %p\n",this));
@@ -8492,9 +9348,9 @@ Stage3end_filter_coverage (List_T hits, int min_coverage) {
Stage3end_T *
-Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
+Stage3end_eval_and_sort (int npaths, int *first_absmq, int *second_absmq,
Stage3end_T *stage3array, int maxpaths, Shortread_T queryseq,
- char *queryuc_ptr, char *queryrc,
+ char *queryuc_ptr,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
char *quality_string, bool displayp) {
float maxlik, loglik;
@@ -8505,19 +9361,19 @@ Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
int randomi, i;
Stage3end_T temp;
- if (*npaths == 0) {
+ if (npaths == 0) {
/* Skip */
*first_absmq = 0;
*second_absmq = 0;
- } else if (*npaths == 1) {
+ } else if (npaths == 1) {
stage3array[0]->mapq_loglik = MAPQ_MAXIMUM_SCORE;
stage3array[0]->mapq_score =
MAPQ_max_quality_score(Shortread_quality_string(queryseq),Shortread_fulllength(queryseq));
stage3array[0]->absmq_score = MAPQ_MAXIMUM_SCORE;
if (displayp == true) {
- Stage3end_display_prep(stage3array[0],queryuc_ptr,queryrc,query_compress_fwd,query_compress_rev,
+ Stage3end_display_prep(stage3array[0],queryuc_ptr,query_compress_fwd,query_compress_rev,
/*amb_resolve*/-1,/*first_read_p*/true);
}
*first_absmq = stage3array[0]->absmq_score;
@@ -8526,25 +9382,25 @@ Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
} else {
/* Determine whether to trim terminal ends */
non_terminal_p = false;
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
if (stage3array[i]->hittype != TERMINAL) {
non_terminal_p = true;
}
}
/* Compute mapq_loglik */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
Stage3end_compute_mapq(stage3array[i],query_compress_fwd,query_compress_rev,
quality_string,/*trim_terminals_p*/non_terminal_p ? false : true);
}
/* Sort by nmatches, then mapq */
- qsort(stage3array,*npaths,sizeof(Stage3end_T),Stage3end_output_cmp);
+ qsort(stage3array,npaths,sizeof(Stage3end_T),Stage3end_output_cmp);
if (want_random_p) {
/* Randomize among best alignments */
i = 1;
- while (i < *npaths && Stage3end_output_cmp(&(stage3array[i]),&(stage3array[0])) == 0) {
+ while (i < npaths && Stage3end_output_cmp(&(stage3array[i]),&(stage3array[0])) == 0) {
i++;
}
if (i > 1) { /* i is number of ties */
@@ -8558,7 +9414,7 @@ Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
}
/* Enforce monotonicity */
- for (i = *npaths - 1; i > 0; i--) {
+ for (i = npaths - 1; i > 0; i--) {
if (stage3array[i-1]->mapq_loglik < stage3array[i]->mapq_loglik) {
stage3array[i-1]->mapq_loglik = stage3array[i]->mapq_loglik;
}
@@ -8566,13 +9422,13 @@ Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
maxlik = stage3array[0]->mapq_loglik;
/* Subtract maxlik to avoid underflow */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
stage3array[i]->mapq_loglik -= maxlik;
}
/* Save on computation if possible */
- if (*npaths < maxpaths) {
- compute_npaths = *npaths;
+ if (npaths < maxpaths) {
+ compute_npaths = npaths;
} else {
compute_npaths = maxpaths;
}
@@ -8594,7 +9450,7 @@ Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
/* Compute Bayesian mapq */
total = 0.0;
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
total += (stage3array[i]->mapq_loglik = fasterexp(stage3array[i]->mapq_loglik));
}
@@ -8615,7 +9471,7 @@ Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
if (displayp == true) {
/* Prepare for display */
for (i = 0; i < compute_npaths; i++) {
- Stage3end_display_prep(stage3array[i],queryuc_ptr,queryrc,query_compress_fwd,query_compress_rev,
+ Stage3end_display_prep(stage3array[i],queryuc_ptr,query_compress_fwd,query_compress_rev,
/*amb_resolve*/-1,/*first_read_p*/true);
}
}
@@ -8708,10 +9564,14 @@ pair_insert_length (Stage3end_T hit5, Stage3end_T hit3) {
static Chrpos_T
pair_insert_length_unpaired (Stage3end_T hit5, Stage3end_T hit3) {
- if (hit5->chrnum != hit3->chrnum) {
+ if (hit5->effective_chrnum != hit3->effective_chrnum) {
debug10(printf("pair_insert_length: hit5->plusp %d != hit3->plusp %d, so returning 0\n",
hit5->plusp,hit3->plusp));
return 0;
+ } else if (hit5->distant_splice_p == true) {
+ return 0;
+ } else if (hit3->distant_splice_p == true) {
+ return 0;
} else if (hit5->high < hit3->low) {
return hit3->low - hit5->high + hit5->querylength + hit3->querylength;
} else if (hit3->high < hit5->low) {
@@ -8723,10 +9583,9 @@ pair_insert_length_unpaired (Stage3end_T hit5, Stage3end_T hit3) {
Stage3end_T *
-Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq, Stage3end_T guide,
+Stage3end_eval_and_sort_guided (int npaths, int *first_absmq, int *second_absmq, Stage3end_T guide,
Stage3end_T *stage3array, int maxpaths, Shortread_T queryseq,
- char *queryuc_ptr, char *queryrc,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
+ char *queryuc_ptr, Compress_T query_compress_fwd, Compress_T query_compress_rev,
char *quality_string, bool displayp) {
float maxlik, loglik;
float total, q; /* For Bayesian mapq calculation */
@@ -8736,19 +9595,19 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
int randomi, i;
Stage3end_T temp;
- if (*npaths == 0) {
+ if (npaths == 0) {
/* Skip */
*first_absmq = 0;
*second_absmq = 0;
- } else if (*npaths == 1) {
+ } else if (npaths == 1) {
stage3array[0]->mapq_loglik = MAPQ_MAXIMUM_SCORE;
stage3array[0]->mapq_score =
MAPQ_max_quality_score(Shortread_quality_string(queryseq),Shortread_fulllength(queryseq));
stage3array[0]->absmq_score = MAPQ_MAXIMUM_SCORE;
if (displayp == true) {
- Stage3end_display_prep(stage3array[0],queryuc_ptr,queryrc,query_compress_fwd,query_compress_rev,
+ Stage3end_display_prep(stage3array[0],queryuc_ptr,query_compress_fwd,query_compress_rev,
/*amb_resolve*/-1,/*first_read_p*/true);
}
*first_absmq = stage3array[0]->absmq_score;
@@ -8757,30 +9616,30 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
} else {
/* Determine whether to trim terminal ends */
non_terminal_p = false;
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
if (stage3array[i]->hittype != TERMINAL) {
non_terminal_p = true;
}
}
/* Compute mapq_loglik */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
Stage3end_compute_mapq(stage3array[i],query_compress_fwd,query_compress_rev,
quality_string,/*trim_terminals_p*/non_terminal_p ? false : true);
}
/* Compute insert_length relative to guide. This is the only change from the unguided procedure. */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
stage3array[i]->guided_insertlength = pair_insert_length_unpaired(stage3array[i],guide);
}
/* Sort by nmatches, then mapq */
- qsort(stage3array,*npaths,sizeof(Stage3end_T),Stage3end_output_cmp);
+ qsort(stage3array,npaths,sizeof(Stage3end_T),Stage3end_output_cmp);
if (want_random_p) {
/* Randomize among best alignments */
i = 1;
- while (i < *npaths && Stage3end_output_cmp(&(stage3array[i]),&(stage3array[0])) == 0) {
+ while (i < npaths && Stage3end_output_cmp(&(stage3array[i]),&(stage3array[0])) == 0) {
i++;
}
if (i > 1) { /* i is number of ties */
@@ -8794,7 +9653,7 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
}
/* Enforce monotonicity */
- for (i = *npaths - 1; i > 0; i--) {
+ for (i = npaths - 1; i > 0; i--) {
if (stage3array[i-1]->mapq_loglik < stage3array[i]->mapq_loglik) {
stage3array[i-1]->mapq_loglik = stage3array[i]->mapq_loglik;
}
@@ -8802,13 +9661,13 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
maxlik = stage3array[0]->mapq_loglik;
/* Subtract maxlik to avoid underflow */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
stage3array[i]->mapq_loglik -= maxlik;
}
/* Save on computation if possible */
- if (*npaths < maxpaths) {
- compute_npaths = *npaths;
+ if (npaths < maxpaths) {
+ compute_npaths = npaths;
} else {
compute_npaths = maxpaths;
}
@@ -8830,7 +9689,7 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
/* Compute Bayesian mapq */
total = 0.0;
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
total += (stage3array[i]->mapq_loglik = fasterexp(stage3array[i]->mapq_loglik));
}
@@ -8851,7 +9710,7 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
if (displayp == true) {
/* Prepare for display */
for (i = 0; i < compute_npaths; i++) {
- Stage3end_display_prep(stage3array[i],queryuc_ptr,queryrc,query_compress_fwd,query_compress_rev,
+ Stage3end_display_prep(stage3array[i],queryuc_ptr,query_compress_fwd,query_compress_rev,
/*amb_resolve*/-1,/*first_read_p*/true);
}
}
@@ -8881,7 +9740,7 @@ Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq
static List_T
-Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level, int suboptimal_mismatches,
+Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
int querylength, bool keep_gmap_p, bool finalp) {
List_T optimal = NULL, p, q;
@@ -8890,12 +9749,12 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
int n;
int minscore = querylength;
int max_nmatches = 0, max_nmatches_posttrim = 0;
- int trim_left = querylength, trim_right = querylength;
+ int trim_left = querylength, trim_right = querylength, trim_left_0, trim_right_0;
int nindelbreaks;
int best_nsegments;
-#ifdef TRANSLOC_SPECIAL
- bool non_translocation_p = false;
+#ifdef DISTANT_SPLICE_SPECIAL
+ bool shortdistance_p = false;
#endif
@@ -8910,9 +9769,9 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
for (p = hitlist; p != NULL; p = p->rest) {
hit = (T) p->first;
-#ifdef TRANSLOC_SPECIAL
- if (hit->chrnum != 0) {
- non_translocation_p = true;
+#ifdef DISTANT_SPLICE_SPECIAL
+ if (hit->distant_splice_p == false) {
+ shortdistance_p = true;
}
#endif
#if 0
@@ -8997,9 +9856,17 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
for (q = hit->substrings_1toN; q != NULL; q = List_next(q)) {
substring = (Substring_T) List_head(q);
- hit->score_eventrim += Substring_count_mismatches_region(substring,trim_left,trim_right,
+ trim_left_0 = trim_left;
+ trim_right_0 = trim_right;
+ if (Substring_mandatory_trim_left(substring) > trim_left_0) {
+ trim_left_0 = Substring_mandatory_trim_left(substring);
+ }
+ if (Substring_mandatory_trim_right(substring) > trim_right_0) {
+ trim_right_0 = Substring_mandatory_trim_right(substring);
+ }
+ hit->score_eventrim += Substring_count_mismatches_region(substring,trim_left_0,trim_right_0,
query_compress_fwd,query_compress_rev);
- debug4(printf(" substring %d.",Substring_count_mismatches_region(substring,trim_left,trim_right,
+ debug4(printf(" substring %d.",Substring_count_mismatches_region(substring,trim_left_0,trim_right_0,
query_compress_fwd,query_compress_rev)));
}
@@ -9022,8 +9889,8 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
hit = (T) p->first;
if (hit->hittype == TERMINAL && finalp == false) {
/* Don't use to determine minscore */
-#ifdef TRANSLOC_SPECIAL
- } else if (hit->chrnum == 0 && non_translocation_p == true) {
+#ifdef DISTANT_SPLICE_SPECIAL
+ } else if (hit->distant_splice_p == true && shortdistance_p == true) {
/* Skip, since we will eliminate */
#endif
} else {
@@ -9043,10 +9910,10 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
}
debug4(printf("Stage3end_optimal_score over %d hits: minscore = %d + subopt:%d\n",
- n,minscore,suboptimal_mismatches));
- minscore += suboptimal_mismatches;
- max_nmatches -= suboptimal_mismatches;
- max_nmatches_posttrim -= suboptimal_mismatches;
+ n,minscore,subopt_levels));
+ minscore += subopt_levels;
+ max_nmatches -= subopt_levels;
+ max_nmatches_posttrim -= subopt_levels;
#if 0
if (non_gmap_terminal_p == false && minscore > cutoff_level) {
@@ -9054,7 +9921,7 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
cutoff_level = minscore;
}
#else
- cutoff_level = minscore;
+ /* cutoff_level = minscore; */
#endif
for (p = hitlist; p != NULL; p = p->rest) {
@@ -9069,8 +9936,8 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
debug4(printf("Keeping a hit of type GMAP\n"));
optimal = List_push(optimal,hit);
-#ifdef TRANSLOC_SPECIAL
- } else if (hit->chrnum == 0 && non_translocation_p == true) {
+#ifdef DISTANT_SPLICE_SPECIAL
+ } else if (hit->distant_splice_p == true && shortdistance_p == true) {
debug4(printf("Eliminating a hit with splice translocation\n"));
*eliminatedp = true;
Stage3end_free(&hit);
@@ -9152,18 +10019,17 @@ Stage3end_optimal_score_aux (bool *eliminatedp, List_T hitlist, int cutoff_level
List_T
-Stage3end_optimal_score (List_T hitlist, int cutoff_level, int suboptimal_mismatches,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
+Stage3end_optimal_score (List_T hitlist, Compress_T query_compress_fwd, Compress_T query_compress_rev,
int querylength, bool keep_gmap_p, bool finalp) {
List_T optimal;
bool eliminatedp;
- optimal = Stage3end_optimal_score_aux(&eliminatedp,hitlist,cutoff_level,suboptimal_mismatches,
+ optimal = Stage3end_optimal_score_aux(&eliminatedp,hitlist,
query_compress_fwd,query_compress_rev,
querylength,keep_gmap_p,finalp);
while (eliminatedp == true) {
- optimal = Stage3end_optimal_score_aux(&eliminatedp,optimal,cutoff_level,suboptimal_mismatches,
+ optimal = Stage3end_optimal_score_aux(&eliminatedp,optimal,
query_compress_fwd,query_compress_rev,
querylength,keep_gmap_p,finalp);
}
@@ -9179,7 +10045,7 @@ unalias_circular (T hit) {
Substring_T substring;
debug12(printf("Calling unalias_circular\n"));
- assert(hit->alias == +1);
+ assert(hit->circularalias == +1);
if (hit->hittype == GMAP) {
Pair_unalias_circular(hit->pairarray,hit->npairs,chrlength);
@@ -9196,7 +10062,7 @@ unalias_circular (T hit) {
hit->low -= chrlength;
hit->high -= chrlength;
- hit->alias = -1;
+ hit->circularalias = -1;
return;
}
@@ -9210,7 +10076,7 @@ Stage3end_unalias_circular (List_T hitlist) {
for (p = hitlist; p != NULL; p = p->rest) {
hit = (T) p->first;
- if (hit->alias == +1) {
+ if (hit->circularalias == +1) {
unalias_circular(hit);
}
}
@@ -9232,13 +10098,13 @@ Stage3end_remove_circular_alias (List_T hitlist) {
for (p = hitlist; p != NULL; p = p->rest) {
hit = (T) p->first;
- if (hit->alias == +1) {
+ if (hit->circularalias == +1) {
/* First, try to salvage alias +1 */
unalias_circular(hit);
}
if (hit->chrnum == 0) {
- /* Distant splice */
+ /* Translocation */
newlist = List_push(newlist,(void *) hit);
} else {
@@ -9299,8 +10165,8 @@ Stage3end_noptimal (List_T hitlist, int querylength) {
static Univcoord_T
-normalize_coord (Univcoord_T orig, int alias, Chrpos_T chrlength) {
- if (alias == +1) {
+normalize_coord (Univcoord_T orig, int circularalias, Chrpos_T chrlength) {
+ if (circularalias == +1) {
return orig - chrlength;
} else {
return orig;
@@ -9314,15 +10180,51 @@ duplicate_sort_cmp (const void *a, const void *b) {
int cmp;
T x = * (T *) a;
T y = * (T *) b;
- Univcoord_T x_genomicstart, x_genomicend, y_genomicstart, y_genomicend;
+ Univcoord_T x_genomicstart, y_genomicstart;
+ Univcoord_T x_genomicend, y_genomicend;
List_T p, q;
Substring_T x_substring, y_substring;
- x_genomicstart = normalize_coord(x->genomicstart,x->alias,x->chrlength);
- x_genomicend = normalize_coord(x->genomicend,x->alias,x->chrlength);
+ if (altlocp[x->chrnum] == true && altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= alias_starts[x->chrnum] &&
+ alias_starts[y->chrnum] <= alias_ends[x->chrnum]) {
+ /* The primary regions overlap */
+ return 0;
+ } else if (alias_starts[x->chrnum] < alias_starts[y->chrnum]) {
+ return -1;
+ } else if (alias_starts[y->chrnum] < alias_starts[x->chrnum]) {
+ return +1;
+ } else if (alias_ends[x->chrnum] < alias_ends[y->chrnum]) {
+ return -1;
+ } else if (alias_ends[y->chrnum] < alias_ends[x->chrnum]) {
+ return +1;
+ } else {
+ return 0;
+ }
+
+ } else if (altlocp[x->chrnum] == true) {
+ if (y->genomicend >= alias_starts[x->chrnum] &&
+ y->genomicstart <= alias_ends[x->chrnum]) {
+ /* y overlaps with the primary region for x */
+ return +1; /* Put primary region first */
+ }
+ /* Don't overlap, so fall through to rest of procedure */
+
+ } else if (altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= x->genomicstart &&
+ alias_starts[y->chrnum] <= x->genomicend) {
+ /* x overlaps with the primary region for y */
+ return -1; /* Put primary region first */
+ }
+ /* Don't overlap, so fall through to rest of procedure */
+ }
+
+
+ x_genomicstart = normalize_coord(x->genomicstart,x->circularalias,x->chrlength);
+ x_genomicend = normalize_coord(x->genomicend,x->circularalias,x->chrlength);
- y_genomicstart = normalize_coord(y->genomicstart,y->alias,y->chrlength);
- y_genomicend = normalize_coord(y->genomicend,y->alias,y->chrlength);
+ y_genomicstart = normalize_coord(y->genomicstart,y->circularalias,y->chrlength);
+ y_genomicend = normalize_coord(y->genomicend,y->circularalias,y->chrlength);
if (x_genomicstart < y_genomicstart) {
@@ -9333,16 +10235,16 @@ duplicate_sort_cmp (const void *a, const void *b) {
return -1;
} else if (x->hittype > y->hittype) {
return +1;
- } else if (x->genomicend < y->genomicend) {
+ } else if (x_genomicend < y_genomicend) {
return -1;
- } else if (x->genomicend > y->genomicend) {
+ } else if (x_genomicend > y_genomicend) {
return +1;
} else {
for (p = x->substrings_1toN, q = y->substrings_1toN; p != NULL && q != NULL; p = List_next(p), q = List_next(q)) {
x_substring = (Substring_T) List_head(p);
y_substring = (Substring_T) List_head(q);
- if ((cmp = Substring_compare(x_substring,y_substring,x->alias,y->alias,x->chrlength,y->chrlength)) != 0) {
+ if ((cmp = Substring_compare(x_substring,y_substring,x->circularalias,y->circularalias,x->chrlength,y->chrlength)) != 0) {
return cmp;
}
}
@@ -9382,11 +10284,33 @@ duplicate_equiv_cmp (const void *a, const void *b) {
Univcoord_T x_genomicstart, x_genomicend, y_genomicstart, y_genomicend;
- x_genomicstart = normalize_coord(x->genomicstart,x->alias,x->chrlength);
- x_genomicend = normalize_coord(x->genomicend,x->alias,x->chrlength);
+ if (altlocp[x->chrnum] == true && altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= alias_starts[x->chrnum] &&
+ alias_starts[y->chrnum] <= alias_ends[x->chrnum]) {
+ /* The primary regions overlap */
+ return 0;
+ }
+
+ } else if (altlocp[x->chrnum] == true) {
+ if (y->genomicend >= alias_starts[x->chrnum] &&
+ y->genomicstart <= alias_ends[x->chrnum]) {
+ /* y overlaps with the primary region for x */
+ return 0;
+ }
+
+ } else if (altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= x->genomicstart &&
+ alias_starts[y->chrnum] <= x->genomicend) {
+ /* x overlaps with the primary region for y */
+ return 0;
+ }
+ }
+
+ x_genomicstart = normalize_coord(x->genomicstart,x->circularalias,x->chrlength);
+ x_genomicend = normalize_coord(x->genomicend,x->circularalias,x->chrlength);
- y_genomicstart = normalize_coord(y->genomicstart,y->alias,y->chrlength);
- y_genomicend = normalize_coord(y->genomicend,y->alias,y->chrlength);
+ y_genomicstart = normalize_coord(y->genomicstart,y->circularalias,y->chrlength);
+ y_genomicend = normalize_coord(y->genomicend,y->circularalias,y->chrlength);
if (x_genomicstart < y_genomicstart) {
return -1;
@@ -9406,7 +10330,7 @@ duplicate_equiv_cmp (const void *a, const void *b) {
for (p = x->substrings_1toN, q = y->substrings_1toN; p != NULL && q != NULL; p = List_next(p), q = List_next(q)) {
x_substring = (Substring_T) List_head(p);
y_substring = (Substring_T) List_head(q);
- if ((cmp = Substring_compare(x_substring,y_substring,x->alias,y->alias,x->chrlength,y->chrlength)) != 0) {
+ if ((cmp = Substring_compare(x_substring,y_substring,x->circularalias,y->circularalias,x->chrlength,y->chrlength)) != 0) {
return cmp;
}
}
@@ -9652,9 +10576,9 @@ Stage3end_remove_duplicates (List_T hitlist) {
debug7(
for (i = 0; i < n; i++) {
x = hits[i];
- printf(" Initial %d (%s): %p #%d:%u..%u, alias %d, nmatches %d, score %d ",
+ printf(" Initial %d (%s): %p #%d:%u..%u, circularalias %d, nmatches %d, score %d ",
i,hittype_string(x->hittype),x,x->chrnum,x->genomicstart - x->chroffset,x->genomicend - x->chroffset,
- x->alias,x->nmatches,x->score);
+ x->circularalias,x->nmatches,x->score);
Stage3end_print_substrings(x);
printf("\n");
}
@@ -9804,11 +10728,46 @@ hit_sort_cmp (const void *a, const void *b) {
Stage3end_T x = * (Stage3end_T *) a;
Stage3end_T y = * (Stage3end_T *) b;
- debug7(printf("Comparing %s: #%d:%u..%u, alias %d, nmatches %d, score %d with %s: #%d:%u..%u, alias %d, nmatches %d, score %d\n",
+ debug7(printf("Comparing %s: #%d:%u..%u, circularalias %d, nmatches %d, score %d with %s: #%d:%u..%u, circularalias %d, nmatches %d, score %d\n",
hittype_string(x->hittype),x->chrnum,x->genomicstart-x->chroffset,x->genomicend-x->chroffset,
- x->alias,x->nmatches,x->score,
+ x->circularalias,x->nmatches,x->score,
hittype_string(y->hittype),y->chrnum,y->genomicstart-y->chroffset,y->genomicend-y->chroffset,
- y->alias,y->nmatches,y->score));
+ y->circularalias,y->nmatches,y->score));
+
+ if (altlocp[x->chrnum] == true && altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= alias_starts[x->chrnum] &&
+ alias_starts[y->chrnum] <= alias_ends[x->chrnum]) {
+ /* The primary regions overlap */
+ return 0;
+ } else if (alias_starts[x->chrnum] < alias_starts[y->chrnum]) {
+ return -1;
+ } else if (alias_starts[y->chrnum] < alias_starts[x->chrnum]) {
+ return +1;
+ } else if (alias_ends[x->chrnum] < alias_ends[y->chrnum]) {
+ return -1;
+ } else if (alias_ends[y->chrnum] < alias_ends[x->chrnum]) {
+ return +1;
+ } else {
+ return 0;
+ }
+
+ } else if (altlocp[x->chrnum] == true) {
+ if (y->genomicend >= alias_starts[x->chrnum] &&
+ y->genomicstart <= alias_ends[x->chrnum]) {
+ /* y overlaps with the primary region for x */
+ return +1; /* Put primary region first */
+ }
+ /* Don't overlap, so fall through to rest of procedure */
+
+ } else if (altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= x->genomicstart &&
+ alias_starts[y->chrnum] <= x->genomicend) {
+ /* x overlaps with the primary region for y */
+ return -1; /* Put primary region first */
+ }
+ /* Don't overlap, so fall through to rest of procedure */
+ }
+
if (x->plusp > y->plusp) {
return -1;
@@ -9887,6 +10846,11 @@ hit_sort_cmp (const void *a, const void *b) {
return +1;
#endif
+ } else if (x->altlocp < y->altlocp) {
+ return -1;
+ } else if (y->altlocp < x->altlocp) {
+ return +1;
+
} else if (x->sensedir != 0 && y->sensedir == 0) {
return -1;
} else if (y->sensedir != 0 && x->sensedir == 0) {
@@ -9905,6 +10869,28 @@ hit_sort_cmp (const void *a, const void *b) {
static int
hit_equiv_cmp (Stage3end_T x, Stage3end_T y) {
+ if (altlocp[x->chrnum] == true && altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= alias_starts[x->chrnum] &&
+ alias_starts[y->chrnum] <= alias_ends[x->chrnum]) {
+ /* The primary regions overlap */
+ return 0;
+ }
+
+ } else if (altlocp[x->chrnum] == true) {
+ if (y->genomicend >= alias_starts[x->chrnum] &&
+ y->genomicstart <= alias_ends[x->chrnum]) {
+ /* y overlaps with the primary region for x */
+ return 0;
+ }
+
+ } else if (altlocp[y->chrnum] == true) {
+ if (alias_ends[y->chrnum] >= x->genomicstart &&
+ alias_starts[y->chrnum] <= x->genomicend) {
+ /* x overlaps with the primary region for y */
+ return 0;
+ }
+ }
+
if (x->plusp > y->plusp) {
return -1;
} else if (y->plusp > x->plusp) {
@@ -10031,22 +11017,14 @@ hit_goodness_cmp (bool *equalp, Stage3end_T hit,
}
#endif
- if (hit->nmatches < best_hit->nmatches) {
- debug7(printf(" => %d loses by nmatches\n",k));
- return -1;
- } else if (hit->nmatches > best_hit->nmatches) {
- debug7(printf(" => %d wins by nmatches\n",k));
- return +1;
-
-#if 0
- /* Causes ambiguous splices to lose to a definitive splice, which could be wrong */
- } else if (hit->nmatches_posttrim < best_hit->nmatches_posttrim) {
- debug7(printf(" => %d loses by nmatches (post-trim)\n",k));
+ /* Favors definitive splices over ambiguous splices. So need to
+ make sure we don't make definitive splices unnecessarily */
+ if (hit->nmatches_posttrim < best_hit->nmatches_posttrim) {
+ debug7(printf(" => %d loses by nmatches_posttrim\n",k));
return -1;
} else if (hit->nmatches_posttrim > best_hit->nmatches_posttrim) {
- debug7(printf(" => %d wins by nmatches (post-trim)\n",k));
+ debug7(printf(" => %d wins by nmatches_posttrim\n",k));
return +1;
-#endif
#if 0
} else if (hit->nsplices > best_hit->nsplices) {
@@ -10082,10 +11060,10 @@ hit_goodness_cmp (bool *equalp, Stage3end_T hit,
debug7(printf(" => %d wins by nindels\n",k));
return +1;
- } else if (hit->chrnum == 0 && best_hit->chrnum != 0) {
+ } else if (hit->distant_splice_p == true && best_hit->distant_splice_p == false) {
debug7(printf(" => %d loses because distant splice\n",k));
return -1;
- } else if (hit->chrnum > 0 && best_hit->chrnum == 0) {
+ } else if (hit->distant_splice_p == false && best_hit->distant_splice_p == true) {
debug7(printf(" => %d wins because not distant splice\n",k));
return +1;
@@ -10120,6 +11098,7 @@ hit_goodness_cmp (bool *equalp, Stage3end_T hit,
}
+/* Not clear how to handle altloc */
static bool
hit_subsumption (Stage3end_T x, Stage3end_T y) {
if (x->plusp != y->plusp) {
@@ -10194,9 +11173,9 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
debug7(
for (i = 0; i < n; i++) {
hit = hits[i];
- printf(" Initial %d (%s): %p #%d:%u..%u, alias %d, nmatches %d, score %d\n",
+ printf(" Initial %d (%s): %p #%d:%u..%u, circularalias %d, nmatches %d, score %d\n",
i,hittype_string(hit->hittype),hit,hit->chrnum,hit->genomicstart-hit->chroffset,hit->genomicend-hit->chroffset,
- hit->alias,hit->nmatches,hit->score);
+ hit->circularalias,hit->nmatches,hit->score);
}
);
@@ -10280,7 +11259,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
i = 0;
while (i < n) {
j = i;
- if (hits[i]->chrnum != 0) {
+ if (hits[i]->distant_splice_p == false) {
while (j+1 < n && hit_subsumption(hits[i],hits[j+1]) == true) {
j = j+1;
}
@@ -10290,7 +11269,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
/* Find bad superstretches */
for (k = i; k <= j; k++) {
- if (hits[k]->chrnum == 0) {
+ if (hits[k]->distant_splice_p == true) {
/* Skip */
} else if (hit_bad_superstretch_p(hits[k],hits,k,j,finalp) == true) {
eliminate[k] = true;
@@ -10369,7 +11348,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
i = 0;
while (i < n) {
j = i;
- if (hits[i]->chrnum != 0) {
+ if (hits[i]->distant_splice_p == false) {
while (j+1 < n && hit_subsumption(hits[i],hits[j+1]) == true) {
j = j+1;
}
@@ -10382,7 +11361,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
debug7(printf("Assume best is %d\n",besti));
for (k = i+1; k <= j; k++) {
- if (hits[k]->chrnum == 0) {
+ if (hits[k]->distant_splice_p == true) {
/* Skip */
} else {
cmp = hit_goodness_cmp(&equalp,hits[k],
@@ -10402,7 +11381,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
for (k = i; k <= j; k++) {
if (k == besti) {
/* Skip */
- } else if (hits[k]->chrnum == 0) {
+ } else if (hits[k]->distant_splice_p == true) {
/* Skip */
} else if (hit_goodness_cmp(&equalp,hits[k],
#ifdef DEBUG7
@@ -10424,7 +11403,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
j = n - 1;
while (j >= 0) {
i = j;
- if (hits[j]->chrnum != 0) {
+ if (hits[j]->distant_splice_p == false) {
while (i-1 >= 0 && hit_subsumption(hits[j],hits[i-1]) == true) {
i = i-1;
}
@@ -10436,7 +11415,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
debug7(printf("Assume best is %d\n",besti));
for (k = i+1; k <= j; k++) {
- if (hits[k]->chrnum == 0) {
+ if (hits[k]->distant_splice_p == true) {
/* Skip */
} else {
cmp = hit_goodness_cmp(&equalp,hits[k],
@@ -10456,7 +11435,7 @@ Stage3end_remove_overlaps (List_T hitlist, bool finalp) {
for (k = i; k <= j; k++) {
if (k == besti) {
/* Skip */
- } else if (hits[k]->chrnum == 0) {
+ } else if (hits[k]->distant_splice_p == true) {
/* Skip */
} else if (hit_goodness_cmp(&equalp,hits[k],
#ifdef DEBUG7
@@ -10736,6 +11715,8 @@ print_alignment_info (Filestring_T fp, int nblocks, int score, int mapq_score, b
Pairtype_T
Stage3_determine_pairtype (T hit5, T hit3) {
+ int pairmax;
+
debug14(printf("Entered Stage3_determine_pairtype\n"));
if (hit5->effective_chrnum != hit3->effective_chrnum) {
debug14(printf("Returning unpaired\n"));
@@ -10747,23 +11728,37 @@ Stage3_determine_pairtype (T hit5, T hit3) {
if (hit3->genomicend < hit5->genomicstart) {
debug14(printf("Returning paired_scramble\n"));
return PAIRED_SCRAMBLE;
- } else if (hit3->genomicstart > hit5->genomicend + pairmax) {
- debug14(printf("Returning paired_toolong\n"));
- return PAIRED_TOOLONG;
} else {
- debug14(printf("Returning concordant\n"));
- return CONCORDANT;
+ if (circularp[hit5->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
+ } else {
+ pairmax = pairmax_linear;
+ }
+ if (hit3->genomicstart > hit5->genomicend + pairmax) {
+ debug14(printf("Returning paired_toolong\n"));
+ return PAIRED_TOOLONG;
+ } else {
+ debug14(printf("Returning concordant\n"));
+ return CONCORDANT;
+ }
}
} else {
if (hit3->genomicend > hit5->genomicstart) {
debug14(printf("Returning paired_scramble\n"));
return PAIRED_SCRAMBLE;
- } else if (hit3->genomicstart + pairmax < hit5->genomicend) {
- debug14(printf("Returning paired_toolong\n"));
- return PAIRED_TOOLONG;
} else {
- debug14(printf("Returning concordant\n"));
- return CONCORDANT;
+ if (circularp[hit3->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
+ } else {
+ pairmax = pairmax_linear;
+ }
+ if (hit3->genomicstart + pairmax < hit5->genomicend) {
+ debug14(printf("Returning paired_toolong\n"));
+ return PAIRED_TOOLONG;
+ } else {
+ debug14(printf("Returning concordant\n"));
+ return CONCORDANT;
+ }
}
}
}
@@ -10779,6 +11774,16 @@ Stage3pair_circularp (Stage3pair_T this) {
return this->circularp;
}
+bool
+Stage3pair_altlocp (Stage3pair_T this) {
+ if (altlocp[this->hit5->chrnum] == true) {
+ return true;
+ } else if (altlocp[this->hit3->chrnum] == true) {
+ return true;
+ } else {
+ return false;
+ }
+}
#if 0
@@ -11096,7 +12101,8 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
bool invertp, int quality_shift) {
Stage3pair_T *stage3pairarray, stage3pair;
T *stage3array, *stage3array_mate, this, hit5, hit3;
- int npaths, npaths_mate, pathnum, first_absmq, second_absmq;
+ int npaths_primary, npaths_altloc, npaths_mate_primary, npaths_mate_altloc, pathnum;
+ int first_absmq, second_absmq;
bool excessivep, translocationp;
@@ -11115,7 +12121,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
/* If failedinput_root != NULL, then this case is handled by calling procedure */
} else if (resulttype == CONCORDANT_UNIQ) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
stage3pair = stage3pairarray[0];
hit5 = stage3pair->hit5;
hit3 = stage3pair->hit3;
@@ -11154,13 +12160,13 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
} else if (resulttype == CONCORDANT_TRANSLOC) {
Filestring_set_split_output(fp,OUTPUT_CT);
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
- if (quiet_if_excessive_p && npaths > maxpaths) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths) {
if (print_m8_p == false) {
/* No xs category for transloc, so ignore quiet-if-excessive_p */
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,CONCORDANT_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT);
FPRINTF(fp," (transloc)");
print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
@@ -11179,7 +12185,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
} else {
if (print_m8_p == false) {
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,CONCORDANT_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT);
FPRINTF(fp," (transloc)");
print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
@@ -11188,7 +12194,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = stage3pair->hit5;
hit3 = stage3pair->hit3;
@@ -11213,13 +12219,13 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
} else if (resulttype == CONCORDANT_MULT) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
- if (quiet_if_excessive_p && npaths > maxpaths) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths) {
Filestring_set_split_output(fp,OUTPUT_CX);
if (print_m8_p == false) {
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,CONCORDANT_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT);
print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
@@ -11238,7 +12244,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Filestring_set_split_output(fp,OUTPUT_CM);
if (print_m8_p == false) {
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,CONCORDANT_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,CONCORDANT_TEXT);
print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
@@ -11246,7 +12252,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = stage3pair->hit5;
hit3 = stage3pair->hit3;
@@ -11271,7 +12277,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
} else if (resulttype == PAIRED_UNIQ) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
stage3pair = stage3pairarray[0];
if (stage3pair->circularp == true) {
@@ -11317,13 +12323,13 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
}
} else if (resulttype == PAIRED_MULT) {
- stage3pairarray = (Stage3pair_T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3pairarray = (Stage3pair_T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
- if (quiet_if_excessive_p && npaths > maxpaths) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths) {
Filestring_set_split_output(fp,OUTPUT_PX);
if (print_m8_p == false) {
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,PAIRED_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,PAIRED_TEXT);
print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
@@ -11342,7 +12348,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Filestring_set_split_output(fp,OUTPUT_PM);
if (print_m8_p == false) {
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,PAIRED_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,PAIRED_TEXT);
print_barcode_and_quality(fp,queryseq,invertp,quality_shift);
@@ -11350,7 +12356,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
Shortread_print_header(fp,headerseq1,headerseq2);
}
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
stage3pair = stage3pairarray[pathnum-1];
hit5 = stage3pair->hit5;
hit3 = stage3pair->hit3;
@@ -11378,20 +12384,20 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
/* Print as singles */
if (firstp == true) {
/* Get stage3array_mate first to avoid incorrect values for npaths */
- stage3array_mate = (T *) Result_array2(&npaths_mate,&first_absmq,&second_absmq,result);
- stage3array = (T *) Result_array(&npaths,&first_absmq,&second_absmq,result);
+ stage3array_mate = (T *) Result_array2(&npaths_mate_primary,&npaths_mate_altloc,&first_absmq,&second_absmq,result);
+ stage3array = (T *) Result_array(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
} else {
/* Get stage3array_mate first to avoid incorrect values for npaths */
- stage3array_mate = (T *) Result_array(&npaths_mate,&first_absmq,&second_absmq,result);
- stage3array = (T *) Result_array2(&npaths,&first_absmq,&second_absmq,result);
+ stage3array_mate = (T *) Result_array(&npaths_mate_primary,&npaths_mate_altloc,&first_absmq,&second_absmq,result);
+ stage3array = (T *) Result_array2(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,result);
}
excessivep = false;
translocationp = false;
if (resulttype == HALFMAPPING_UNIQ) {
- if (npaths > 0 && Stage3end_circularpos(stage3array[0]) > 0) {
+ if (npaths_primary + npaths_altloc > 0 && Stage3end_circularpos(stage3array[0]) > 0) {
Filestring_set_split_output(fp,OUTPUT_HC);
- } else if (npaths_mate > 0 && Stage3end_circularpos(stage3array_mate[0]) > 0) {
+ } else if (npaths_mate_primary + npaths_mate_altloc > 0 && Stage3end_circularpos(stage3array_mate[0]) > 0) {
Filestring_set_split_output(fp,OUTPUT_HC);
} else {
Filestring_set_split_output(fp,OUTPUT_HU);
@@ -11402,7 +12408,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
translocationp = true;
} else if (resulttype == HALFMAPPING_MULT) {
- if (quiet_if_excessive_p && npaths > maxpaths) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths) {
Filestring_set_split_output(fp,OUTPUT_HX);
excessivep = true;
} else {
@@ -11410,9 +12416,9 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
}
} else if (resulttype == UNPAIRED_UNIQ) {
- if (npaths > 0 && Stage3end_circularpos(stage3array[0]) > 0) {
+ if (npaths_primary + npaths_altloc > 0 && Stage3end_circularpos(stage3array[0]) > 0) {
Filestring_set_split_output(fp,OUTPUT_UC);
- } else if (npaths_mate > 0 && Stage3end_circularpos(stage3array_mate[0]) > 0) {
+ } else if (npaths_mate_primary + npaths_mate_altloc > 0 && Stage3end_circularpos(stage3array_mate[0]) > 0) {
Filestring_set_split_output(fp,OUTPUT_UC);
} else {
Filestring_set_split_output(fp,OUTPUT_UU);
@@ -11423,7 +12429,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
translocationp = true;
} else if (resulttype == UNPAIRED_MULT) {
- if (quiet_if_excessive_p && npaths > maxpaths) {
+ if (quiet_if_excessive_p && npaths_primary + npaths_altloc > maxpaths) {
Filestring_set_split_output(fp,OUTPUT_UX);
excessivep = true;
} else {
@@ -11437,7 +12443,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
if (print_m8_p == false) {
print_query_header(fp,initchar,queryseq,invertp);
- FPRINTF(fp,"\t%d %s",npaths,UNPAIRED_TEXT);
+ FPRINTF(fp,"\t%d %s",npaths_primary + npaths_altloc,UNPAIRED_TEXT);
if (translocationp == true) {
FPRINTF(fp," (transloc)");
}
@@ -11456,7 +12462,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
} else {
if (firstp == true) {
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
this = stage3array[pathnum-1];
Stage3end_print(fp,this,this->score,
chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/1",
@@ -11464,7 +12470,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
/*insertlength*/0,/*pairscore*/0,/*pairtype*/UNPAIRED,this->mapq_score);
}
} else {
- for (pathnum = 1; pathnum <= npaths && pathnum <= maxpaths; pathnum++) {
+ for (pathnum = 1; pathnum <= npaths_primary + npaths_altloc && pathnum <= maxpaths; pathnum++) {
this = stage3array[pathnum-1];
Stage3end_print(fp,this,this->score,
chromosome_iit,queryseq,headerseq1,/*acc_suffix*/"/2",
@@ -11521,9 +12527,8 @@ strip_gaps_at_tail (List_T pairs) {
static List_T
Stage3end_convert_to_pairs (List_T pairs, T hit, Shortread_T queryseq,
int hardclip_low, int hardclip_high, int queryseq_offset) {
- Pair_T pair;
- List_T newpairs = NULL, p, q;
- Chrpos_T genomicpos1, genomicpos2;
+ List_T p, q;
+ /* Chrpos_T genomicpos1, genomicpos2; */
Substring_T substring, prev_substring;
Junction_T junction;
Junctiontype_T type;
@@ -11915,10 +12920,7 @@ overlap3_gmap_minus (int *querypos, Chrpos_T *genomicstart, Chrpos_T *genomicend
static void
resolve_inside_ambiguous_splice_plus (int *unresolved_amb_length, int *amb_resolve_5, int *amb_resolve_3,
- int *amb_status_inside, T hit5, T hit3, Univcoord_T *splicesites,
- Compress_T query5_compress_fwd, Compress_T query3_compress_fwd,
- int localsplicing_penalty, int querylength5, int querylength3,
- int genestrand) {
+ int *amb_status_inside, T hit5, T hit3, int querylength5, int querylength3) {
int insertlength;
Univcoord_T genomicstart, genomicend;
int nbingo, bingoi5, bingoi3;
@@ -11926,11 +12928,6 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_length, int *amb_resol
int best_nmismatches, nmismatches;
Substring_T substring5, substring3;
-#ifdef LARGE_GENOMES
- Uint8list_T ambcoords;
-#else
- Uintlist_T ambcoords;
-#endif
Univcoord_T *end_ambcoords, *start_ambcoords;
int *end_amb_nmismatches, *start_amb_nmismatches;
int end_amb_length_5, start_amb_length_3;
@@ -12131,23 +13128,14 @@ resolve_inside_ambiguous_splice_plus (int *unresolved_amb_length, int *amb_resol
static void
resolve_inside_ambiguous_splice_minus (int *unresolved_amb_length, int *amb_resolve_5, int *amb_resolve_3,
- int *amb_status_inside, T hit5, T hit3, Univcoord_T *splicesites,
- Compress_T query5_compress_rev, Compress_T query3_compress_rev,
- int localsplicing_penalty, int querylength5, int querylength3,
- int genestrand) {
+ int *amb_status_inside, T hit5, T hit3, int querylength5, int querylength3) {
int insertlength;
Univcoord_T genomicstart, genomicend;
int nbingo, bingoi5, bingoi3;
int nbest, besti5, besti3, i, j;
int best_nmismatches, nmismatches;
- bool new5p = false, new3p = false;
Substring_T substring5, substring3;
-#ifdef LARGE_GENOMES
- Uint8list_T ambcoords;
-#else
- Uintlist_T ambcoords;
-#endif
Univcoord_T *end_ambcoords, *start_ambcoords;
int *end_amb_nmismatches, *start_amb_nmismatches;
int end_amb_length_5, start_amb_length_3;
@@ -12219,6 +13207,8 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_length, int *amb_reso
debug9(printf("\nnbest is zero: amb_length = %d...%d",
end_amb_length(hit5),start_amb_length(hit3)));
*unresolved_amb_length = end_amb_length_5 + start_amb_length_3;
+ *amb_resolve_5 = -1; /* Signifies cannot resolve */
+ *amb_resolve_3 = -1;
*amb_status_inside = AMB_UNRESOLVED_TOOCLOSE;
} else if (nbest == 1) {
@@ -12275,6 +13265,7 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_length, int *amb_reso
debug9(printf("\nnbest is zero: amb_length = %d...%d",
end_amb_length(hit5),start_amb_length(hit3)));
*unresolved_amb_length = end_amb_length_5;
+ *amb_resolve_5 = -1;
*amb_status_inside = AMB_UNRESOLVED_TOOCLOSE;
} else if (nbest == 1) {
@@ -12328,6 +13319,7 @@ resolve_inside_ambiguous_splice_minus (int *unresolved_amb_length, int *amb_reso
debug9(printf("\nnbest is zero: amb_length = %d...%d",
end_amb_length(hit5),start_amb_length(hit3)));
*unresolved_amb_length = start_amb_length_3;
+ *amb_resolve_3 = -1;
*amb_status_inside = AMB_UNRESOLVED_TOOCLOSE;
} else if (nbest == 1) {
@@ -12354,7 +13346,7 @@ alias_circular (T hit) {
List_T p;
Substring_T substring;
- assert(hit->alias == -1);
+ assert(hit->circularalias == -1);
if (hit->hittype == GMAP) {
Pair_alias_circular(hit->pairarray,hit->npairs,chrlength);
@@ -12371,7 +13363,7 @@ alias_circular (T hit) {
hit->low += chrlength;
hit->high += chrlength;
- hit->alias = +1;
+ hit->circularalias = +1;
return;
}
@@ -12522,19 +13514,17 @@ compute_insertlength (Stage3pair_T this) {
Stage3pair_T
-Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
- Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
- Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- int genestrand, Pairtype_T pairtype, int localsplicing_penalty,
+Stage3pair_new (T hit5, T hit3, int genestrand, Pairtype_T pairtype,
bool private5p, bool private3p, bool expect_concordant_p) {
Stage3pair_T new;
- Stage3end_T copy;
+ /* Stage3end_T copy; */
Substring_T substring1, substringN;
Chrpos_T chrstart, chrend, chrpos;
int querypos;
int unresolved_amb_length = 0;
- int found_score = 0;
+ /* int found_score = 0; */
bool overreach5p, overreach3p;
+ int pairmax;
int querylength5 = hit5->querylength;
int querylength3 = hit3->querylength;
@@ -12624,9 +13614,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
if (expect_concordant_p == true) {
/* Try to resolve ambiguity on inside of concordant ends */
resolve_inside_ambiguous_splice_plus(&unresolved_amb_length,&new->amb_resolve_5,&new->amb_resolve_3,
- &new->amb_status_inside,hit5,hit3,
- splicesites,query5_compress_fwd,query3_compress_fwd,
- localsplicing_penalty,querylength5,querylength3,genestrand);
+ &new->amb_status_inside,hit5,hit3,querylength5,querylength3);
}
/* Have 5-start..end and 3-start..end */
@@ -12670,9 +13658,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
if (expect_concordant_p == true) {
/* Try to resolve ambiguity on inside of concordant ends */
resolve_inside_ambiguous_splice_minus(&unresolved_amb_length,&new->amb_resolve_5,&new->amb_resolve_3,
- &new->amb_status_inside,hit5,hit3,
- splicesites,query5_compress_rev,query3_compress_rev,
- localsplicing_penalty,querylength5,querylength3,genestrand);
+ &new->amb_status_inside,hit5,hit3,querylength5,querylength3);
}
/* Have 3-end..start and 5-end..start */
@@ -12724,9 +13710,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
if (expect_concordant_p == true) {
/* Try to resolve ambiguity on inside of concordant ends */
resolve_inside_ambiguous_splice_plus(&unresolved_amb_length,&new->amb_resolve_5,&new->amb_resolve_3,
- &new->amb_status_inside,hit5,hit3,
- splicesites,query5_compress_fwd,query3_compress_fwd,
- localsplicing_penalty,querylength5,querylength3,genestrand);
+ &new->amb_status_inside,hit5,hit3,querylength5,querylength3);
}
/* Have 5-start..end and 3-start..end */
@@ -12770,9 +13754,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
if (expect_concordant_p == true) {
/* Try to resolve ambiguity on inside of concordant ends */
resolve_inside_ambiguous_splice_minus(&unresolved_amb_length,&new->amb_resolve_5,&new->amb_resolve_3,
- &new->amb_status_inside,hit5,hit3,
- splicesites,query5_compress_rev,query3_compress_rev,
- localsplicing_penalty,querylength5,querylength3,genestrand);
+ &new->amb_status_inside,hit5,hit3,querylength5,querylength3);
}
/* Have 3-end..start and 5-end..start */
@@ -12956,9 +13938,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
/* Try to resolve ambiguity on inside of concordant ends */
resolve_inside_ambiguous_splice_plus(&unresolved_amb_length,&new->amb_resolve_5,&new->amb_resolve_3,
- &new->amb_status_inside,hit5,hit3,
- splicesites,query5_compress_fwd,query3_compress_fwd,
- localsplicing_penalty,querylength5,querylength3,genestrand);
+ &new->amb_status_inside,hit5,hit3,querylength5,querylength3);
}
/* Have 5-start..end and 3-start..end */
@@ -13090,9 +14070,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
/* Try to resolve ambiguity on inside of concordant ends */
resolve_inside_ambiguous_splice_minus(&unresolved_amb_length,&new->amb_resolve_5,&new->amb_resolve_3,
- &new->amb_status_inside,hit5,hit3,
- splicesites,query5_compress_rev,query3_compress_rev,
- localsplicing_penalty,querylength5,querylength3,genestrand);
+ &new->amb_status_inside,hit5,hit3,querylength5,querylength3);
}
/* Have 3-end..start and 5-end..start */
@@ -13141,32 +14119,39 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
return (Stage3pair_T) NULL;
}
- } else if (new->insertlength > pairmax && expect_concordant_p == true) {
- debug5(printf(" Returning NULL because insertlength %d > pairmax %d\n",new->insertlength,pairmax));
- if (private5p == true) {
- Stage3end_free(&hit5);
- }
- if (private3p == true) {
- Stage3end_free(&hit3);
- }
- FREE_OUT(new);
- return (Stage3pair_T) NULL;
-
} else {
-#ifdef USE_ABSDIFFLENGTH
- if (new->insertlength < expected_pairlength) {
- new->absdifflength = expected_pairlength - new->insertlength;
+ if (circularp[hit5->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
} else {
- new->absdifflength = new->insertlength - expected_pairlength;
+ pairmax = pairmax_linear;
}
+ if (new->insertlength > pairmax && expect_concordant_p == true) {
+ debug5(printf(" Returning NULL because insertlength %d > pairmax %d\n",new->insertlength,pairmax));
+ if (private5p == true) {
+ Stage3end_free(&hit5);
+ }
+ if (private3p == true) {
+ Stage3end_free(&hit3);
+ }
+ FREE_OUT(new);
+ return (Stage3pair_T) NULL;
+
+ } else {
+#ifdef USE_ABSDIFFLENGTH
+ if (new->insertlength < expected_pairlength) {
+ new->absdifflength = expected_pairlength - new->insertlength;
+ } else {
+ new->absdifflength = new->insertlength - expected_pairlength;
+ }
#endif
#ifdef USE_BINGO
- if (new->absdifflength <= pairlength_deviation) {
- new->absdifflength_bingo_p = true;
- } else {
- new->absdifflength_bingo_p = false;
- }
+ if (new->absdifflength <= pairlength_deviation) {
+ new->absdifflength_bingo_p = true;
+ } else {
+ new->absdifflength_bingo_p = false;
+ }
#endif
+ }
}
if (SENSE_CONSISTENT_P(hit5->sensedir,hit3->sensedir)) {
@@ -13230,11 +14215,11 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
}
/* Fixing insertlength for circular pairs */
- if (new->insertlength > hit5->chrlength) {
+ if (new->insertlength > (int) hit5->chrlength) {
new->insertlength -= hit5->chrlength;
}
- if (hit5->alias == +1) {
+ if (hit5->circularalias == +1) {
debug0(printf("Unaliasing 5' end\n"));
if (private5p == false) {
new->hit5 = Stage3end_copy(hit5);
@@ -13243,7 +14228,7 @@ Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
unalias_circular(new->hit5);
}
- if (hit3->alias == +1) {
+ if (hit3->circularalias == +1) {
debug0(printf("Unaliasing 3' end\n"));
if (private3p == false) {
new->hit3 = Stage3end_copy(hit3);
@@ -13293,40 +14278,40 @@ hitpair_sort_cmp (const void *a, const void *b) {
Univcoord_T x_hit3_high, x_hit3_low, y_hit3_high, y_hit3_low;
Univcoord_T x_low, x_high, y_low, y_high;
- debug8(printf(" Comparing (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), alias %d|%d, nmatches: %d (%d posttrim), amb_lengths %d and %d, sensedirs %d-%d\n",
+ debug8(printf(" Comparing (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), circularalias %d|%d, nmatches: %d (%d posttrim), amb_lengths %d and %d, sensedirs %d-%d\n",
Pairtype_string(x->pairtype),hittype_string(x->hit5->hittype),
hittype_string(x->hit3->hittype),x,
x->hit5->low - x->hit5->chroffset,x->hit5->high - x->hit5->chroffset,
x->hit3->low - x->hit3->chroffset,x->hit3->high - x->hit3->chroffset,
- x->dir,x->hit5->alias,x->hit3->alias,x->nmatches,x->nmatches_posttrim,
+ x->dir,x->hit5->circularalias,x->hit3->circularalias,x->nmatches,x->nmatches_posttrim,
start_amb_length(x->hit5) + end_amb_length(x->hit5),start_amb_length(x->hit3) + end_amb_length(x->hit3),
x->hit5->sensedir,x->hit3->sensedir));
- debug8(printf(" with (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), alias %d|%d, nmatches: %d (%d posttrim), amb_lengths %d and %d, sensedirs %d-%d\n",
+ debug8(printf(" with (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), circularalias %d|%d, nmatches: %d (%d posttrim), amb_lengths %d and %d, sensedirs %d-%d\n",
Pairtype_string(y->pairtype),hittype_string(y->hit5->hittype),
hittype_string(y->hit3->hittype),y,
y->hit5->low - y->hit5->chroffset,y->hit5->high - y->hit5->chroffset,
y->hit3->low - y->hit3->chroffset,y->hit3->high - y->hit3->chroffset,
- y->dir,y->hit5->alias,y->hit3->alias,y->nmatches,y->nmatches_posttrim,
+ y->dir,y->hit5->circularalias,y->hit3->circularalias,y->nmatches,y->nmatches_posttrim,
start_amb_length(y->hit5) + end_amb_length(y->hit5),start_amb_length(y->hit3) + end_amb_length(y->hit3),
y->hit5->sensedir,y->hit3->sensedir));
- x_hit5_low = normalize_coord(x->hit5->low,x->hit5->alias,x->hit5->chrlength);
- x_hit5_high = normalize_coord(x->hit5->high,x->hit5->alias,x->hit5->chrlength);
+ x_hit5_low = normalize_coord(x->hit5->low,x->hit5->circularalias,x->hit5->chrlength);
+ x_hit5_high = normalize_coord(x->hit5->high,x->hit5->circularalias,x->hit5->chrlength);
- x_hit3_low = normalize_coord(x->hit3->low,x->hit3->alias,x->hit3->chrlength);
- x_hit3_high = normalize_coord(x->hit3->high,x->hit3->alias,x->hit3->chrlength);
+ x_hit3_low = normalize_coord(x->hit3->low,x->hit3->circularalias,x->hit3->chrlength);
+ x_hit3_high = normalize_coord(x->hit3->high,x->hit3->circularalias,x->hit3->chrlength);
x_low = (x_hit5_low < x_hit3_low) ? x_hit5_low : x_hit3_low;
x_high = (x_hit5_high > x_hit3_high) ? x_hit5_high : x_hit3_high;
- y_hit5_low = normalize_coord(y->hit5->low,y->hit5->alias,y->hit5->chrlength);
- y_hit5_high = normalize_coord(y->hit5->high,y->hit5->alias,y->hit5->chrlength);
+ y_hit5_low = normalize_coord(y->hit5->low,y->hit5->circularalias,y->hit5->chrlength);
+ y_hit5_high = normalize_coord(y->hit5->high,y->hit5->circularalias,y->hit5->chrlength);
- y_hit3_low = normalize_coord(y->hit3->low,y->hit3->alias,y->hit3->chrlength);
- y_hit3_high = normalize_coord(y->hit3->high,y->hit3->alias,y->hit3->chrlength);
+ y_hit3_low = normalize_coord(y->hit3->low,y->hit3->circularalias,y->hit3->chrlength);
+ y_hit3_high = normalize_coord(y->hit3->high,y->hit3->circularalias,y->hit3->chrlength);
y_low = (y_hit5_low < y_hit3_low) ? y_hit5_low : y_hit3_low;
y_high = (y_hit5_high > y_hit3_high) ? y_hit5_high : y_hit3_high;
@@ -13502,21 +14487,21 @@ hitpair_equiv_cmp (Stage3pair_T x, Stage3pair_T y) {
Univcoord_T x_hit3_high, x_hit3_low, y_hit3_high, y_hit3_low;
Univcoord_T x_low, x_high, y_low, y_high;
- x_hit5_low = normalize_coord(x->hit5->low,x->hit5->alias,x->hit5->chrlength);
- x_hit5_high = normalize_coord(x->hit5->high,x->hit5->alias,x->hit5->chrlength);
+ x_hit5_low = normalize_coord(x->hit5->low,x->hit5->circularalias,x->hit5->chrlength);
+ x_hit5_high = normalize_coord(x->hit5->high,x->hit5->circularalias,x->hit5->chrlength);
- x_hit3_low = normalize_coord(x->hit3->low,x->hit3->alias,x->hit3->chrlength);
- x_hit3_high = normalize_coord(x->hit3->high,x->hit3->alias,x->hit3->chrlength);
+ x_hit3_low = normalize_coord(x->hit3->low,x->hit3->circularalias,x->hit3->chrlength);
+ x_hit3_high = normalize_coord(x->hit3->high,x->hit3->circularalias,x->hit3->chrlength);
x_low = (x_hit5_low < x_hit3_low) ? x_hit5_low : x_hit3_low;
x_high = (x_hit5_high > x_hit3_high) ? x_hit5_high : x_hit3_high;
- y_hit5_low = normalize_coord(y->hit5->low,y->hit5->alias,y->hit5->chrlength);
- y_hit5_high = normalize_coord(y->hit5->high,y->hit5->alias,y->hit5->chrlength);
+ y_hit5_low = normalize_coord(y->hit5->low,y->hit5->circularalias,y->hit5->chrlength);
+ y_hit5_high = normalize_coord(y->hit5->high,y->hit5->circularalias,y->hit5->chrlength);
- y_hit3_low = normalize_coord(y->hit3->low,y->hit3->alias,y->hit3->chrlength);
- y_hit3_high = normalize_coord(y->hit3->high,y->hit3->alias,y->hit3->chrlength);
+ y_hit3_low = normalize_coord(y->hit3->low,y->hit3->circularalias,y->hit3->chrlength);
+ y_hit3_high = normalize_coord(y->hit3->high,y->hit3->circularalias,y->hit3->chrlength);
y_low = (y_hit5_low < y_hit3_low) ? y_hit5_low : y_hit3_low;
y_high = (y_hit5_high > y_hit3_high) ? y_hit5_high : y_hit3_high;
@@ -13875,12 +14860,12 @@ Stage3pair_remove_duplicates_exact (List_T hitpairlist) {
debug8(
for (i = 0; i < n; i++) {
hitpair = hitpairs[i];
- printf(" Initial %d (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), alias %d|%d, nmatches: %d\n",
+ printf(" Initial %d (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), circularalias %d|%d, nmatches: %d\n",
i,Pairtype_string(hitpair->pairtype),hittype_string(hitpair->hit5->hittype),
hittype_string(hitpair->hit3->hittype),hitpair,
hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
- hitpair->dir,hitpair->hit5->alias,hitpair->hit3->alias,hitpair->nmatches);
+ hitpair->dir,hitpair->hit5->circularalias,hitpair->hit3->circularalias,hitpair->nmatches);
}
);
@@ -14046,17 +15031,9 @@ hitpair_goodness_cmp (bool *equalp, Stage3pair_T hitpair,
#endif
- if (hitpair->nmatches < best_hitpair->nmatches) {
- /* k is worse */
- debug8(printf(" => loses by nmatches\n"));
- return -1;
- } else if (hitpair->nmatches > best_hitpair->nmatches) {
- /* k is better */
- debug8(printf(" => wins by nmatches\n"));
- return +1;
-
-#if 0
- } else if (hitpair->nmatches_posttrim < best_hitpair->nmatches_posttrim) {
+ /* Favors definitive splices over ambiguous splices. So need to
+ make sure we don't make definitive splices unnecessarily */
+ if (hitpair->nmatches_posttrim < best_hitpair->nmatches_posttrim) {
/* k is worse */
debug8(printf(" => loses by nmatches_posttrim\n"));
return -1;
@@ -14064,7 +15041,6 @@ hitpair_goodness_cmp (bool *equalp, Stage3pair_T hitpair,
/* k is better */
debug8(printf(" => wins by nmatches_posttrim\n"));
return +1;
-#endif
#if 0
} else if (hitpair->nsplices > best_hitpair->nsplices) {
@@ -14438,12 +15414,12 @@ pair_remove_overlaps (List_T hitpairlist, bool translocp, bool finalp) {
debug8(
for (i = 0; i < n; i++) {
hitpair = hitpairs[i];
- printf(" Initial %d (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), alias %d|%d, nmatches: %d (%d posttrim), amb_lengths %d and %d, sensedirs %d and %d\n",
+ printf(" Initial %d (%s, %s-%s): %p, %u..%u|%u..%u (dir = %d), circularalias %d|%d, nmatches: %d (%d posttrim), amb_lengths %d and %d, sensedirs %d and %d\n",
i,Pairtype_string(hitpair->pairtype),hittype_string(hitpair->hit5->hittype),
hittype_string(hitpair->hit3->hittype),hitpair,
hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
- hitpair->dir,hitpair->hit5->alias,hitpair->hit3->alias,hitpair->nmatches,hitpair->nmatches_posttrim,
+ hitpair->dir,hitpair->hit5->circularalias,hitpair->hit3->circularalias,hitpair->nmatches,hitpair->nmatches_posttrim,
start_amb_length(hitpair->hit5) + end_amb_length(hitpair->hit5),start_amb_length(hitpair->hit3) + end_amb_length(hitpair->hit3),
hitpair->hit5->sensedir,hitpair->hit3->sensedir);
}
@@ -14744,11 +15720,10 @@ Stage3pair_filter_coverage (List_T hits, int min_coverage_5, int min_coverage_3)
Stage3pair_T *
-Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
+Stage3pair_eval_and_sort (int npaths, int *first_absmq, int *second_absmq,
Stage3pair_T *stage3pairarray, int maxpaths,
Shortread_T queryseq5, Shortread_T queryseq3,
- char *queryuc_ptr_5, char *queryrc5,
- char *queryuc_ptr_3, char *queryrc3,
+ char *queryuc_ptr_5, char *queryuc_ptr_3,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
char *quality_string_5, char *quality_string_3) {
@@ -14762,12 +15737,12 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
int randomi, i;
Stage3pair_T temp;
- if (*npaths == 0) {
+ if (npaths == 0) {
/* Skip */
*first_absmq = 0;
*second_absmq = 0;
- } else if (*npaths == 1) {
+ } else if (npaths == 1) {
stage3pairarray[0]->mapq_loglik = MAPQ_MAXIMUM_SCORE;
stage3pairarray[0]->mapq_score = MAPQ_max_quality_score(quality_string_5,Shortread_fulllength(queryseq5));
if ((mapq_score = MAPQ_max_quality_score(quality_string_3,Shortread_fulllength(queryseq3))) > stage3pairarray[0]->mapq_score) {
@@ -14777,23 +15752,22 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
assert(stage3pairarray[0]->private5p == true);
assert(stage3pairarray[0]->private3p == true);
- Stage3end_display_prep(stage3pairarray[0]->hit5,queryuc_ptr_5,queryrc5,query5_compress_fwd,query5_compress_rev,
+ Stage3end_display_prep(stage3pairarray[0]->hit5,queryuc_ptr_5,query5_compress_fwd,query5_compress_rev,
stage3pairarray[0]->amb_resolve_5,/*first_read_p*/true);
- Stage3end_display_prep(stage3pairarray[0]->hit3,queryuc_ptr_3,queryrc3,query3_compress_fwd,query3_compress_rev,
+ Stage3end_display_prep(stage3pairarray[0]->hit3,queryuc_ptr_3,query3_compress_fwd,query3_compress_rev,
stage3pairarray[0]->amb_resolve_3,/*first_read_p*/false);
if (stage3pairarray[0]->amb_resolve_5 >= 0 || stage3pairarray[0]->amb_resolve_3 >= 0) {
stage3pairarray[0]->insertlength = compute_insertlength(stage3pairarray[0]);
- assert((int) stage3pairarray[0]->insertlength > 0);
+ /* assert((int) stage3pairarray[0]->insertlength > 0); -- can fail for bad resolutions */
}
-
*first_absmq = stage3pairarray[0]->absmq_score;
*second_absmq = 0;
} else {
/* Determine whether to trim terminal ends */
non_terminal_5p = non_terminal_3p = false;
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
if (stage3pairarray[i]->hit5->hittype != TERMINAL) {
non_terminal_5p = true;
}
@@ -14803,12 +15777,12 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
}
/* Resolve ambiguities, needed for computing mapq */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
assert(stage3pairarray[i]->private5p == true);
assert(stage3pairarray[i]->private3p == true);
- Stage3end_display_prep(stage3pairarray[i]->hit5,queryuc_ptr_5,queryrc5,query5_compress_fwd,query5_compress_rev,
+ Stage3end_display_prep(stage3pairarray[i]->hit5,queryuc_ptr_5,query5_compress_fwd,query5_compress_rev,
stage3pairarray[i]->amb_resolve_5,/*first_read_p*/true);
- Stage3end_display_prep(stage3pairarray[i]->hit3,queryuc_ptr_3,queryrc3,query3_compress_fwd,query3_compress_rev,
+ Stage3end_display_prep(stage3pairarray[i]->hit3,queryuc_ptr_3,query3_compress_fwd,query3_compress_rev,
stage3pairarray[i]->amb_resolve_3,/*first_read_p*/false);
if (stage3pairarray[i]->amb_resolve_5 >= 0 || stage3pairarray[i]->amb_resolve_3 >= 0) {
stage3pairarray[i]->insertlength = compute_insertlength(stage3pairarray[i]);
@@ -14817,7 +15791,7 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
/* Compute mapq_loglik */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
stage3pairarray[i]->mapq_loglik =
Stage3end_compute_mapq(stage3pairarray[i]->hit5,query5_compress_fwd,query5_compress_rev,
quality_string_5,/*trim_terminals_p*/non_terminal_5p ? false : true);
@@ -14827,12 +15801,12 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
}
/* Sort by nmatches, then mapq, and then insert length */
- qsort(stage3pairarray,*npaths,sizeof(Stage3pair_T),Stage3pair_output_cmp);
+ qsort(stage3pairarray,npaths,sizeof(Stage3pair_T),Stage3pair_output_cmp);
if (want_random_p) {
/* Randomize among best alignments */
i = 1;
- while (i < *npaths && Stage3pair_output_cmp(&(stage3pairarray[i]),&(stage3pairarray[0])) == 0) {
+ while (i < npaths && Stage3pair_output_cmp(&(stage3pairarray[i]),&(stage3pairarray[0])) == 0) {
i++;
}
if (i > 1) { /* i is number of ties */
@@ -14846,7 +15820,7 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
}
/* Enforce monotonicity */
- for (i = *npaths - 1; i > 0; i--) {
+ for (i = npaths - 1; i > 0; i--) {
if (stage3pairarray[i-1]->mapq_loglik < stage3pairarray[i]->mapq_loglik) {
stage3pairarray[i-1]->mapq_loglik = stage3pairarray[i]->mapq_loglik;
}
@@ -14854,13 +15828,13 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
maxlik = stage3pairarray[0]->mapq_loglik;
/* Subtract maxlik to avoid underflow */
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
stage3pairarray[i]->mapq_loglik -= maxlik;
}
/* Save on computation if possible */
- if (*npaths < maxpaths) {
- compute_npaths = *npaths;
+ if (npaths < maxpaths) {
+ compute_npaths = npaths;
} else {
compute_npaths = maxpaths;
}
@@ -14882,7 +15856,7 @@ Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
/* Compute Bayesian mapq */
total = 0.0;
- for (i = 0; i < *npaths; i++) {
+ for (i = 0; i < npaths; i++) {
total += (stage3pairarray[i]->mapq_loglik = fasterexp(stage3pairarray[i]->mapq_loglik));
}
@@ -14969,7 +15943,7 @@ Stage3pair_remove_excess_terminals (List_T hitpairlist) {
static List_T
-Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_level, int suboptimal_mismatches,
+Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
int querylength5, int querylength3, bool keep_gmap_p, bool finalp) {
@@ -14977,20 +15951,20 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
Stage3pair_T hitpair;
T hit5, hit3;
Substring_T substring;
- int cutoff_level_5, cutoff_level_3, score;
+ int cutoff_level_5, cutoff_level_3, cutoff_level;
int n;
int minscore5 = querylength5, minscore3 = querylength3, minscore = querylength5 + querylength3;
- int best_nsegments;
- /* int max_nmatches = 0, max_nmatches_posttrim; */
+ int best_nsegments, best_nsegments_5, best_nsegments_3;
+ int max_nmatches = 0;
#ifdef USE_OPTIMAL_SCORE_BINGO
int minscore_bingo = querylength5 + querylength3;
#endif
int trim_left_5 = querylength5, trim_right_5 = querylength5,
- trim_left_3 = querylength3, trim_right_3 = querylength3;
+ trim_left_3 = querylength3, trim_right_3 = querylength3, trim_left, trim_right;
int nindelbreaks;
-#ifdef TRANSLOC_SPECIAL
- bool non_translocation_p = false;
+#if 0 /* DISTANT_SPLICE_SPECIAL */
+ bool shortdistance_p = false;
#endif
@@ -15140,10 +16114,18 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
for (q = hit5->substrings_1toN; q != NULL; q = List_next(q)) {
substring = (Substring_T) List_head(q);
- hit5->score_eventrim += Substring_count_mismatches_region(substring,trim_left_5,trim_right_5,
+ trim_left = trim_left_5;
+ trim_right = trim_right_5;
+ if (Substring_mandatory_trim_left(substring) > trim_left) {
+ trim_left = Substring_mandatory_trim_left(substring);
+ }
+ if (Substring_mandatory_trim_right(substring) > trim_right) {
+ trim_right = Substring_mandatory_trim_right(substring);
+ }
+ hit5->score_eventrim += Substring_count_mismatches_region(substring,trim_left,trim_right,
query5_compress_fwd,query5_compress_rev);
- debug6(printf(" substring (%d..%d) %d.",trim_left_5,trim_right_5,
- Substring_count_mismatches_region(substring,trim_left_5,trim_right_5,
+ debug6(printf(" substring (%d..%d) %d.",trim_left,trim_right,
+ Substring_count_mismatches_region(substring,trim_left,trim_right,
query5_compress_fwd,query5_compress_rev)));
}
@@ -15223,10 +16205,18 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
for (q = hit3->substrings_1toN; q != NULL; q = List_next(q)) {
substring = (Substring_T) List_head(q);
- hit3->score_eventrim += Substring_count_mismatches_region(substring,trim_left_3,trim_right_3,
+ trim_left = trim_left_3;
+ trim_right = trim_right_3;
+ if (Substring_mandatory_trim_left(substring) > trim_left) {
+ trim_left = Substring_mandatory_trim_left(substring);
+ }
+ if (Substring_mandatory_trim_right(substring) > trim_right) {
+ trim_right = Substring_mandatory_trim_right(substring);
+ }
+ hit3->score_eventrim += Substring_count_mismatches_region(substring,trim_left,trim_right,
query3_compress_fwd,query3_compress_rev);
debug6(printf(" substring (%d..%d) %d.",trim_left_3,trim_right_3,
- Substring_count_mismatches_region(substring,trim_left_3,trim_right_3,
+ Substring_count_mismatches_region(substring,trim_left,trim_right,
query3_compress_fwd,query3_compress_rev)));
}
@@ -15249,30 +16239,29 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
}
}
-
- for (p = hitpairlist; p != NULL; p = p->rest) {
- hitpair = (Stage3pair_T) p->first;
- debug6(printf("%u..%u|%u..%u types %s and %s, score_eventrim %d+%d, pairlength %d, outerlength %u\n",
- hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
- hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
- hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),
- hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim,
- hitpair->insertlength,hitpair->outerlength));
-
- if (hitpair->hit5->score_eventrim < minscore5) {
- minscore5 = hitpair->hit5->score_eventrim;
- }
- if (hitpair->hit3->score_eventrim < minscore3) {
- minscore3 = hitpair->hit3->score_eventrim;
+ if (finalp == false) {
+ for (p = hitpairlist; p != NULL; p = p->rest) {
+ hitpair = (Stage3pair_T) p->first;
+ debug6(printf("%u..%u|%u..%u types %s and %s, score_eventrim %d+%d, pairlength %d, outerlength %u\n",
+ hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
+ hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
+ hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),
+ hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim,
+ hitpair->insertlength,hitpair->outerlength));
+
+ if (hitpair->hit5->score_eventrim < minscore5) {
+ minscore5 = hitpair->hit5->score_eventrim;
+ }
+ if (hitpair->hit3->score_eventrim < minscore3) {
+ minscore3 = hitpair->hit3->score_eventrim;
+ }
}
- }
- debug6(printf("Stage3pair_optimal_score over %d pairs: minscore = %d and %d + subopt:%d\n",
- n,minscore5,minscore3,suboptimal_mismatches));
+ debug6(printf("Stage3pair_optimal_score over %d pairs: minscore = %d and %d + subopt:%d\n",
+ n,minscore5,minscore3,subopt_levels));
- if (finalp == false) {
/* finalp == false. Add suboptimal_mismatches to each end. */
- minscore5 += suboptimal_mismatches;
- minscore3 += suboptimal_mismatches;
+ minscore5 += subopt_levels;
+ minscore3 += subopt_levels;
cutoff_level_5 = minscore5;
cutoff_level_3 = minscore3;
@@ -15281,73 +16270,74 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
if (keep_gmap_p == true && (hitpair->hit5->hittype == GMAP || hitpair->hit3->hittype == GMAP)) {
/* GMAP hits already found to be better than their corresponding terminals */
- debug6(printf("Prefinal: Keeping a hit pair of type %s-%s with score_eventrim %d and %d, because keep_gmap_p is true\n",
- hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),
+ debug6(printf("Prefinal: Keeping hit pair %p of type %s-%s with score_eventrim %d and %d, because keep_gmap_p is true\n",
+ hitpair,hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),
hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim));
optimal = List_push(optimal,hitpair);
} else if (hitpair->hit5->score_eventrim > cutoff_level_5 && hitpair->hit3->score_eventrim > cutoff_level_3) {
- debug6(printf("Prefinal: Eliminating a hit pair at %u..%u|%u..%u with score_eventrim_5 %d > cutoff_level_5 %d and score_eventrim_3 %d > cutoff_level_3 %d (finalp %d)\n",
- hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
+ debug6(printf("Prefinal: Eliminating hit pair %p at %u..%u|%u..%u with score_eventrim_5 %d > cutoff_level_5 %d and score_eventrim_3 %d > cutoff_level_3 %d (finalp %d)\n",
+ hitpair,hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
hitpair->hit5->score_eventrim,cutoff_level_5,hitpair->hit3->score_eventrim,cutoff_level_3,finalp));
*eliminatedp = true;
Stage3pair_free(&hitpair);
} else {
- debug6(printf("Prefinal: Keeping a hit pair with score_eventrim %d and %d (cutoff_level %d and %d)\n",
- hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim,cutoff_level_5,cutoff_level_3));
+ debug6(printf("Prefinal: Keeping hit pair %p with score_eventrim %d and %d (cutoff_level %d and %d)\n",
+ hitpair,hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim,cutoff_level_5,cutoff_level_3));
optimal = List_push(optimal,hitpair);
}
}
} else {
- /* finalp == true. Add suboptimal_mismatches to overall score. */
-#if 0
- if (minscore5 + minscore3 < minscore) {
- cutoff_level = minscore + suboptimal_mismatches;
- debug6(printf("cutoff level %d = minscore %d + subopt %d\n",cutoff_level,minscore,suboptimal_mismatches));
- } else {
- cutoff_level = minscore5 + minscore3 + suboptimal_mismatches;
- debug6(printf("cutoff level %d = minscore5 %d + minscore3 %d + subopt %d\n",cutoff_level,minscore5,minscore3,suboptimal_mismatches));
- }
-#else
- cutoff_level = minscore + suboptimal_mismatches;
- debug6(printf("cutoff level %d = minscore %d + subopt %d\n",cutoff_level,minscore,suboptimal_mismatches));
-#endif
-
-
+ /* Final */
+ max_nmatches = 0;
for (p = hitpairlist; p != NULL; p = p->rest) {
hitpair = (Stage3pair_T) p->first;
- debug6(printf("Final: %u..%u|%u..%u types %s and %s, score_eventrim %d (%d+%d), pairlength %d, outerlength %u\n",
+ debug6(printf("%u..%u|%u..%u types %s and %s, score_eventrim %d+%d, pairlength %d, outerlength %u\n",
hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),
- hitpair->score_eventrim,hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim,
+ hitpair->hit5->score_eventrim,hitpair->hit3->score_eventrim,
hitpair->insertlength,hitpair->outerlength));
+
+ if (hitpair->nmatches > max_nmatches) {
+ max_nmatches = hitpair->nmatches;
+ }
+ }
- score = hitpair->score_eventrim;
+ /* finalp == true. Add suboptimal_mismatches to overall score. */
+ cutoff_level = max_nmatches - subopt_levels;
+ debug6(printf("cutoff level %d = max_nmatches %d - subopt %d\n",cutoff_level,max_nmatches,subopt_levels));
- if (keep_gmap_p == true && (hitpair->hit5->hittype == GMAP || hitpair->hit3->hittype == GMAP)) {
+ /* For comparison within loci (as in hit_goodness_cmp), use hitpair->nmatches_posttrim */
+ /* For comparison across loci, use hitpair->nmatches, not hitpair->nmatches_posttrim, hitpair->score_eventrim or hitpair->score */
+ for (p = hitpairlist; p != NULL; p = p->rest) {
+ hitpair = (Stage3pair_T) p->first;
+ debug6(printf("Final (%p): %u..%u|%u..%u types %s and %s, score %d, pairlength %d, outerlength %u\n",
+ hitpair,hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
+ hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
+ hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),
+ hitpair->score,hitpair->insertlength,hitpair->outerlength));
+
+ if (0 && keep_gmap_p == true && (hitpair->hit5->hittype == GMAP || hitpair->hit3->hittype == GMAP)) {
/* GMAP hits already found to be better than their corresponding terminals */
- debug6(printf("Final: Keeping a hit pair of type %s-%s with score_eventrim %d, because keep_gmap_p is true\n",
- hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),hitpair->score_eventrim));
+ debug6(printf("Final: Keeping hit pair %p of type %s-%s with score %d, because keep_gmap_p is true\n",
+ hitpair,hittype_string(hitpair->hit5->hittype),hittype_string(hitpair->hit3->hittype),hitpair->score));
optimal = List_push(optimal,hitpair);
-#if 0
- } else if (score > cutoff_level) {
- /* Turning off, because it eliminates some shorter, but good, alignments unnecessarily */
- debug6(printf("Final: Eliminating a hit pair at %u..%u|%u..%u with score %d > cutoff_level %d (finalp %d)\n",
- hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
+ } else if (hitpair->nmatches < cutoff_level) {
+ debug6(printf("Final: Eliminating hit pair %p at %u..%u|%u..%u with nmatches %d < cutoff_level %d (finalp %d)\n",
+ hitpair,hitpair->hit5->low - hitpair->hit5->chroffset,hitpair->hit5->high - hitpair->hit5->chroffset,
hitpair->hit3->low - hitpair->hit3->chroffset,hitpair->hit3->high - hitpair->hit3->chroffset,
- score,cutoff_level,finalp));
+ hitpair->nmatches,cutoff_level,finalp));
*eliminatedp = true;
Stage3pair_free(&hitpair);
-#endif
} else {
- debug6(printf("Final: Keeping a hit pair with score_eventrim %d (cutoff_level %d)\n",
- hitpair->score_eventrim,cutoff_level));
+ debug6(printf("Final: Keeping hit pair %p with nmatches %d (vs cutoff_level %d)\n",
+ hitpair,hitpair->nmatches,cutoff_level));
optimal = List_push(optimal,hitpair);
}
}
@@ -15363,22 +16353,54 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
hitpair = (Stage3pair_T) hitpairlist->first;
best_nsegments = hitpair->hit5->nsegments + hitpair->hit3->nsegments;
+ best_nsegments_5 = hitpair->hit5->nsegments;
+ best_nsegments_3 = hitpair->hit3->nsegments;
for (p = hitpairlist; p != NULL; p = p->rest) {
hitpair = (Stage3pair_T) p->first;
if (hitpair->hit5->nsegments + hitpair->hit3->nsegments < best_nsegments) {
best_nsegments = hitpair->hit5->nsegments + hitpair->hit3->nsegments;
}
+ if (hitpair->hit5->nsegments < best_nsegments_5) {
+ best_nsegments_5 = hitpair->hit5->nsegments;
+ }
+ if (hitpair->hit3->nsegments < best_nsegments_3) {
+ best_nsegments_3 = hitpair->hit3->nsegments;
+ }
}
for (p = hitpairlist; p != NULL; p = p->rest) {
hitpair = (Stage3pair_T) p->first;
- if (hitpair->hit5->nsegments + hitpair->hit3->nsegments > best_nsegments + 2) {
- debug6(printf("Eliminating a hit pair with nsegments %d+%d\n",hitpair->hit5->nsegments,hitpair->hit3->nsegments));
+ if (hitpair->hit5->hittype == GMAP && hitpair->hit3->hittype == GMAP) {
+ /* Skip, since this criterion is unfavorable to GMAP improvements */
+ optimal = List_push(optimal,hitpair);
+
+ } else if (hitpair->hit5->hittype == GMAP && hitpair->hit3->hittype != GMAP) {
+ if (hitpair->hit3->nsegments > best_nsegments_3 + 2) {
+ debug6(printf("Eliminating hit pair %p with nsegments (%d)+%d\n",hitpair,hitpair->hit5->nsegments,hitpair->hit3->nsegments));
+ *eliminatedp = true;
+ Stage3pair_free(&hitpair);
+ } else {
+ debug6(printf("Keeping hit pair %p with nsegments (%d)+%d\n",hitpair,hitpair->hit5->nsegments,hitpair->hit3->nsegments));
+ optimal = List_push(optimal,hitpair);
+ }
+
+ } else if (hitpair->hit5->hittype != GMAP && hitpair->hit3->hittype == GMAP) {
+ if (hitpair->hit5->nsegments > best_nsegments_5 + 2) {
+ debug6(printf("Eliminating hit pair %p with nsegments %d+(%d)\n",hitpair,hitpair->hit5->nsegments,hitpair->hit3->nsegments));
+ *eliminatedp = true;
+ Stage3pair_free(&hitpair);
+ } else {
+ debug6(printf("Keeping hit pair %p with nsegments %d+(%d)\n",hitpair,hitpair->hit5->nsegments,hitpair->hit3->nsegments));
+ optimal = List_push(optimal,hitpair);
+ }
+
+ } else if (hitpair->hit5->nsegments + hitpair->hit3->nsegments > best_nsegments + 2) {
+ debug6(printf("Eliminating hit pair %p with nsegments %d+%d\n",hitpair,hitpair->hit5->nsegments,hitpair->hit3->nsegments));
*eliminatedp = true;
Stage3pair_free(&hitpair);
} else {
- debug6(printf("Keeping a hit pair with nsegments %d+%d\n",hitpair->hit5->nsegments,hitpair->hit3->nsegments));
+ debug6(printf("Keeping hit pair %p with nsegments %d+%d\n",hitpair,hitpair->hit5->nsegments,hitpair->hit3->nsegments));
optimal = List_push(optimal,hitpair);
}
}
@@ -15412,16 +16434,16 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
for (p = hitpairlist; p != NULL; p = p->rest) {
hitpair = (Stage3pair_T) p->first;
if (hitpair->absdifflength > best_absdifflength) {
- debug6(printf("Eliminating a hit pair with absdifflength %d\n",hitpair->absdifflength));
+ debug6(printf("Eliminating hit pair %p with absdifflength %d\n",hitpair,hitpair->absdifflength));
*eliminatedp = true;
Stage3pair_free(&hitpair);
} else if (hitpair->outerlength > best_outerlength + OUTERLENGTH_SLOP) {
- debug6(printf("Eliminating a hit pair with outerlength %u\n",hitpair->outerlength));
+ debug6(printf("Eliminating hit pair %p with outerlength %u\n",hitpair,hitpair->outerlength));
*eliminatedp = true;
Stage3pair_free(&hitpair);
} else {
- debug6(printf("Keeping a hit pair with absdifflength %d and outerlength %d\n",
- hitpair->absdifflength,hitpair->outerlength));
+ debug6(printf("Keeping hit pair %p with absdifflength %d and outerlength %d\n",
+ hitpair,hitpair->absdifflength,hitpair->outerlength));
optimal = List_push(optimal,hitpair);
}
}
@@ -15435,19 +16457,19 @@ Stage3pair_optimal_score_aux (bool *eliminatedp, List_T hitpairlist, int cutoff_
List_T
-Stage3pair_optimal_score (List_T hitpairlist, int cutoff_level, int suboptimal_mismatches,
+Stage3pair_optimal_score (List_T hitpairlist,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
int querylength5, int querylength3, bool keep_gmap_p, bool finalp) {
List_T optimal;
bool eliminatedp;
- optimal = Stage3pair_optimal_score_aux(&eliminatedp,hitpairlist,cutoff_level,suboptimal_mismatches,
+ optimal = Stage3pair_optimal_score_aux(&eliminatedp,hitpairlist,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,keep_gmap_p,finalp);
while (eliminatedp == true) {
- optimal = Stage3pair_optimal_score_aux(&eliminatedp,optimal,cutoff_level,suboptimal_mismatches,
+ optimal = Stage3pair_optimal_score_aux(&eliminatedp,optimal,
query5_compress_fwd,query5_compress_rev,
query3_compress_fwd,query3_compress_rev,
querylength5,querylength3,keep_gmap_p,finalp);
@@ -15485,9 +16507,11 @@ Stage3pair_sense_consistent_p (List_T hitpairlist) {
/* Want to unalias plus and alias minus */
List_T
Stage3end_linearize_5 (List_T hitlist) {
- Chrpos_T chrlength;
T hit;
List_T p;
+#ifdef DEBUG12
+ Chrpos_T chrlength;
+#endif
for (p = hitlist; p != NULL; p = List_next(p)) {
hit = (T) List_head(p);
@@ -15495,15 +16519,15 @@ Stage3end_linearize_5 (List_T hitlist) {
debug12(printf("Looking at 5' end %u..%u against chrlength %u\n",
hit->genomicstart - hit->chroffset,hit->genomicend - hit->chroffset,chrlength));
- if (hit->alias == 0) {
+ if (hit->circularalias == 0) {
/* Skip */
- } else if (hit->alias == +1) {
+ } else if (hit->circularalias == +1) {
if (hit->plusp == true) {
unalias_circular(hit);
}
- } else if (hit->alias == -1) {
+ } else if (hit->circularalias == -1) {
if (hit->plusp == false) {
alias_circular(hit);
}
@@ -15517,9 +16541,11 @@ Stage3end_linearize_5 (List_T hitlist) {
/* Want to alias plus and unalias minus */
List_T
Stage3end_linearize_3 (List_T hitlist) {
- Chrpos_T chrlength;
T hit;
List_T p;
+#ifdef DEBUG12
+ Chrpos_T chrlength;
+#endif
for (p = hitlist; p != NULL; p = List_next(p)) {
hit = (T) List_head(p);
@@ -15527,15 +16553,15 @@ Stage3end_linearize_3 (List_T hitlist) {
debug12(printf("Looking at 3' end %u..%u against chrlength %u\n",
hit->genomicstart - hit->chroffset,hit->genomicend - hit->chroffset,chrlength));
- if (hit->alias == 0) {
+ if (hit->circularalias == 0) {
/* Skip */
- } else if (hit->alias == -1) {
+ } else if (hit->circularalias == -1) {
if (hit->plusp == true) {
alias_circular(hit);
}
- } else if (hit->alias == +1) {
+ } else if (hit->circularalias == +1) {
if (hit->plusp == false) {
unalias_circular(hit);
}
@@ -15560,7 +16586,7 @@ Stage3pair_remove_circular_alias (List_T hitpairlist) {
#if 0
/* Not sure if this is necessary */
- if (hitpair->hit5->alias == +1 && hitpair->hit3->alias == +1) {
+ if (hitpair->hit5->circularalias == +1 && hitpair->hit3->circularalias == +1) {
/* First, try to salvage alias +1 */
unalias_circular(hitpair->hit5);
unalias_circular(hitpair->hit3);
@@ -15593,14 +16619,9 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
List_T *samechr, List_T *conc_transloc, List_T hitpairs,
T **hits5_plus, int *nhits5_plus, T **hits5_minus, int *nhits5_minus,
T **hits3_plus, int *nhits3_plus, T **hits3_minus, int *nhits3_minus,
- bool *sorted5p, bool *sorted3p,
- int cutoff_level_5, int cutoff_level_3, int subopt_levels,
-
- Univcoord_T *splicesites,
- Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
- Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- int querylength5, int querylength3, int maxpairedpaths,
- int splicing_penalty, int genestrand) {
+ bool *sorted5p, bool *sorted3p, int cutoff_level_5, int cutoff_level_3,
+
+ int querylength5, int querylength3, int maxpairedpaths, int genestrand) {
int new_found_score = *found_score;
int frontier_score, score5_start, score5_end, score5, score3, i, j;
List_T q, prev_start;
@@ -15608,10 +16629,11 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
T *hits5, *hits3, hit5, hit3;
int nhits5, nhits3;
Univcoord_T insert_start;
-
+ int pairmax;
prev_start = hitpairs;
frontier_score = 0;
+ /* Eliminating check on frontier_score against *found_score, because too greedy and can miss correct result */
while (*abort_pairing_p == false && frontier_score <= *found_score + subopt_levels &&
frontier_score <= cutoff_level_5 + cutoff_level_3) {
debug5a(printf("frontier_score = %d\n",frontier_score));
@@ -15650,80 +16672,79 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
hits3 = hits3_plus[score3];
nhits5 = nhits5_plus[score5];
nhits3 = nhits3_plus[score3];
- debug5(printf("at score %d, nhits5_plus = %d; at score %d, nhits3_plus = %d\n",
- score5,nhits5,score3,nhits3));
+ debug5(printf("at score %d+%d, nhits5_plus = %d, nhits3_plus = %d\n",
+ score5,score3,nhits5,nhits3));
if (nhits5 > 0 && nhits3 > 0) {
i = j = 0;
while (*abort_pairing_p == false && i < nhits5) {
hit5 = hits5[i];
+ if (circularp[hit5->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
+ } else {
+ pairmax = pairmax_linear;
+ }
+
insert_start = hit5->genomicend - querylength5;
- debug5(printf("plus/plus: i=%d/%d %u..%u %s %s %p\n",
+ debug5(printf("plus/plus: i=%d/%d %u..%u %s %s circularalias:%d %p\n",
i,nhits5,hit5->genomicstart - hit5->chroffset,hit5->genomicend - hit5->chroffset,
- print_sense(hit5->sensedir),hittype_string(hit5->hittype),hit5));
+ print_sense(hit5->sensedir),hittype_string(hit5->hittype),hit5->circularalias,hit5));
while (j >= 0 &&
hits3[j]->genomicstart + querylength3 /* for scramble: */ + pairmax > insert_start) {
- debug5(printf(" backup: j=%d/%d %u..%u %s %s %p\n",
+ debug5(printf(" backup: j=%d/%d %u..%u %s %s circularalias:%d %p\n",
j,nhits3,hits3[j]->genomicstart - hits3[j]->chroffset,hits3[j]->genomicend - hits3[j]->chroffset,
- print_sense(hits3[j]->sensedir),hittype_string(hits3[j]->hittype),hits3[j]));
+ print_sense(hits3[j]->sensedir),hittype_string(hits3[j]->hittype),hits3[j]->circularalias,hits3[j]));
j--;
}
j++; /* Finish backup */
while (j < nhits3 &&
hits3[j]->genomicstart + querylength3 /* for scramble: */ + pairmax <= insert_start) {
- debug5(printf(" advance: j=%d/%d %u..%u %s %s %p\n",
+ debug5(printf(" advance: j=%d/%d %u..%u %s %s circularalias:%d %p\n",
j,nhits3,hits3[j]->genomicstart - hits3[j]->chroffset,hits3[j]->genomicend - hits3[j]->chroffset,
- print_sense(hits3[j]->sensedir),hittype_string(hits3[j]->hittype),hits3[j]));
+ print_sense(hits3[j]->sensedir),hittype_string(hits3[j]->hittype),hits3[j]->circularalias,hits3[j]));
j++;
}
while (j < nhits3 && hits3[j]->genomicstart + querylength3 <= pairmax + insert_start) {
- debug5(printf(" overlap: j=%d/%d %u..%u %s %s %p",
+ debug5(printf(" overlap: j=%d/%d %u..%u %s %s circularalias:%d %p",
j,nhits3,hits3[j]->genomicstart - hits3[j]->chroffset,hits3[j]->genomicend - hits3[j]->chroffset,
- print_sense(hits3[j]->sensedir),hittype_string(hits3[j]->hittype),hits3[j]));
+ print_sense(hits3[j]->sensedir),hittype_string(hits3[j]->hittype),hits3[j]->circularalias,hits3[j]));
hit3 = hits3[j];
/* Want only pairs not previously seen */
if (hit5->paired_seenp == false || hit3->paired_seenp == false) {
if (hit5->effective_chrnum != hit3->effective_chrnum) {
debug5(printf(" => diff chrs %d and %d",hit5->effective_chrnum,hit3->effective_chrnum));
- } else if (hit5->chrnum == 0 && hit3->chrnum == 0 /* && hit5->other_chrnum != hit3->other_chrnum */) {
+ } else if (hit5->distant_splice_p == true && hit3->distant_splice_p == true /* && hit5->other_chrnum != hit3->other_chrnum */) {
/* Could potentially miss an alignment if the two ends overlap */
debug5(printf(" => double splice translocations"));
- } else if (hit5->chrnum == 0 || hit3->chrnum == 0) {
+ } else if (hit5->distant_splice_p == true || hit3->distant_splice_p == true) {
debug5(printf(" => conc_transloc effchr %d (chrnum5 %d, chrnum3 %d)",
hit5->effective_chrnum,hit5->chrnum,hit3->chrnum));
- if ((stage3pair = Stage3pair_new(hit5,hit3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT_TRANSLOCATIONS,splicing_penalty,
+ if ((stage3pair = Stage3pair_new(hit5,hit3,genestrand,/*pairtype*/CONCORDANT_TRANSLOCATIONS,
/*private5p*/false,/*private3p*/false,/*expect_concordant_p*/true)) != NULL) {
*conc_transloc = List_push(*conc_transloc,(void *) stage3pair);
}
} else if (SENSE_INCONSISTENT_P(hit5->sensedir,hit3->sensedir)) {
debug5(printf(" => sense inconsistent: %d | %d = %d",hit5->sensedir,hit3->sensedir,hit5->sensedir|hit3->sensedir));
+
} else if (hit3->genomicend < hit5->genomicstart) {
debug5(printf(" => scramble because end3 %llu < start5 %llu\n",
(unsigned long long) hit3->genomicend,(unsigned long long) hit5->genomicstart));
if (*nsamechr <= maxpairedpaths &&
- (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/PAIRED_SCRAMBLE,splicing_penalty,
+ (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),genestrand,/*pairtype*/PAIRED_SCRAMBLE,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/false)) != NULL) {
*samechr = List_push(*samechr,(void *) stage3pair);
(*nsamechr)++;
}
+
} else {
debug5(printf(" => concordant effchr %d (chrnum5 %d, chrnum3 %d)",
hit5->effective_chrnum,hit5->chrnum,hit3->chrnum));
- if ((stage3pair = Stage3pair_new(hit5,hit3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,splicing_penalty,
+ if ((stage3pair = Stage3pair_new(hit5,hit3,genestrand,/*pairtype*/CONCORDANT,
/*private5p*/false,/*private3p*/false,/*expect_concordant_p*/true)) != NULL) {
debug5(printf("Have new pair with scores %d + %d, compared with new_found_score %d\n",hit5->score,hit3->score,new_found_score));
@@ -15737,7 +16758,13 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
} /*else*/
#endif
- if (hit5->score + hit3->score < new_found_score) {
+
+ if (hit5->hittype == GMAP || hit3->hittype == GMAP) {
+ /* Don't use GMAP scores to set new_found_score */
+ hitpairs = List_push(hitpairs,(void *) stage3pair);
+ (*nconcordant)++;
+
+ } else if (hit5->score + hit3->score < new_found_score) {
/* Don't use frontier_score here, which is the trimmed_score. Use the full score, to motivate stage1hr to find longer alignments */
new_found_score = hit5->score + hit3->score;
debug5(printf(" => tentatively updating found_score to be %d = %d + %d\n",new_found_score,hit5->score,hit3->score));
@@ -15771,81 +16798,79 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
hits5 = hits5_minus[score5];
nhits3 = nhits3_minus[score3];
nhits5 = nhits5_minus[score5];
- debug5(printf("at score %d, nhits5_minus = %d; at score %d, nhits3_minus = %d\n",
- score5,nhits5,score3,nhits3));
+ debug5(printf("at score %d+%d, nhits5_minus = %d, nhits3_minus = %d\n",
+ score5,score3,nhits5,nhits3));
if (nhits3 > 0 && nhits5 > 0) {
i = j = 0;
while (*abort_pairing_p == false && i < nhits3) {
hit3 = hits3[i];
+ if (circularp[hit3->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
+ } else {
+ pairmax = pairmax_linear;
+ }
insert_start = hit3->genomicstart - querylength3;
- debug5(printf("minus/minus: i=%d/%d %u..%u %s %s %p\n",
+ debug5(printf("minus/minus: i=%d/%d %u..%u %s %s circularalias:%d %p\n",
i,nhits3,hit3->genomicstart - hit3->chroffset,hit3->genomicend - hit3->chroffset,
- print_sense(hit3->sensedir),hittype_string(hit3->hittype),hit3));
+ print_sense(hit3->sensedir),hittype_string(hit3->hittype),hit3->circularalias,hit3));
while (j >= 0 &&
hits5[j]->genomicend + querylength5 /* for scramble: */ + pairmax > insert_start) {
- debug5(printf(" backup: j=%d/%d %u..%u %s %s %p\n",
+ debug5(printf(" backup: j=%d/%d %u..%u %s %s circularalias:%d %p\n",
j,nhits5,hits5[j]->genomicstart - hits5[j]->chroffset,hits5[j]->genomicend - hits5[j]->chroffset,
- print_sense(hits5[j]->sensedir),hittype_string(hits5[j]->hittype),hits5[j]));
+ print_sense(hits5[j]->sensedir),hittype_string(hits5[j]->hittype),hits5[j]->circularalias,hits5[j]));
j--;
}
j++; /* Finish backup */
while (j < nhits5 &&
hits5[j]->genomicend + querylength5 /* for scramble: */ + pairmax <= insert_start) {
- debug5(printf(" advance: j=%d/%d %u..%u %s %s %p\n",
+ debug5(printf(" advance: j=%d/%d %u..%u %s %s circularalias:%d %p\n",
j,nhits5,hits5[j]->genomicstart - hits5[j]->chroffset,hits5[j]->genomicend - hits5[j]->chroffset,
- print_sense(hits5[j]->sensedir),hittype_string(hits5[j]->hittype),hits5[j]));
+ print_sense(hits5[j]->sensedir),hittype_string(hits5[j]->hittype),hits5[j]->circularalias,hits5[j]));
j++;
}
while (j < nhits5 && hits5[j]->genomicend + querylength5 <= pairmax + insert_start) {
- debug5(printf(" overlap: j=%d/%d %u..%u %s %s %p",
+ debug5(printf(" overlap: j=%d/%d %u..%u %s %s circularalias:%d %p",
j,nhits5,hits5[j]->genomicstart - hits5[j]->chroffset,hits5[j]->genomicend - hits5[j]->chroffset,
- print_sense(hits5[j]->sensedir),hittype_string(hits5[j]->hittype),hits5[j]));
+ print_sense(hits5[j]->sensedir),hittype_string(hits5[j]->hittype),hits5[j]->circularalias,hits5[j]));
hit5 = hits5[j];
/* Want only pairs not previously seen */
if (hit3->paired_seenp == false || hit5->paired_seenp == false) {
if (hit3->effective_chrnum != hit5->effective_chrnum) {
debug5(printf(" => diff chrs %d and %d",hit5->effective_chrnum,hit3->effective_chrnum));
- } else if (hit5->chrnum == 0 && hit3->chrnum == 0 /* && hit5->other_chrnum != hit3->other_chrnum */) {
+ } else if (hit5->distant_splice_p == true && hit3->distant_splice_p == true /* && hit5->other_chrnum != hit3->other_chrnum */) {
/* Could potentially miss an alignment if the two ends overlap */
debug5(printf(" => double splice translocations"));
- } else if (hit5->chrnum == 0 || hit3->chrnum == 0) {
+ } else if (hit5->distant_splice_p == true || hit3->distant_splice_p == true) {
debug5(printf(" => conc_transloc effchr %d (chrnum5 %d, chrnum3 %d)",
hit3->effective_chrnum,hit5->chrnum,hit3->chrnum));
- if ((stage3pair = Stage3pair_new(hit5,hit3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT_TRANSLOCATIONS,splicing_penalty,
+ if ((stage3pair = Stage3pair_new(hit5,hit3,genestrand,/*pairtype*/CONCORDANT_TRANSLOCATIONS,
/*private5p*/false,/*private3p*/false,/*expect_concordant_p*/true)) != NULL) {
*conc_transloc = List_push(*conc_transloc,(void *) stage3pair);
}
} else if (SENSE_INCONSISTENT_P(hit3->sensedir,hit5->sensedir)) {
debug5(printf(" => sense inconsistent: %d | %d = %d",hit5->sensedir,hit3->sensedir,hit5->sensedir|hit3->sensedir));
+
} else if (hit5->genomicstart < hit3->genomicend) {
debug5(printf(" => scramble because start5 %llu < end3 %llu\n",
(unsigned long long) hit5->genomicstart,(unsigned long long) hit3->genomicend));
if (*nsamechr <= maxpairedpaths &&
- (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/PAIRED_SCRAMBLE,splicing_penalty,
+ (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),genestrand,/*pairtype*/PAIRED_SCRAMBLE,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/false)) != NULL) {
*samechr = List_push(*samechr,(void *) stage3pair);
(*nsamechr)++;
}
+
} else {
debug5(printf(" => concordant effchr %d (chrnum5 %d, chrnum3 %d)",
hit3->effective_chrnum,hit5->chrnum,hit3->chrnum));
- if ((stage3pair = Stage3pair_new(hit5,hit3,splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/CONCORDANT,splicing_penalty,
+ if ((stage3pair = Stage3pair_new(hit5,hit3,genestrand,/*pairtype*/CONCORDANT,
/*private5p*/false,/*private3p*/false,/*expect_concordant_p*/true)) != NULL) {
debug5(printf("Have new pair with scores %d + %d, compared with new_found_score %d\n",hit5->score,hit3->score,new_found_score));
@@ -15859,7 +16884,13 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
} /*else*/
#endif
- if (hit5->score + hit3->score < new_found_score) {
+
+ if (hit5->hittype == GMAP || hit3->hittype == GMAP) {
+ /* Don't use GMAP scores to set new_found_score */
+ hitpairs = List_push(hitpairs,(void *) stage3pair);
+ (*nconcordant)++;
+
+ } else if (hit5->score + hit3->score < new_found_score) {
/* Don't use frontier_score here, which is the trimmed_score. Use the full score, to motivate stage1hr to find longer alignments */
new_found_score = hit5->score + hit3->score;
debug5(printf(" => tentatively updating found_score to be %d = %d + %d\n",new_found_score,hit5->score,hit3->score));
@@ -15893,13 +16924,18 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
hits3 = hits3_minus[score3];
nhits5 = nhits5_plus[score5];
nhits3 = nhits3_minus[score3];
- debug5(printf("at score %d, nhits5_plus = %d; at score %d, nhits3_minus = %d\n",
- score5,nhits5,score3,nhits3));
+ debug5(printf("at score %d+%d, nhits5_plus = %d, nhits3_minus = %d\n",
+ score5,score3,nhits5,nhits3));
if (nhits5 > 0 && nhits3 > 0) {
i = j = 0;
while (*abort_pairing_p == false && i < nhits5) {
hit5 = hits5[i];
+ if (circularp[hit5->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
+ } else {
+ pairmax = pairmax_linear;
+ }
insert_start = hit5->genomicend - querylength5;
debug5(printf("plus/minus: i=%d/%d %u..%u %s %s %p\n",
i,nhits5,hit5->genomicstart - hit5->chroffset,hit5->genomicend - hit5->chroffset,
@@ -15932,7 +16968,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
if (hit5->paired_seenp == false || hit3->paired_seenp == false) {
if (hit5->effective_chrnum != hit3->effective_chrnum) {
debug5(printf(" => diff chrs %d and %d",hit5->effective_chrnum,hit3->effective_chrnum));
- } else if (hit5->chrnum == 0 && hit3->chrnum == 0 /* && hit5->other_chrnum != hit3->other_chrnum */) {
+ } else if (hit5->distant_splice_p == true && hit3->distant_splice_p == true /* && hit5->other_chrnum != hit3->other_chrnum */) {
debug5(printf(" => double splice translocations"));
} else if (SENSE_INCONSISTENT_FOR_INVERSION_P(hit5->sensedir,hit3->sensedir)) {
debug5(printf(" => sense inconsistent for inversion"));
@@ -15940,10 +16976,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
} else if (hits3[j]->genomicstart + querylength3 <= insert_start) {
debug5(printf(" => scramble"));
if (*nsamechr <= maxpairedpaths &&
- (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/PAIRED_SCRAMBLE,splicing_penalty,
+ (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),genestrand,/*pairtype*/PAIRED_SCRAMBLE,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/false)) != NULL) {
*samechr = List_push(*samechr,(void *) stage3pair);
(*nsamechr)++;
@@ -15953,10 +16986,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
debug5(printf(" => inversion effchr %d (chrnum5 %d, chrnum3 %d)",
hit5->effective_chrnum,hit5->chrnum,hit3->chrnum));
if (*nsamechr <= maxpairedpaths &&
- (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/PAIRED_INVERSION,splicing_penalty,
+ (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),genestrand,/*pairtype*/PAIRED_INVERSION,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/false)) != NULL) {
*samechr = List_push(*samechr,(void *) stage3pair);
(*nsamechr)++;
@@ -15978,13 +17008,18 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
hits5 = hits5_minus[score5];
nhits3 = nhits3_plus[score3];
nhits5 = nhits5_minus[score5];
- debug5(printf("at score %d, nhits5_minus = %d; at score %d, nhits3_plus = %d\n",
- score5,nhits5,score3,nhits3));
+ debug5(printf("at score %d+%d, nhits5_minus = %d, nhits3_plus = %d\n",
+ score5,score3,nhits5,nhits3));
if (nhits3 > 0 && nhits5 > 0) {
i = j = 0;
while (*abort_pairing_p == false && i < nhits3) {
hit3 = hits3[i];
+ if (circularp[hit3->effective_chrnum] == true) {
+ pairmax = pairmax_circular;
+ } else {
+ pairmax = pairmax_linear;
+ }
insert_start = hit3->genomicstart - querylength3;
debug5(printf("minus/plus: i=%d/%d %u..%u %s %s %p\n",
i,nhits3,hit3->genomicstart - hit3->chroffset,hit3->genomicend - hit3->chroffset,
@@ -16017,7 +17052,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
if (hit3->paired_seenp == false || hit5->paired_seenp == false) {
if (hit3->effective_chrnum != hit5->effective_chrnum) {
debug5(printf(" => diff chrs %d and %d",hit5->effective_chrnum,hit3->effective_chrnum));
- } else if (hit5->chrnum == 0 && hit3->chrnum == 0 /* && hit5->other_chrnum != hit3->other_chrnum */) {
+ } else if (hit5->distant_splice_p == true && hit3->distant_splice_p == true /* && hit5->other_chrnum != hit3->other_chrnum */) {
debug5(printf(" => double splice translocations"));
} else if (SENSE_INCONSISTENT_FOR_INVERSION_P(hit3->sensedir,hit5->sensedir)) {
debug5(printf(" => sense inconsistent for inversion"));
@@ -16025,10 +17060,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
} else if (hits5[j]->genomicend + querylength5 <= insert_start) {
debug5(printf(" => scramble"));
if (*nsamechr <= maxpairedpaths &&
- (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/PAIRED_SCRAMBLE,splicing_penalty,
+ (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),genestrand,/*pairtype*/PAIRED_SCRAMBLE,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/false)) != NULL) {
*samechr = List_push(*samechr,(void *) stage3pair);
(*nsamechr)++;
@@ -16038,10 +17070,7 @@ pair_up_concordant_aux (bool *abort_pairing_p, int *found_score, int *nconcordan
debug5(printf(" => inversion effchr %d (chrnum5 %d, chrnum3 %d)",
hit3->effective_chrnum,hit5->chrnum,hit3->chrnum));
if (*nsamechr <= maxpairedpaths &&
- (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),splicesites,
- query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,genestrand,
- /*pairtype*/PAIRED_INVERSION,splicing_penalty,
+ (stage3pair = Stage3pair_new(Stage3end_copy(hit5),Stage3end_copy(hit3),genestrand,/*pairtype*/PAIRED_INVERSION,
/*private5p*/true,/*private3p*/true,/*expect_concordant_p*/false)) != NULL) {
*samechr = List_push(*samechr,(void *) stage3pair);
(*nsamechr)++;
@@ -16170,28 +17199,24 @@ List_T
Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcordant, int *nsamechr,
List_T *samechr, List_T *conc_transloc,
List_T hitpairs, List_T *hitarray5, int narray5, List_T *hitarray3, int narray3,
- int cutoff_level_5, int cutoff_level_3, int subopt_levels,
- Univcoord_T *splicesites,
- Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
- Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- int querylength5, int querylength3, int maxpairedpaths,
- int splicing_penalty, int genestrand) {
+ int cutoff_level_5, int cutoff_level_3,
+ int querylength5, int querylength3, int maxpairedpaths, int genestrand) {
T **hits5_plus, **hits5_minus, **hits3_plus, **hits3_minus;
int *nhits5_plus, *nhits5_minus, *nhits3_plus, *nhits3_minus;
- T **terminals5_plus, **terminals5_minus, **terminals3_plus, **terminals3_minus;
- int *nterminals5_plus, *nterminals5_minus, *nterminals3_plus, *nterminals3_minus;
int score5, score3;
- bool *sorted_hits5_p, *sorted_hits3_p, *sorted_terminals5_p = NULL, *sorted_terminals3_p = NULL;
- int cutoff_level_hits5, cutoff_level_hits3, cutoff_level_terminals5 = 0, cutoff_level_terminals3 = 0;
- int ignore_found_score;
-
+ bool *sorted_hits5_p, *sorted_hits3_p;
+ /* bool *sorted_terminals5_p = NULL, *sorted_terminals3_p = NULL; */
+ int cutoff_level_hits5, cutoff_level_hits3;
+ /* int cutoff_level_terminals5 = 0, cutoff_level_terminals3 = 0; */
+ /* int ignore_found_score; */
+
int i;
int min_score_5 = -1, min_score_3 = -1;
List_T q;
T hit;
-
- debug5(printf("Starting Stage3_pair_up_concordant with %d concordant, narray5 %d, narray3 %d, terminals5 %p, terminals3 %p, found_score %d\n",
- *nconcordant,narray5,narray3,terminals5,terminals3,*found_score));
+
+ debug5(printf("Starting Stage3_pair_up_concordant with %d concordant, narray5 %d, narray3 %d, found_score %d\n",
+ *nconcordant,narray5,narray3,*found_score));
/* Re-adjust cutoff_levels for best hit5 and best hit3 */
for (i = 0; i < narray5; i++) {
@@ -16229,6 +17254,7 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
nhits5_minus = (int *) CALLOCA(cutoff_level_5+1,sizeof(int));
cutoff_level_hits5 = sort_hits_by_trimmed_score(hits5_plus,hits5_minus,nhits5_plus,nhits5_minus,
hitarray5,narray5,cutoff_level_5);
+ debug5(printf("cutoff_level for hits5 is %d\n",cutoff_level_hits5));
sorted_hits5_p = (bool *) CALLOCA(cutoff_level_hits5+1,sizeof(bool));
@@ -16239,6 +17265,7 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
nhits3_minus = (int *) CALLOCA(cutoff_level_3+1,sizeof(int));
cutoff_level_hits3 = sort_hits_by_trimmed_score(hits3_plus,hits3_minus,nhits3_plus,nhits3_minus,
hitarray3,narray3,cutoff_level_3);
+ debug5(printf("cutoff_level for hits3 is %d\n",cutoff_level_hits3));
sorted_hits3_p = (bool *) CALLOCA(cutoff_level_hits3+1,sizeof(bool));
/* Look for concordant pairs among the non-terminals */
@@ -16247,10 +17274,8 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
hits5_plus,nhits5_plus,hits5_minus,nhits5_minus,
hits3_plus,nhits3_plus,hits3_minus,nhits3_minus,
/*sorted5p*/sorted_hits5_p,/*sorted3p*/sorted_hits3_p,
- cutoff_level_hits5,cutoff_level_hits3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,querylength5,querylength3,
- maxpairedpaths,splicing_penalty,genestrand);
+ cutoff_level_hits5,cutoff_level_hits3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
#if 0
/* Look for single terminals */
@@ -16270,10 +17295,8 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
hits5_plus,nhits5_plus,hits5_minus,nhits5_minus,
terminals3_plus,nterminals3_plus,terminals3_minus,nterminals3_minus,
/*sorted5p*/sorted_hits5_p,/*sorted3p*/sorted_terminals3_p,
- cutoff_level_hits5,cutoff_level_terminals3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,querylength5,querylength3,
- maxpairedpaths,splicing_penalty,genestrand);
+ cutoff_level_hits5,cutoff_level_terminals3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
}
if (terminals5 != NULL) {
@@ -16292,10 +17315,8 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
terminals5_plus,nterminals5_plus,terminals5_minus,nterminals5_minus,
hits3_plus,nhits3_plus,hits3_minus,nhits3_minus,
/*sorted5p*/sorted_terminals5_p,/*sorted3p*/sorted_hits3_p,
- cutoff_level_terminals5,cutoff_level_hits3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,querylength5,querylength3,
- maxpairedpaths,splicing_penalty,genestrand);
+ cutoff_level_terminals5,cutoff_level_hits3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
}
/* Previously required *with_terminal to be NULL also */
@@ -16308,10 +17329,8 @@ Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcor
terminals5_plus,nterminals5_plus,terminals5_minus,nterminals5_minus,
terminals3_plus,nterminals3_plus,terminals3_minus,nterminals3_minus,
/*sorted5p*/sorted_terminals5_p,/*sorted3p*/sorted_terminals3_p,
- cutoff_level_terminals5,cutoff_level_terminals3,subopt_levels,
- splicesites,query5_compress_fwd,query5_compress_rev,
- query3_compress_fwd,query3_compress_rev,querylength5,querylength3,
- maxpairedpaths,splicing_penalty,genestrand);
+ cutoff_level_terminals5,cutoff_level_terminals3,
+ querylength5,querylength3,maxpairedpaths,genestrand);
}
if (sorted_terminals3_p != NULL) {
diff --git a/src/stage3hr.h b/src/stage3hr.h
index 47aa59d..a3642dd 100644
--- a/src/stage3hr.h
+++ b/src/stage3hr.h
@@ -1,4 +1,4 @@
-/* $Id: stage3hr.h 173896 2015-09-12 00:11:40Z twu $ */
+/* $Id: stage3hr.h 184484 2016-02-18 03:11:53Z twu $ */
#ifndef STAGE3HR_INCLUDED
#define STAGE3HR_INCLUDED
@@ -38,14 +38,14 @@ Stage3hr_setup (bool invert_first_p_in, bool invert_second_p_in, Genome_T genome
IIT_T genes_iit_in, int *genes_divint_crosstable_in,
IIT_T tally_iit_in, int *tally_divint_crosstable_in,
IIT_T runlength_iit_in, int *runlength_divint_crosstable_in,
- bool distances_observed_p, int pairmax_in,
+ bool distances_observed_p, int pairmax_linear_in, int pairmax_circular_in,
Chrpos_T expected_pairlength, Chrpos_T pairlength_deviation,
int localsplicing_penalty_in, int indel_penalty_middle_in,
int antistranded_penalty_in, bool favor_multiexon_p_in,
- int gmap_min_nconsecutive_in, int index1part, int index1interval,
- bool novelsplicingp_in, bool merge_samechr_p_in,
- bool *circularp_in, char *failedinput_root_in,
- bool print_m8_p_in, bool want_random_p_in);
+ int gmap_min_nconsecutive_in, int end_detail, int subopt_levels_in,
+ bool novelsplicingp_in, Chrpos_T shortsplicedist_in, bool merge_samechr_p_in,
+ bool *circularp_in, bool *altlocp_in, Univcoord_T *alias_starts_in, Univcoord_T *alias_ends_in,
+ char *failedinput_root_in, bool print_m8_p_in, bool want_random_p_in);
extern char *
Stage3end_deletion_string (T this);
@@ -136,9 +136,6 @@ extern int
Stage3end_circularpos (T this);
-extern char *
-Stage3end_deletion_string (T this);
-
extern Junction_T
Stage3end_junctionD (T this);
extern Junction_T
@@ -152,7 +149,7 @@ Stage3end_junctions_LtoH (T this);
extern Substring_T
Stage3end_substring1 (T this);
extern Substring_T
-Stage3end_substring2 (T this);
+Stage3end_substringN (T this);
extern Substring_T
Stage3end_substring_donor (T this);
@@ -239,6 +236,9 @@ extern int
Stage3end_terminal_trim (T this);
extern int
Stage3end_trimlength (T this);
+extern void
+Stage3end_count_hits (int *npaths_primary, int *npaths_altloc, List_T hits);
+
extern bool
Stage3end_contains_known_splicesite (T this);
extern bool
@@ -275,6 +275,9 @@ extern int
Stage3pair_nmatches_posttrim (int *nmatches5, int *nmatches3, Stage3pair_T this);
extern bool
Stage3pair_concordantp (List_T hitpairs);
+extern void
+Stage3pair_count_hits (int *npaths_primary, int *npaths_altloc, List_T hitpairs);
+
extern List_T
Stage3pair_filter_nonconcordant (List_T hitpairs);
extern int
@@ -305,54 +308,61 @@ Stage3end_new_substrings (int *found_score, Intlist_T endpoints,
Intlist_T nmismatches_list, List_T junctions, int querylength,
Compress_T query_compress,
Substring_T right_ambig, Substring_T left_ambig,
- bool plusp, int genestrand, int sensedir, bool first_read_p,
+ bool plusp, int genestrand, int sensedir,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh,
Chrpos_T chrlength, bool sarrayp);
extern T
-Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength,
- int genestrand, bool first_read_p,
+Stage3end_substrings_run_gmap_plus (T this, char *queryuc_ptr, int querylength, int genestrand,
int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool);
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool extend_ends_p);
extern T
-Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength,
- int genestrand, bool first_read_p,
+Stage3end_substrings_run_gmap_minus (T this, char *queryuc_ptr, int querylength, int genestrand,
int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
- Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool);
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool,
+ bool extend_ends_p);
+
+extern T
+Stage3end_gmap_run_gmap_plus (T this, char *queryuc_ptr, int querylength, int genestrand,
+ int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool);
+extern T
+Stage3end_gmap_run_gmap_minus (T this, char *queryuc_ptr, int querylength, int genestrand,
+ int maxpeelback, Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR,
+ Oligoindex_array_T oligoindices_minor, Diagpool_T diagpool, Cellpool_T cellpool);
extern T
Stage3end_new_exact (int *found_score, Univcoord_T left, int genomiclength, Compress_T query_compress,
- bool plusp, int genestrand, bool first_read_p,
+ bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
bool sarrayp);
extern T
Stage3end_new_substitution (int *found_score, int nmismatches, Univcoord_T left,
int genomiclength, Compress_T query_compress,
- bool plusp, int genestrand, bool first_read_p,
+ bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
bool sarrayp);
extern T
Stage3end_new_insertion (int *found_score, int nindels, int indel_pos, int nmismatches1, int nmismatches2,
- Univcoord_T left, int genomiclength, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int indel_penalty, bool sarrayp);
extern T
Stage3end_new_deletion (int *found_score, int nindels, int indel_pos, int nmismatches1, int nmismatches2,
- Univcoord_T left, int genomiclength, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int indel_penalty, bool sarrayp);
extern T
Stage3end_new_terminal (int querystart, int queryend, Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ int querylength, bool plusp, int genestrand,
Endtype_T start_endtype, Endtype_T end_endtype,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int max_mismatches_allowed, bool sarrayp);
extern T
Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmismatches,
Substring_T donor, Substring_T acceptor, double donor_prob, double acceptor_prob, Chrpos_T distance,
- bool shortdistancep, int splicing_penalty, int querylength, int amb_length, double amb_prob,
+ bool shortdistancep, int splicing_penalty, int querylength,
#ifdef LARGE_GENOMES
Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
#else
@@ -366,7 +376,7 @@ Stage3end_new_splice (int *found_score, int donor_nmismatches, int acceptor_nmis
extern T
Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T acceptor, Substring_T shortexon,
double donor_prob, double shortexonA_prob, double shortexonD_prob, double acceptor_prob,
- int amb_length_donor, int amb_length_acceptor, double amb_prob_donor, double amb_prob_acceptor,
+ int amb_length_donor, int amb_length_acceptor,
#ifdef LARGE_GENOMES
Uint8list_T ambcoords_donor, Uint8list_T ambcoords_acceptor,
#else
@@ -376,15 +386,15 @@ Stage3end_new_shortexon (int *found_score, Substring_T donor, Substring_T accept
Intlist_T amb_nmismatches_donor, Intlist_T amb_nmismatches_acceptor,
Doublelist_T amb_probs_donor, Doublelist_T amb_probs_acceptor,
bool copy_donor_p, bool copy_acceptor_p, bool copy_shortexon_p,
- int splicing_penalty, int querylength, bool first_read_p, int sensedir, bool sarrayp);
+ int splicing_penalty, int querylength, int sensedir, bool sarrayp);
extern T
Stage3end_new_gmap (int nmismatches_whole, int nmatches_posttrim, int max_match_length,
int ambig_end_length_5, int ambig_end_length_3,
Splicetype_T ambig_splicetype_5, Splicetype_T ambig_splicetype_3,
- double ambig_prob_5, double ambig_prob_3, double min_splice_prob,
+ double min_splice_prob,
struct Pair_T *pairarray, int npairs, int nsegments, int nintrons, int nindelbreaks,
- Univcoord_T left, int genomiclength, bool plusp, int genestrand, bool first_read_p,
+ Univcoord_T left, int genomiclength, bool plusp, int genestrand,
char *accession, int querylength,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength,
int cdna_direction, int sensedir, GMAP_source_T gmap_source);
@@ -398,22 +408,19 @@ extern List_T
Stage3end_filter_coverage (List_T hits, int min_coverage);
extern Stage3end_T *
-Stage3end_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
+Stage3end_eval_and_sort (int npaths, int *first_absmq, int *second_absmq,
Stage3end_T *stage3array, int maxpaths, Shortread_T queryseq,
- char *queryuc_ptr, char *queryrc,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
+ char *queryuc_ptr, Compress_T query_compress_fwd, Compress_T query_compress_rev,
char *quality_string, bool displayp);
extern Stage3end_T *
-Stage3end_eval_and_sort_guided (int *npaths, int *first_absmq, int *second_absmq, Stage3end_T guide,
+Stage3end_eval_and_sort_guided (int npaths, int *first_absmq, int *second_absmq, Stage3end_T guide,
Stage3end_T *stage3array, int maxpaths, Shortread_T queryseq,
- char *queryuc_ptr, char *queryrc,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
+ char *queryuc_ptr, Compress_T query_compress_fwd, Compress_T query_compress_rev,
char *quality_string, bool displayp);
extern List_T
Stage3pair_remove_excess_terminals (List_T hitpairlist);
extern List_T
-Stage3end_optimal_score (List_T hitlist, int cutoff_level, int suboptimal_mismatches,
- Compress_T query_compress_fwd, Compress_T query_compress_rev,
+Stage3end_optimal_score (List_T hitlist, Compress_T query_compress_fwd, Compress_T query_compress_rev,
int querylength, bool keep_gmap_p, bool finalp);
extern bool
Stage3pair_sense_consistent_p (List_T hitpairlist);
@@ -447,6 +454,8 @@ extern Pairtype_T
Stage3pair_pairtype (Stage3pair_T this);
extern bool
Stage3pair_circularp (Stage3pair_T this);
+extern bool
+Stage3pair_altlocp (Stage3pair_T this);
extern void
Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
@@ -457,10 +466,7 @@ Stage3pair_print_end (Filestring_T fp, Filestring_T fp_failedinput,
bool invertp, int quality_shift);
extern Stage3pair_T
-Stage3pair_new (T hit5, T hit3, Univcoord_T *splicesites,
- Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
- Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- int genestrand, Pairtype_T pairtype, int splicing_penalty,
+Stage3pair_new (T hit5, T hit3, int genestrand, Pairtype_T pairtype,
bool private5p, bool private3p, bool expect_concordant_p);
struct Pair_T *
@@ -485,17 +491,16 @@ extern List_T
Stage3pair_filter_coverage (List_T hits, int min_coverage_5, int min_coverage_3);
extern Stage3pair_T *
-Stage3pair_eval_and_sort (int *npaths, int *first_absmq, int *second_absmq,
+Stage3pair_eval_and_sort (int npaths, int *first_absmq, int *second_absmq,
Stage3pair_T *stage3pairarray, int maxpaths,
Shortread_T queryseq1, Shortread_T queryseq2,
- char *queryuc_ptr_5, char *queryrc5,
- char *queryuc_ptr_3, char *queryrc3,
+ char *queryuc_ptr_5, char *queryuc_ptr_3,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
char *quality_string_5, char *quality_string_3);
extern List_T
-Stage3pair_optimal_score (List_T hitpairlist, int cutoff_level, int suboptimal_mismatches,
+Stage3pair_optimal_score (List_T hitpairlist,
Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
int querylength5, int querylength3, bool keep_gmap_p, bool finalp);
@@ -512,12 +517,8 @@ extern List_T
Stage3_pair_up_concordant (bool *abort_pairing_p, int *found_score, int *nconcordant, int *nsamechr,
List_T *samechr, List_T *conc_transloc,
List_T hitpairs, List_T *hitarray5, int narray5, List_T *hitarray3, int narray3,
- int cutoff_level_5, int cutoff_level_3, int subopt_levels,
- Univcoord_T *splicesites,
- Compress_T query5_compress_fwd, Compress_T query5_compress_rev,
- Compress_T query3_compress_fwd, Compress_T query3_compress_rev,
- int querylength5, int querylength3, int maxpairedpaths,
- int splicing_penalty, int genestrand);
+ int cutoff_level_5, int cutoff_level_3,
+ int querylength5, int querylength3, int maxpairedpaths, int genestrand);
#undef T
#endif
diff --git a/src/substring.c b/src/substring.c
index 69aa9f1..45ab519 100644
--- a/src/substring.c
+++ b/src/substring.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: substring.c 184487 2016-02-18 03:28:42Z twu $";
+static char rcsid[] = "$Id: substring.c 184582 2016-02-19 14:40:24Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -30,6 +30,10 @@ static char rcsid[] = "$Id: substring.c 184487 2016-02-18 03:28:42Z twu $";
#define INVERSION_TEXT "inversion"
#define SCRAMBLE_TEXT "scramble"
+#define END_SPLICESITE_SEARCH 10
+#define END_SPLICESITE_PROB_MATCH 0.90
+#define END_SPLICESITE_PROB_MISMATCH 0.95
+
#ifdef DEBUG
#define debug(x) x
@@ -98,6 +102,14 @@ static char rcsid[] = "$Id: substring.c 184487 2016-02-18 03:28:42Z twu $";
#endif
+/* trim_novel_spliceends */
+#ifdef DEBUG13
+#define debug13(x) x
+#else
+#define debug13(x)
+#endif
+
+
#define LOG_99 -0.01005033585
#define LOG_01 -4.605170186
@@ -227,6 +239,9 @@ struct T {
int trim_left;
int trim_right;
+ int mandatory_trim_left; /* Resulting from unalias, plus SOFT_CLIPS_AVOID_CIRCULARIZATION */
+ int mandatory_trim_right; /* Resulting from alias, plus SOFT_CLIPS_AVOID_CIRCULARIZATION */
+
bool trim_left_splicep;
bool trim_right_splicep;
@@ -259,10 +274,8 @@ struct T {
Univcoord_T alignstart_trim; /* For part that aligns to genome, excluding part that is trimmed (post-trim) */
Univcoord_T alignend_trim;
- int genomiclength; /* Can replace with querylength */
bool plusp;
int genestrand;
- bool first_read_p;
char *genomic_bothdiff; /* In same direction as query. NULL if same
as query. Has dashes outside of
@@ -325,6 +338,16 @@ Substring_alias_circular (T this) {
if (this != NULL) {
chrlength = this->chrlength;
+ if (this->left + this->querylength > chrlength) {
+ if (this->plusp == true) {
+ this->mandatory_trim_right = chrlength - (this->left + this->querylength);
+ debug2(printf("For alias, setting mandatory_trim_right to be %d\n",this->mandatory_trim_right));
+ } else {
+ this->mandatory_trim_left = chrlength - (this->left + this->querylength);
+ debug2(printf("For alias, setting mandatory_trim_left to be %d\n",this->mandatory_trim_left));
+ }
+ }
+
this->left += chrlength;
this->genomicstart += chrlength;
this->genomicend += chrlength;
@@ -347,6 +370,16 @@ Substring_unalias_circular (T this) {
if (this != NULL) {
chrlength = this->chrlength;
+ if (this->left < chrlength) {
+ if (this->plusp == true) {
+ this->mandatory_trim_left = chrlength - this->left;
+ debug2(printf("For alias, setting mandatory_trim_left to be %d\n",this->mandatory_trim_left));
+ } else {
+ this->mandatory_trim_right = chrlength - this->left;
+ debug2(printf("For alias, setting mandatory_trim_right to be %d\n",this->mandatory_trim_right));
+ }
+ }
+
this->left -= chrlength;
this->genomicstart -= chrlength;
this->genomicend -= chrlength;
@@ -590,8 +623,8 @@ count_mismatches_dibase (char *genome, char *query, int start, int end, bool plu
static int
-trim_left_end (Compress_T query_compress, Univcoord_T left, int querystart, int queryend,
- int querylength, bool plusp, int genestrand, bool first_read_p, int trim_mismatch_score) {
+trim_left_end (int *nmismatches_end, Compress_T query_compress, Univcoord_T left, int querystart, int queryend,
+ int querylength, bool plusp, int genestrand, int trim_mismatch_score) {
int bestscore, score;
int trim5, alignlength, pos, prevpos, i;
int nmismatches;
@@ -615,7 +648,7 @@ trim_left_end (Compress_T query_compress, Univcoord_T left, int querystart, int
left,querystart,queryend));
nmismatches = Genome_mismatches_right_trim(mismatch_positions,/*max_mismatches*/alignlength,
query_compress,left,/*pos5*/querystart,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug8(printf("%d mismatches:",nmismatches));
debug8(
for (i = 0; i < nmismatches; i++) {
@@ -641,12 +674,26 @@ trim_left_end (Compress_T query_compress, Univcoord_T left, int querystart, int
prevpos = pos - 1; /* On the mismatch */
}
+ score += prevpos*TRIM_MATCH_SCORE;
+ if (score >= bestscore) { /* want >= and not >, so ties go to end */
+ /* bestscore = score; */
+ trim5 = 0;
+ }
+
+ *nmismatches_end = 0;
+ for (i = 0; i < nmismatches; i++) {
+ pos = mismatch_positions[i]; /* the position of the mismatch */
+ if (mismatch_positions[i] < trim5) {
+ *nmismatches_end += 1;
+ }
+ }
+
} else {
debug8(printf("Calling Genome_mismatches_left_trim with left %u, pos5 %d - %d, pos3 %d - %d\n",
left,querylength,queryend,querylength,querystart));
nmismatches = Genome_mismatches_left_trim(mismatch_positions,/*max_mismatches*/alignlength,
query_compress,left,/*pos5*/querylength - queryend,
- /*pos3*/querylength - querystart,plusp,genestrand,first_read_p);
+ /*pos3*/querylength - querystart,plusp,genestrand);
debug8(printf("%d mismatches:",nmismatches));
debug8(
@@ -672,15 +719,24 @@ trim_left_end (Compress_T query_compress, Univcoord_T left, int querystart, int
}
prevpos = pos - 1; /* On the mismatch */
}
- }
- score += prevpos*TRIM_MATCH_SCORE;
- if (score >= bestscore) { /* want >= and not >, so ties go to end */
- bestscore = score;
- trim5 = 0;
+ score += prevpos*TRIM_MATCH_SCORE;
+ if (score >= bestscore) { /* want >= and not >, so ties go to end */
+ /* bestscore = score; */
+ trim5 = 0;
+ }
+
+ *nmismatches_end = 0;
+ for (i = 0; i < nmismatches; i++) {
+ pos = querylength - 1 - mismatch_positions[i]; /* the position of the mismatch */
+ if (pos < trim5) {
+ *nmismatches_end += 1;
+ }
+ }
}
- debug8(printf("Trim left pos 0, score %d, trim5 %d\n",score,trim5));
+
+ debug8(printf("Trim left pos 0, score %d, trim5 %d, nmismatches_end %d\n",score,trim5,*nmismatches_end));
debug8(printf("\n"));
return trim5;
@@ -691,8 +747,8 @@ trim_left_end (Compress_T query_compress, Univcoord_T left, int querystart, int
/* querystart (typically 0) and queryend (typically querylength) are exclusive */
/* sequences may have had lower case characters marked */
static int
-trim_right_end (Compress_T query_compress, Univcoord_T left, int querystart, int queryend,
- int querylength, bool plusp, int genestrand, bool first_read_p, int trim_mismatch_score) {
+trim_right_end (int *nmismatches_end, Compress_T query_compress, Univcoord_T left, int querystart, int queryend,
+ int querylength, bool plusp, int genestrand, int trim_mismatch_score) {
int bestscore, score;
int trim3, alignlength, pos, prevpos, i;
int nmismatches;
@@ -713,7 +769,7 @@ trim_right_end (Compress_T query_compress, Univcoord_T left, int querystart, int
if (plusp == true) {
nmismatches = Genome_mismatches_left_trim(mismatch_positions,/*max_mismatches*/alignlength,
query_compress,left,/*pos5*/querystart,/*pos3*/queryend,
- plusp,genestrand,first_read_p);
+ plusp,genestrand);
debug8(printf("%d mismatches:",nmismatches));
debug8(
@@ -740,10 +796,24 @@ trim_right_end (Compress_T query_compress, Univcoord_T left, int querystart, int
prevpos = pos + 1; /* On the mismatch */
}
+ score += (queryend - 1 - prevpos)*TRIM_MATCH_SCORE;
+ if (score >= bestscore) { /* want >= and not >, so ties go to end */
+ /* bestscore = score; */
+ trim3 = 0;
+ }
+
+ *nmismatches_end = 0;
+ for (i = 0; i < nmismatches; i++) {
+ pos = mismatch_positions[i]; /* the position of the mismatch */
+ if (pos > querylength - 1 - trim3) {
+ *nmismatches_end += 1;
+ }
+ }
+
} else {
nmismatches = Genome_mismatches_right_trim(mismatch_positions,/*max_mismatches*/alignlength,
query_compress,left,/*pos5*/querylength - queryend,
- /*pos3*/querylength - querystart,plusp,genestrand,first_read_p);
+ /*pos3*/querylength - querystart,plusp,genestrand);
debug8(printf("%d mismatches:",nmismatches));
debug8(
@@ -769,21 +839,31 @@ trim_right_end (Compress_T query_compress, Univcoord_T left, int querystart, int
}
prevpos = pos + 1; /* On the mismatch */
}
- }
- score += (queryend - 1 - prevpos)*TRIM_MATCH_SCORE;
- if (score >= bestscore) { /* want >= and not >, so ties go to end */
- bestscore = score;
- trim3 = 0;
+ score += (queryend - 1 - prevpos)*TRIM_MATCH_SCORE;
+ if (score >= bestscore) { /* want >= and not >, so ties go to end */
+ /* bestscore = score; */
+ trim3 = 0;
+ }
+
+ *nmismatches_end = 0;
+ for (i = 0; i < nmismatches; i++) {
+ pos = querylength - 1 - mismatch_positions[i]; /* the position of the mismatch */
+ if (pos > querylength - 1 - trim3) {
+ *nmismatches_end += 1;
+ }
+ }
}
- debug8(printf("Trim right pos %d, score %d, trim3 %d\n",queryend-1,score,trim3));
+
+ debug8(printf("Trim right pos %d, score %d, trim3 %d, nmismatches_end %d\n",queryend-1,score,trim3,*nmismatches_end));
debug8(printf("\n"));
return trim3;
}
+#if 0
/* Uses hmm */
/* Modified for Stage3_bad_stretch_p */
bool
@@ -817,7 +897,7 @@ Substring_bad_stretch_p (T this, Compress_T query_compress_fwd, Compress_T query
#ifdef DEBUG9
nmismatches = Genome_mismatches_left(mismatch_positions,/*max_mismatches*/alignlength,
query_compress_fwd,this->left,/*pos5*/startpos,/*pos3*/endpos,
- /*plusp*/true,this->genestrand,this->first_read_p);
+ /*plusp*/true,this->genestrand);
#endif
} else {
startpos = this->querylength - this->queryend_orig;
@@ -826,7 +906,7 @@ Substring_bad_stretch_p (T this, Compress_T query_compress_fwd, Compress_T query
#ifdef DEBUG9
nmismatches = Genome_mismatches_left(mismatch_positions,/*max_mismatches*/alignlength,
query_compress_rev,this->left,/*pos5*/startpos,/*pos3*/endpos,
- /*plusp*/false,this->genestrand,this->first_read_p);
+ /*plusp*/false,this->genestrand);
#endif
}
@@ -1003,6 +1083,7 @@ Substring_bad_stretch_p (T this, Compress_T query_compress_fwd, Compress_T query
#endif
}
+#endif
void
@@ -1656,7 +1737,7 @@ embellish_genomic (char *genomic_diff, char *query, int querystart, int queryend
static char *
embellish_genomic_sam (char *genomic_diff, char *query, int querystart, int queryend, int querylength,
- int genomiclength, int genestrand, bool exactp) {
+ int genestrand, bool exactp) {
char *result;
int i, j, k;
@@ -1706,26 +1787,782 @@ embellish_genomic_sam (char *genomic_diff, char *query, int querystart, int quer
}
+/* Modified from trim_novel_spliceends in stage3.c */
+void
+substring_trim_novel_spliceends (T substring1, T substringN, int *ambig_end_length_5, int *ambig_end_length_3,
+ Splicetype_T *ambig_splicetype_5, Splicetype_T *ambig_splicetype_3,
+ double *ambig_prob_5, double *ambig_prob_3, int *sensedir,
+ Univcoord_T chroffset) {
+
+ Univcoord_T genomicpos, start_genomicpos, middle_genomicpos, end_genomicpos;
+ Univcoord_T splice_genomepos_5, splice_genomepos_3, splice_genomepos_5_mm, splice_genomepos_3_mm;
+ Univcoord_T start, middle, end; /* start to middle has mismatches, while middle to end has none */
+ double donor_prob, acceptor_prob;
+ double max_prob_5 = 0.0, max_prob_3 = 0.0,
+ max_prob_sense_forward_5 = 0.0, max_prob_sense_anti_5 = 0.0,
+ max_prob_sense_forward_3 = 0.0, max_prob_sense_anti_3 = 0.0;
+ double max_prob_5_mm = 0.0, max_prob_3_mm = 0.0,
+ max_prob_sense_forward_5_mm = 0.0, max_prob_sense_anti_5_mm = 0.0,
+ max_prob_sense_forward_3_mm = 0.0, max_prob_sense_anti_3_mm = 0.0;
+ Splicetype_T splicetype5, splicetype3, splicetype5_mm, splicetype3_mm;
+ int splice_sensedir_5, splice_sensedir_3, splice_sensedir_5_mm, splice_sensedir_3_mm;
+
+
+ debug13(printf("\nEntered Substring_trim_novel_spliceends with sensedir %d\n",*sensedir));
+ *ambig_end_length_5 = 0;
+ *ambig_end_length_3 = 0;
+
+ /* start is distal, end is medial */
+ if (substringN == NULL) {
+ /* Skip 3' end*/
+ } else if (substringN->plusp == true) {
+ start = substringN->genomicend;
+ middle = substringN->alignend_trim + 1;
+ if ((end = middle - END_SPLICESITE_SEARCH) < substringN->alignstart_trim) {
+ end = substringN->alignstart_trim;
+ }
+ } else {
+ start = substringN->genomicend;
+ middle = substringN->alignend_trim - 1;
+ if ((end = middle + END_SPLICESITE_SEARCH) > substringN->alignstart_trim) {
+ end = substringN->alignstart_trim;
+ }
+ }
+
+ if (substringN == NULL) {
+ /* Skip 3' end */
+ } else if (*sensedir == SENSE_FORWARD) {
+ if (substringN->plusp) {
+ splicetype3 = splicetype3_mm = DONOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos >= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 1 */
+ debug13(printf("3', watson, sense anti %u %u %f mm\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 1 */
+ debug13(printf("3', watson, sense anti %u %u %f\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_3) {
+ max_prob_3 = donor_prob;
+ splice_genomepos_3 = genomicpos;
+ }
+ genomicpos--;
+ }
+ debug13(printf("\n"));
+
+ } else {
+ splicetype3 = splicetype3_mm = ANTIDONOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos <= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 3 */
+ debug13(printf("3', crick, sense forward %u %u %f mm\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 3 */
+ debug13(printf("3', crick, sense forward %u %u %f\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_3) {
+ max_prob_3 = donor_prob;
+ splice_genomepos_3 = genomicpos;
+ }
+ genomicpos++;
+ }
+ debug13(printf("\n"));
+ }
+
+ } else if (*sensedir == SENSE_ANTI) {
+ if (substringN->plusp) {
+ splicetype3 = splicetype3_mm = ANTIACCEPTOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos >= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 5 */
+ debug13(printf("3', watson, sense forward %u %u %f mm\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 5 */
+ debug13(printf("3', watson, sense forward %u %u %f\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_3) {
+ max_prob_3 = acceptor_prob;
+ splice_genomepos_3 = genomicpos;
+ }
+ genomicpos--;
+ }
+ debug13(printf("\n"));
+
+ } else {
+ splicetype3 = splicetype3_mm = ACCEPTOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos <= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 7 */
+ debug13(printf("3', crick, sense anti %u %u %f mm\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 7 */
+ debug13(printf("3', crick, sense anti %u %u %f\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_3) {
+ max_prob_3 = acceptor_prob;
+ splice_genomepos_3 = genomicpos;
+ }
+ genomicpos++;
+ }
+ debug13(printf("\n"));
+ }
+
+ } else {
+ if (substringN->plusp) {
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos >= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 1 */
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 5 */
+ debug13(printf("3', watson, sense null %u %u %f %f mm\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (donor_prob > max_prob_sense_forward_3_mm) {
+ max_prob_sense_forward_3_mm = donor_prob;
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ /* splice_cdna_direction_3_mm = +1; */
+ splice_sensedir_3_mm = SENSE_FORWARD;
+ splicetype3_mm = DONOR;
+ }
+ }
+ if (acceptor_prob > max_prob_sense_anti_3_mm) {
+ max_prob_sense_anti_3_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ /* splice_cdna_direction_3_mm = -1; */
+ splice_sensedir_3_mm = SENSE_ANTI;
+ splicetype3_mm = ANTIACCEPTOR;
+ }
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 1 */
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 5 */
+ debug13(printf("3', watson, sense null %u %u %f %f\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (donor_prob > max_prob_sense_forward_3) {
+ max_prob_sense_forward_3 = donor_prob;
+ if (donor_prob > max_prob_3) {
+ max_prob_3 = donor_prob;
+ splice_genomepos_3 = genomicpos;
+ /* splice_cdna_direction_3 = +1; */
+ splice_sensedir_3 = SENSE_FORWARD;
+ splicetype3 = DONOR;
+ }
+ }
+ if (acceptor_prob > max_prob_sense_anti_3) {
+ max_prob_sense_anti_3 = acceptor_prob;
+ if (acceptor_prob > max_prob_3) {
+ max_prob_3 = acceptor_prob;
+ splice_genomepos_3 = genomicpos;
+ /* splice_cdna_direction_3 = -1; */
+ splice_sensedir_3 = SENSE_ANTI;
+ splicetype3 = ANTIACCEPTOR;
+ }
+ }
+ genomicpos--;
+ }
+ debug13(printf("\n"));
+
+ } else {
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos <= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 3 */
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 7 */
+ debug13(printf("3', crick, sense null %u %u %f %f mm\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (donor_prob > max_prob_sense_forward_3_mm) {
+ max_prob_sense_forward_3_mm = donor_prob;
+ if (donor_prob > max_prob_3_mm) {
+ max_prob_3_mm = donor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ /* splice_cdna_direction_3_mm = +1; */
+ splice_sensedir_3_mm = SENSE_FORWARD;
+ splicetype3_mm = ANTIDONOR;
+ }
+ }
+ if (acceptor_prob > max_prob_sense_anti_3_mm) {
+ max_prob_sense_anti_3_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_3_mm) {
+ max_prob_3_mm = acceptor_prob;
+ splice_genomepos_3_mm = genomicpos;
+ /* splice_cdna_direction_3_mm = -1; */
+ splice_sensedir_3_mm = SENSE_ANTI;
+ splicetype3_mm = ACCEPTOR;
+ }
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 3 */
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 7 */
+ debug13(printf("3', crick, sense null %u %u %f %f\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (donor_prob > max_prob_sense_forward_3) {
+ max_prob_sense_forward_3 = donor_prob;
+ if (donor_prob > max_prob_3) {
+ max_prob_3 = donor_prob;
+ splice_genomepos_3 = genomicpos;
+ /* splice_cdna_direction_3 = +1; */
+ splice_sensedir_3 = SENSE_FORWARD;
+ splicetype3 = ANTIDONOR;
+ }
+ }
+ if (acceptor_prob > max_prob_sense_anti_3) {
+ max_prob_sense_anti_3 = acceptor_prob;
+ if (acceptor_prob > max_prob_3) {
+ max_prob_3 = acceptor_prob;
+ splice_genomepos_3 = genomicpos;
+ /* splice_cdna_direction_3 = -1; */
+ splice_sensedir_3 = SENSE_ANTI;
+ splicetype3 = ACCEPTOR;
+ }
+ }
+ genomicpos++;
+ }
+ debug13(printf("\n"));
+ }
+ }
+
+ if (substringN == NULL) {
+ /* Skip 3' end */
+ } else if (*sensedir != SENSE_NULL) {
+ if (max_prob_3 > END_SPLICESITE_PROB_MATCH) {
+ debug13(printf("Found good splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3),splice_genomepos_3-chroffset,max_prob_3));
+ if (substringN->plusp) {
+ *ambig_end_length_3 = substringN->genomicend - splice_genomepos_3;
+ } else {
+ *ambig_end_length_3 = splice_genomepos_3 - substringN->genomicend;
+ }
+ *ambig_splicetype_3 = splicetype3;
+ *ambig_prob_3 = max_prob_3;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+
+ } else if (max_prob_3_mm > END_SPLICESITE_PROB_MISMATCH) {
+ debug13(printf("Found good mismatch splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3_mm),splice_genomepos_3_mm-chroffset,max_prob_3_mm));
+ if (substringN->plusp) {
+ *ambig_end_length_3 = substringN->genomicend - splice_genomepos_3_mm;
+ } else {
+ *ambig_end_length_3 = splice_genomepos_3_mm - substringN->genomicend;
+ }
+ *ambig_splicetype_3 = splicetype3_mm;
+ *ambig_prob_3 = max_prob_3_mm;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ }
+ }
+
+
+ /* start is distal, end is medial */
+ if (substring1 == NULL) {
+ /* Skip 5' end */
+ } else if (substring1->plusp == true) {
+ start = substring1->genomicstart;
+ middle = substring1->alignstart_trim - 1;
+ if ((end = middle + END_SPLICESITE_SEARCH) > substring1->alignend_trim) {
+ end = substring1->alignend_trim;
+ }
+ } else {
+ start = substring1->genomicstart;
+ middle = substring1->alignstart_trim + 1;
+ if ((end = middle - END_SPLICESITE_SEARCH) < substring1->alignend_trim) {
+ end = substring1->alignend_trim;
+ }
+ }
+
+ if (substring1 == NULL) {
+ /* Skip 5' end */
+ } else if (*sensedir == SENSE_FORWARD) {
+ if (substring1->plusp) {
+ splicetype5 = splicetype5_mm = ACCEPTOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos <= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 2 */
+ debug13(printf("5', watson, sense forward %u %u %f mm\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 2 */
+ debug13(printf("5', watson, sense forward %u %u %f\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_5) {
+ max_prob_5 = acceptor_prob;
+ splice_genomepos_5 = genomicpos;
+ }
+ genomicpos++;
+ }
+ debug13(printf("\n"));
+
+ } else {
+ splicetype5 = splicetype5_mm = ANTIACCEPTOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos >= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 4 */
+ debug13(printf("5', crick, sense anti %u %u %f mm\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 4 */
+ debug13(printf("5', crick, sense anti %u %u %f\n",genomicpos,genomicpos-chroffset,acceptor_prob));
+ if (acceptor_prob > max_prob_5) {
+ max_prob_5 = acceptor_prob;
+ splice_genomepos_5 = genomicpos;
+ }
+ genomicpos--;
+ }
+ debug13(printf("\n"));
+ }
+
+ } else if (*sensedir == SENSE_ANTI) {
+ if (substring1->plusp) {
+ splicetype5 = splicetype5_mm = ANTIDONOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos <= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 6 */
+ debug13(printf("5', watson, sense anti %u %u %f mm\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 6 */
+ debug13(printf("5', watson, sense anti %u %u %f\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_5) {
+ max_prob_5 = donor_prob;
+ splice_genomepos_5 = genomicpos;
+ }
+ genomicpos++;
+ }
+ debug13(printf("\n"));
+
+ } else {
+ splicetype5 = splicetype5_mm = DONOR;
+
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos >= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 8 */
+ debug13(printf("5', crick, sense forward %u %u %f mm\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 8 */
+ debug13(printf("5', crick, sense forward %u %u %f\n",genomicpos,genomicpos-chroffset,donor_prob));
+ if (donor_prob > max_prob_5) {
+ max_prob_5 = donor_prob;
+ splice_genomepos_5 = genomicpos;
+ }
+ genomicpos--;
+ }
+ debug13(printf("\n"));
+ }
+
+ } else {
+ if (substring1->plusp) {
+ start_genomicpos = start;
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos <= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos <= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 2 */
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 6 */
+ debug13(printf("5', watson, sense null %u %u %f %f mm\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (acceptor_prob > max_prob_sense_forward_5_mm) {
+ max_prob_sense_forward_5_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ /* splice_cdna_direction_5_mm = +1; */
+ splice_sensedir_5_mm = SENSE_FORWARD;
+ splicetype5_mm = ACCEPTOR;
+ }
+ }
+ if (donor_prob > max_prob_sense_anti_5_mm) {
+ max_prob_sense_anti_5_mm = donor_prob;
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ /* splice_cdna_direction_5_mm = -1; */
+ splice_sensedir_5_mm = SENSE_ANTI;
+ splicetype5_mm = ANTIDONOR;
+ }
+ }
+ genomicpos++;
+ }
+ while (genomicpos <= end_genomicpos) {
+ acceptor_prob = Maxent_hr_acceptor_prob(genomicpos,chroffset); /* Case 2 */
+ donor_prob = Maxent_hr_antidonor_prob(genomicpos,chroffset); /* Case 6 */
+ debug13(printf("5', watson, sense null %u %u %f %f\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (acceptor_prob > max_prob_sense_forward_5) {
+ max_prob_sense_forward_5 = acceptor_prob;
+ if (acceptor_prob > max_prob_5) {
+ max_prob_5 = acceptor_prob;
+ splice_genomepos_5 = genomicpos;
+ /* splice_cdna_direction_5 = +1; */
+ splice_sensedir_5 = SENSE_FORWARD;
+ splicetype5 = ACCEPTOR;
+ }
+ }
+ if (donor_prob > max_prob_sense_anti_5) {
+ max_prob_sense_anti_5 = donor_prob;
+ if (donor_prob > max_prob_5) {
+ max_prob_5 = donor_prob;
+ splice_genomepos_5 = genomicpos;
+ /* splice_cdna_direction_5 = -1; */
+ splice_sensedir_5 = SENSE_ANTI;
+ splicetype5 = ANTIDONOR;
+ }
+ }
+ genomicpos++;
+ }
+ debug13(printf("\n"));
+
+ } else {
+ start_genomicpos = start; /* check */
+ middle_genomicpos = middle;
+ end_genomicpos = end;
+
+ assert(start_genomicpos >= end_genomicpos);
+ genomicpos = start_genomicpos;
+ while (genomicpos >= middle_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 4 */
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 8 */
+ debug13(printf("5', crick, sense null %u %u %f %f mm\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (acceptor_prob > max_prob_sense_forward_5_mm) {
+ max_prob_sense_forward_5_mm = acceptor_prob;
+ if (acceptor_prob > max_prob_5_mm) {
+ max_prob_5_mm = acceptor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ /* splice_cdna_direction_5_mm = +1; */
+ splice_sensedir_5_mm = SENSE_FORWARD;
+ splicetype5_mm = ANTIACCEPTOR;
+ }
+ }
+ if (donor_prob > max_prob_sense_anti_5_mm) {
+ max_prob_sense_anti_5_mm = donor_prob;
+ if (donor_prob > max_prob_5_mm) {
+ max_prob_5_mm = donor_prob;
+ splice_genomepos_5_mm = genomicpos;
+ /* splice_cdna_direction_5_mm = -1; */
+ splice_sensedir_5_mm = SENSE_ANTI;
+ splicetype5_mm = DONOR;
+ }
+ }
+ genomicpos--;
+ }
+ while (genomicpos >= end_genomicpos) {
+ acceptor_prob = Maxent_hr_antiacceptor_prob(genomicpos,chroffset); /* Case 4 */
+ donor_prob = Maxent_hr_donor_prob(genomicpos,chroffset); /* Case 8 */
+ debug13(printf("5', crick, sense null %u %u %f %f\n",genomicpos,genomicpos-chroffset,donor_prob,acceptor_prob));
+ if (acceptor_prob > max_prob_sense_forward_5) {
+ max_prob_sense_forward_5 = acceptor_prob;
+ if (acceptor_prob > max_prob_5) {
+ max_prob_5 = acceptor_prob;
+ splice_genomepos_5 = genomicpos;
+ /* splice_cdna_direction_5 = +1; */
+ splice_sensedir_5 = SENSE_FORWARD;
+ splicetype5 = ANTIACCEPTOR;
+ }
+ }
+ if (donor_prob > max_prob_sense_anti_5) {
+ max_prob_sense_anti_5 = donor_prob;
+ if (donor_prob > max_prob_5) {
+ max_prob_5 = donor_prob;
+ splice_genomepos_5 = genomicpos;
+ /* splice_cdna_direction_5 = -1; */
+ splice_sensedir_5 = SENSE_ANTI;
+ splicetype5 = DONOR;
+ }
+ }
+ genomicpos--;
+ }
+ debug13(printf("\n"));
+ }
+ }
+
+ if (substring1 == NULL) {
+ /* Skip 5' end */
+ } else if (*sensedir != SENSE_NULL) {
+ if (max_prob_5 > END_SPLICESITE_PROB_MATCH) {
+ debug13(printf("Found good splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5),splice_genomepos_5-chroffset,max_prob_5));
+ if (substring1->plusp) {
+ *ambig_end_length_5 = splice_genomepos_5 - substring1->genomicstart;
+ } else {
+ *ambig_end_length_5 = substring1->genomicstart - splice_genomepos_5;
+ }
+ *ambig_splicetype_5 = splicetype5;
+ *ambig_prob_5 = max_prob_5;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ } else if (max_prob_5_mm > END_SPLICESITE_PROB_MISMATCH) {
+ debug13(printf("Found good mismatch splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5_mm),splice_genomepos_5_mm-chroffset,max_prob_5_mm));
+ if (substring1->plusp) {
+ *ambig_end_length_5 = splice_genomepos_5 - substring1->genomicstart;
+ } else {
+ *ambig_end_length_5 = substring1->genomicstart - splice_genomepos_5;
+ }
+ *ambig_splicetype_5 = splicetype5_mm;
+ *ambig_prob_5 = max_prob_5_mm;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ }
+ }
+
+ if (*sensedir == SENSE_NULL) {
+ if (max_prob_3 >= END_SPLICESITE_PROB_MATCH || max_prob_5 >= END_SPLICESITE_PROB_MATCH) {
+ if (max_prob_3 >= END_SPLICESITE_PROB_MATCH && max_prob_5 >= END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_5 < END_SPLICESITE_PROB_MATCH) {
+ /* Forward sense wins on both sides */
+ if (substringN->plusp) {
+ *ambig_end_length_3 = substringN->genomicend - splice_genomepos_3;
+ *ambig_end_length_5 = splice_genomepos_5 - substring1->genomicstart;
+ } else {
+ *ambig_end_length_3 = splice_genomepos_3 - substringN->genomicend;
+ *ambig_end_length_5 = substring1->genomicstart - splice_genomepos_5;
+ }
+ *ambig_splicetype_3 = splicetype3;
+ *ambig_prob_3 = max_prob_3;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ *ambig_splicetype_5 = splicetype5;
+ *ambig_prob_5 = max_prob_5;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ *sensedir = SENSE_FORWARD; /* = splice_sensedir_3 */
+
+ } else if (max_prob_3 >= END_SPLICESITE_PROB_MATCH && max_prob_5 >= END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_5 < END_SPLICESITE_PROB_MATCH) {
+ /* Anti sense wins on both sides */
+ if (substringN->plusp) {
+ *ambig_end_length_3 = substringN->genomicend - splice_genomepos_3;
+ *ambig_end_length_5 = splice_genomepos_5 - substring1->genomicstart;
+ } else {
+ *ambig_end_length_3 = splice_genomepos_3 - substringN->genomicend;
+ *ambig_end_length_5 = substring1->genomicstart - splice_genomepos_5;
+ }
+ *ambig_splicetype_3 = splicetype3;
+ *ambig_prob_3 = max_prob_3;
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ *ambig_splicetype_5 = splicetype5;
+ *ambig_prob_5 = max_prob_5;
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ *sensedir = SENSE_ANTI; /* = splice_sensedir_3 */
+
+ } else if (max_prob_3 > max_prob_5) {
+ /* Consider just 3' end */
+ debug13(printf("Found good splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3),splice_genomepos_3-chroffset,max_prob_3));
+ if (substringN->plusp) {
+ *ambig_end_length_3 = substringN->genomicend - splice_genomepos_3;
+ } else {
+ *ambig_end_length_3 = splice_genomepos_3 - substringN->genomicend;
+ }
+ *ambig_splicetype_3 = splicetype3;
+ *ambig_prob_3 = max_prob_3;
+ /* *cdna_direction = splice_cdna_direction_3; */
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ if (max_prob_sense_forward_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_5 < END_SPLICESITE_PROB_MATCH) {
+ *sensedir = splice_sensedir_3;
+ } else if (max_prob_sense_anti_3 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_3 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_5 < END_SPLICESITE_PROB_MATCH) {
+ *sensedir = splice_sensedir_3;
+ } else {
+ /* Not enough evidence to set sensedir */
+ }
+
+ } else {
+ /* Consider just 5' end */
+ debug13(printf("Found good splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5),splice_genomepos_5-chroffset,max_prob_5));
+ if (substring1->plusp) {
+ *ambig_end_length_5 = splice_genomepos_5 - substring1->genomicstart;
+ } else {
+ *ambig_end_length_5 = substring1->genomicstart - splice_genomepos_5;
+ }
+ *ambig_splicetype_5 = splicetype5;
+ *ambig_prob_5 = max_prob_5;
+ /* *cdna_direction = splice_cdna_direction_5; */
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ if (max_prob_sense_forward_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_anti_5 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_anti_3 < END_SPLICESITE_PROB_MATCH) {
+ *sensedir = splice_sensedir_5;
+ } else if (max_prob_sense_anti_5 >= END_SPLICESITE_PROB_MATCH && max_prob_sense_forward_5 < END_SPLICESITE_PROB_MATCH
+ && max_prob_sense_forward_3 < END_SPLICESITE_PROB_MATCH) {
+ *sensedir = splice_sensedir_5;
+ } else {
+ /* Not enough evidence to set sensedir */
+ }
+ }
+
+ } else if (max_prob_3_mm >= END_SPLICESITE_PROB_MISMATCH || max_prob_5_mm >= END_SPLICESITE_PROB_MISMATCH) {
+ if (max_prob_3_mm > max_prob_5_mm) {
+ debug13(printf("Found good mismatch splice %s on 3' end at %u with probability %f\n",
+ Splicetype_string(splicetype3_mm),splice_genomepos_3_mm-chroffset,max_prob_3_mm));
+ if (substringN->plusp) {
+ *ambig_end_length_3 = substringN->genomicend - splice_genomepos_3_mm;
+ } else {
+ *ambig_end_length_3 = splice_genomepos_3_mm - substringN->genomicend;
+ }
+ *ambig_splicetype_3 = splicetype3_mm;
+ *ambig_prob_3 = max_prob_3_mm;
+ /* *cdna_direction = splice_cdna_direction_3_mm; */
+ debug13(printf("Set ambig_end_length_3 to be %d\n",*ambig_end_length_3));
+ if (max_prob_sense_forward_3_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_anti_3_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_anti_5_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_3_mm;
+ } else if (max_prob_sense_anti_3_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_forward_3_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_forward_5_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_3_mm;
+ } else {
+ /* Not enough evidence to set sensedir */
+ }
+ } else {
+ debug13(printf("Found good mismatch splice %s on 5' end at %u with probability %f\n",
+ Splicetype_string(splicetype5_mm),splice_genomepos_5_mm-chroffset,max_prob_5_mm));
+ if (substring1->plusp) {
+ *ambig_end_length_5 = splice_genomepos_5_mm - substring1->genomicstart;
+ } else {
+ *ambig_end_length_5 = substring1->genomicstart - splice_genomepos_5_mm;
+ }
+ *ambig_splicetype_5 = splicetype5_mm;
+ *ambig_prob_5 = max_prob_5_mm;
+ /* *cdna_direction = splice_cdna_direction_5_mm; */
+ debug13(printf("Set ambig_end_length_5 to be %d\n",*ambig_end_length_5));
+ if (max_prob_sense_forward_5_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_anti_5_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_anti_3_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_5_mm;
+ } else if (max_prob_sense_anti_5_mm >= END_SPLICESITE_PROB_MISMATCH && max_prob_sense_forward_5_mm < END_SPLICESITE_PROB_MISMATCH
+ && max_prob_sense_forward_3_mm < END_SPLICESITE_PROB_MISMATCH) {
+ *sensedir = splice_sensedir_5_mm;
+ } else {
+ /* Not enough evidence to set sensedir */
+ }
+ }
+ }
+ }
+
+ debug13(printf("Returning ambig_end_length_5 %d and ambig_end_length_3 %d\n",*ambig_end_length_5,*ambig_end_length_3));
+ return;
+}
+
+
+
/* Want querylength and not querylength_adj */
T
Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
Univcoord_T chrhigh, Chrpos_T chrlength,
Compress_T query_compress, Endtype_T start_endtype, Endtype_T end_endtype,
int querystart, int queryend, int querylength,
- Univcoord_T alignstart, Univcoord_T alignend, int genomiclength,
- bool exactp, bool plusp, int genestrand, bool first_read_p,
- bool trim_left_p, bool trim_right_p, int outofbounds_start, int outofbounds_end,
- int minlength) {
+ Univcoord_T alignstart, Univcoord_T alignend,
+ bool exactp, bool plusp, int genestrand,
+ Trimaction_T trim_left_action, Trimaction_T trim_right_action,
+ int outofbounds_start, int outofbounds_end, int minlength, int sensedir) {
T new;
int nmatches;
- double prob1, prob2;
int nonterminal_trim = 0;
+ int ambig_end_length_5, ambig_end_length_3;
+ Splicetype_T ambig_splicetype_5, ambig_splicetype_3;
+ double ambig_prob_5, ambig_prob_3;
+ int nmismatches_end_left, nmismatches_end_right;
+
/* General test for goodness over original region */
nmatches = queryend - querystart - nmismatches_whole;
debug2(printf("Initial nmatches %d = queryend %d - querystart %d - nmismatches_whole %d\n",
nmatches,queryend,querystart,nmismatches_whole));
+
if (nmatches - 3*nmismatches_whole < 0) {
debug2(printf("Substring fails general test 1 for goodness with %d matches and %d mismatches\n",
nmatches,nmismatches_whole));
@@ -1760,10 +2597,8 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
new->alignstart = new->alignstart_trim = alignstart;
new->alignend = new->alignend_trim = alignend;
- new->genomiclength = genomiclength;
new->plusp = plusp;
new->genestrand = genestrand;
- new->first_read_p = first_read_p;
new->chimera_prob = 0.0;
new->chimera_knownp = false;
@@ -1771,8 +2606,10 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
new->chimera_novelp = false;
new->chimera_novelp_2 = false;
- debug2(printf("\n***Entered Substring_new with query %d..%d, chrnum %d (chroffset %u, chrhigh %u), plusp %d\n",
- querystart,queryend,chrnum,chroffset,chrhigh,plusp));
+ debug2(printf("\n***Entered Substring_new with query %d..%d, chrnum %d (chroffset %u, chrhigh %u), plusp %d, outofbounds start %d and end %d\n",
+ querystart,queryend,chrnum,chroffset,chrhigh,plusp,outofbounds_start,outofbounds_end));
+ /* assert(queryend > querystart); -- Assertion does not hold. Sometimes queryend == querystart */
+
/* Compute coordinates */
if (plusp == true) {
@@ -1781,8 +2618,7 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
new->genomicend = new->left + querylength;
debug2(printf("left is %u\n",new->left));
- debug2(printf("querylength is %d, genomiclength is %d, alignstart is %u, alignend is %u\n",
- querylength,genomiclength,alignstart,alignend));
+ debug2(printf("querylength is %d, alignstart is %u, alignend is %u\n",querylength,alignstart,alignend));
assert(alignstart + outofbounds_start >= chroffset);
assert(alignend - outofbounds_end <= chrhigh);
@@ -1792,8 +2628,7 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
new->genomicstart = new->left + querylength;
debug2(printf("left is %u\n",new->left));
- debug2(printf("querylength is %d, genomiclength is %d, alignstart is %u, alignend is %u\n",
- querylength,genomiclength,alignstart,alignend));
+ debug2(printf("querylength is %d, alignstart is %u, alignend is %u\n",querylength,alignstart,alignend));
assert(alignstart - outofbounds_start <= chrhigh);
assert(alignend + outofbounds_end >= chroffset);
}
@@ -1803,11 +2638,11 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
if (plusp == true) {
nmismatches_whole =
Genome_count_mismatches_substring(query_compress,new->left,/*pos5*/querystart,
- /*pos3*/queryend,/*plusp*/true,genestrand,first_read_p);
+ /*pos3*/queryend,/*plusp*/true,genestrand);
} else {
nmismatches_whole =
Genome_count_mismatches_substring(query_compress,new->left,/*pos5*/querylength - queryend,
- /*pos3*/querylength - querystart,/*plusp*/false,genestrand,first_read_p);
+ /*pos3*/querylength - querystart,/*plusp*/false,genestrand);
}
}
@@ -1820,9 +2655,15 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
new->genomic_refdiff = (char *) NULL;
/* Do trimming */
- debug8(printf("trim_left_p %d, trim_right_p %d\n",trim_left_p,trim_right_p));
+ debug8(printf("trim_left_action %d, trim_right_action %d\n",trim_left_action,trim_right_action));
- if (trim_left_p == false) {
+ new->mandatory_trim_left = 0;
+ new->mandatory_trim_right = 0;
+
+ if (trim_left_action == PRE_TRIMMED) {
+ new->trim_left = querystart;
+
+ } else if (trim_left_action == NO_TRIM) {
if (outofbounds_start > 0) {
/* Not allowed to trim */
debug2(printf("outofbounds_start %d > 0, so returning NULL\n",outofbounds_start));
@@ -1834,22 +2675,28 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
} else if (new->start_endtype == TERM) {
/* Accept true terminals generated by GSNAP procedure */
- new->trim_left = trim_left_end(query_compress,new->left,querystart,queryend,querylength,plusp,genestrand,first_read_p,
- /*trim_mismatch_score*/-3);
+ new->trim_left = trim_left_end(&nmismatches_end_left,query_compress,new->left,querystart,queryend,querylength,
+ plusp,genestrand,/*trim_mismatch_score*/-3);
if (outofbounds_start > new->trim_left) {
new->trim_left = outofbounds_start;
}
+ new->querystart += new->trim_left;
} else {
- new->trim_left = trim_left_end(query_compress,new->left,querystart,queryend,querylength,plusp,genestrand,first_read_p,
- trim_mismatch_score);
+ new->trim_left = trim_left_end(&nmismatches_end_left,query_compress,new->left,querystart,queryend,querylength,
+ plusp,genestrand,trim_mismatch_score);
+ debug13(printf("trim_left %d, nmismatches_end_left = %d\n",new->trim_left,nmismatches_end_left));
if (outofbounds_start > new->trim_left) {
new->trim_left = outofbounds_start;
}
nonterminal_trim += new->trim_left;
+ new->querystart += new->trim_left;
}
- if (trim_right_p == false) {
+ if (trim_right_action == PRE_TRIMMED) {
+ new->trim_right = querylength - queryend;
+
+ } else if (trim_right_action == NO_TRIM) {
if (outofbounds_end > 0) {
/* Not allowed to trim */
Substring_free(&new);
@@ -1861,22 +2708,24 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
} else if (new->end_endtype == TERM) {
/* Accept true terminals generated by GSNAP procedure */
- new->trim_right = trim_right_end(query_compress,new->left,querystart,queryend,querylength,plusp,genestrand,first_read_p,
- /*trim_mismatch_score*/-3);
+ new->trim_right = trim_right_end(&nmismatches_end_right,query_compress,new->left,querystart,queryend,querylength,
+ plusp,genestrand,/*trim_mismatch_score*/-3);
if (outofbounds_end > new->trim_right) {
new->trim_right = outofbounds_end;
}
+ new->queryend -= new->trim_right;
} else {
- new->trim_right = trim_right_end(query_compress,new->left,querystart,queryend,querylength,plusp,genestrand,first_read_p,
- trim_mismatch_score);
+ new->trim_right = trim_right_end(&nmismatches_end_right,query_compress,new->left,querystart,queryend,querylength,
+ plusp,genestrand,trim_mismatch_score);
+ debug13(printf("trim_right %d, nmismatches_end_right = %d\n",new->trim_right,nmismatches_end_right));
if (outofbounds_end > new->trim_right) {
new->trim_right = outofbounds_end;
}
nonterminal_trim += new->trim_right;
+ new->queryend -= new->trim_right;
}
- debug8(printf("Nonterminal trim %d vs reject_trimlength %d\n",nonterminal_trim,reject_trimlength));
#if 0
if (nonterminal_trim >= reject_trimlength) {
/* Reject non-terminal alignments (including those by sarray search) with excessive trim */
@@ -1887,8 +2736,6 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
return (T) NULL;
} else {
#endif
- new->querystart += new->trim_left;
- new->queryend -= new->trim_right;
/* Check for minlength. Needed to avoid nonsensical terminal alignments */
if (new->queryend - new->querystart <= minlength) {
debug8(printf("queryend %d - querystart %d <= minlength %d, so returning NULL\n",
@@ -1901,44 +2748,96 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
#endif
+ new->mandatory_trim_left = 0;
+ new->mandatory_trim_right = 0;
+
/* ? Should we spend the time to determine trim_left_splicep and
trim_right_splicep, especially since trimming may not be perfect */
if (plusp == true) {
/* nmatches: Counts matches over whole region including trims */
new->nmatches = (new->alignend - new->alignstart) - new->nmismatches_whole;
- new->alignstart_trim += new->trim_left;
- new->alignend_trim -= new->trim_right;
+ if (trim_left_action == COMPUTE_TRIM) {
+ if (nmismatches_end_left == 0) {
+ trim_left_action = NO_TRIM;
+ } else {
+ new->alignstart_trim += new->trim_left;
+ }
+ }
+ if (trim_right_action == COMPUTE_TRIM) {
+ if (nmismatches_end_right == 0) {
+ trim_right_action = NO_TRIM;
+ } else {
+ new->alignend_trim -= new->trim_right;
+ }
+ }
debug2(printf("Got trims of %d and %d => Revised alignstart_trim and alignend_trim to be %u..%u (%u..%u)\n",
new->trim_left,new->trim_right,new->alignstart_trim,new->alignend_trim,
new->alignstart_trim - new->chroffset,new->alignend_trim - new->chroffset));
- if (novelsplicingp == false) {
- new->trim_left_splicep = new->trim_right_splicep = false;
- } else {
- if (new->trim_left == 0) {
- new->trim_left_splicep = false;
- } else {
- prob1 = Maxent_hr_acceptor_prob(new->left + new->trim_left,chroffset);
- prob2 = Maxent_hr_antidonor_prob(new->left + new->trim_left,chroffset);
- /* fprintf(stderr,"At %u, acceptor prob %f, antidonor prob %f\n",left+new->trim_left,prob1,prob2); */
- if (prob1 > 0.90 || prob2 > 0.90) {
+ new->trim_left_splicep = new->trim_right_splicep = false;
+ if (novelsplicingp == true) {
+ if (trim_left_action == COMPUTE_TRIM && trim_right_action == COMPUTE_TRIM) {
+ substring_trim_novel_spliceends(/*substring1*/new,/*substringN*/new,&ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,&ambig_prob_5,&ambig_prob_3,
+ &sensedir,chroffset);
+ if (ambig_end_length_5 > 0) {
new->trim_left_splicep = true;
- } else {
- new->trim_left_splicep = false;
+ new->querystart += (ambig_end_length_5 - new->trim_left);
+ new->alignstart_trim += (ambig_end_length_5 - new->trim_left);
+ new->trim_left = ambig_end_length_5;
+ if (ambig_splicetype_5 == DONOR || ambig_splicetype_5 == ANTIDONOR) {
+ new->start_endtype = DON;
+ } else {
+ new->start_endtype = ACC;
+ }
+ new->chimera_prob = ambig_prob_5;
+ }
+ if (ambig_end_length_3 > 0) {
+ new->trim_right_splicep = true;
+ new->queryend -= (ambig_end_length_3 - new->trim_right);
+ new->alignend_trim -= (ambig_end_length_3 - new->trim_right);
+ new->trim_right = ambig_end_length_3;
+ if (ambig_splicetype_3 == DONOR || ambig_splicetype_3 == ANTIDONOR) {
+ new->end_endtype = DON;
+ } else {
+ new->end_endtype = ACC;
+ }
+ new->chimera_prob_2 = ambig_prob_3;
}
- }
- if (new->trim_right == 0) {
- new->trim_right_splicep = false;
- } else {
- prob1 = Maxent_hr_donor_prob(new->left + querylength - new->trim_right,chroffset);
- prob2 = Maxent_hr_antiacceptor_prob(new->left + querylength - new->trim_right,chroffset);
- /* fprintf(stderr,"At %u, donor prob %f, antiacceptor prob %f\n",left + querylength - new->trim_right,prob1,prob2); */
- if (prob1 > 0.90 || prob2 > 0.90) {
+ } else if (trim_left_action == COMPUTE_TRIM) {
+ substring_trim_novel_spliceends(/*substring1*/new,/*substringN*/NULL,&ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,&ambig_prob_5,&ambig_prob_3,
+ &sensedir,chroffset);
+ if (ambig_end_length_5 > 0) {
+ new->trim_left_splicep = true;
+ new->querystart += (ambig_end_length_5 - new->trim_left);
+ new->alignstart_trim += (ambig_end_length_5 - new->trim_left);
+ new->trim_left = ambig_end_length_5;
+ if (ambig_splicetype_5 == DONOR || ambig_splicetype_5 == ANTIDONOR) {
+ new->start_endtype = DON;
+ } else {
+ new->start_endtype = ACC;
+ }
+ new->chimera_prob = ambig_prob_5;
+ }
+
+ } else if (trim_right_action == COMPUTE_TRIM) {
+ substring_trim_novel_spliceends(/*substring1*/NULL,/*substringN*/new,&ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,&ambig_prob_5,&ambig_prob_3,
+ &sensedir,chroffset);
+ if (ambig_end_length_3 > 0) {
new->trim_right_splicep = true;
- } else {
- new->trim_right_splicep = false;
+ new->queryend -= (ambig_end_length_3 - new->trim_right);
+ new->alignend_trim -= (ambig_end_length_3 - new->trim_right);
+ new->trim_right = ambig_end_length_3;
+ if (ambig_splicetype_3 == DONOR || ambig_splicetype_3 == ANTIDONOR) {
+ new->end_endtype = DON;
+ } else {
+ new->end_endtype = ACC;
+ }
+ new->chimera_prob_2 = ambig_prob_3;
}
}
}
@@ -1947,41 +2846,89 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
/* nmatches: Counts matches over whole region including trims */
new->nmatches = (new->alignstart - new->alignend) - new->nmismatches_whole;
- new->alignstart_trim -= new->trim_left;
- new->alignend_trim += new->trim_right;
+ if (trim_left_action == COMPUTE_TRIM) {
+ if (nmismatches_end_left == 0) {
+ trim_left_action = NO_TRIM;
+ } else {
+ new->alignstart_trim -= new->trim_left;
+ }
+ }
+ if (trim_right_action == COMPUTE_TRIM) {
+ if (nmismatches_end_right == 0) {
+ trim_right_action = NO_TRIM;
+ } else {
+ new->alignend_trim += new->trim_right;
+ }
+ }
debug2(printf("Revised alignstart_trim and alignend_trim to be %u..%u (%u..%u)\n",
new->alignstart_trim,new->alignend_trim,
new->alignstart_trim - new->chroffset,new->alignend_trim - new->chroffset));
-
- if (novelsplicingp == false) {
- new->trim_left_splicep = new->trim_right_splicep = false;
- } else {
- if (new->trim_left == 0) {
- new->trim_left_splicep = false;
- } else {
- prob1 = Maxent_hr_donor_prob(new->left + querylength - new->trim_left,chroffset);
- prob2 = Maxent_hr_antiacceptor_prob(new->left + querylength - new->trim_left,chroffset);
- /* fprintf(stderr,"At %u, donor prob %f, antiacceptor prob %f\n",new->left + querylength - new->trim_left,prob1,prob2); */
- if (prob1 > 0.90 || prob2 > 0.90) {
+ new->trim_left_splicep = new->trim_right_splicep = false;
+ if (novelsplicingp == true) {
+ if (trim_left_action == COMPUTE_TRIM && trim_right_action == COMPUTE_TRIM) {
+ substring_trim_novel_spliceends(/*substring1*/new,/*substringN*/new,&ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,&ambig_prob_5,&ambig_prob_3,
+ &sensedir,chroffset);
+ if (ambig_end_length_5 > 0) {
new->trim_left_splicep = true;
- } else {
- new->trim_left_splicep = false;
+ new->querystart += (ambig_end_length_5 - new->trim_left);
+ new->alignstart_trim -= (ambig_end_length_5 - new->trim_left);
+ new->trim_left = ambig_end_length_5;
+ if (ambig_splicetype_5 == DONOR || ambig_splicetype_5 == ANTIDONOR) {
+ new->start_endtype = DON;
+ } else {
+ new->start_endtype = ACC;
+ }
+ new->chimera_prob = ambig_prob_5;
+ }
+ if (ambig_end_length_3 > 0) {
+ new->trim_right_splicep = true;
+ new->queryend -= (ambig_end_length_3 - new->trim_right);
+ new->alignend_trim += (ambig_end_length_3 - new->trim_right);
+ new->trim_right = ambig_end_length_3;
+ if (ambig_splicetype_3 == DONOR || ambig_splicetype_3 == ANTIDONOR) {
+ new->end_endtype = DON;
+ } else {
+ new->end_endtype = ACC;
+ }
+ new->chimera_prob_2 = ambig_prob_3;
}
- }
- if (new->trim_right == 0) {
- new->trim_right_splicep = false;
- } else {
- prob1 = Maxent_hr_acceptor_prob(new->left + new->trim_right,chroffset);
- prob2 = Maxent_hr_antidonor_prob(new->left + new->trim_right,chroffset);
- /* fprintf(stderr,"At %u, acceptor prob %f, antidonor prob %f\n",new->left+new->trim_right,prob1,prob2); */
- if (prob1 > 0.90 || prob2 > 0.90) {
+ } else if (trim_left_action == COMPUTE_TRIM) {
+ substring_trim_novel_spliceends(/*substring1*/new,/*substringN*/NULL,&ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,&ambig_prob_5,&ambig_prob_3,
+ &sensedir,chroffset);
+ if (ambig_end_length_5 > 0) {
+ new->trim_left_splicep = true;
+ new->querystart += (ambig_end_length_5 - new->trim_left);
+ new->alignstart_trim -= (ambig_end_length_5 - new->trim_left);
+ new->trim_left = ambig_end_length_5;
+ if (ambig_splicetype_5 == DONOR || ambig_splicetype_5 == ANTIDONOR) {
+ new->start_endtype = DON;
+ } else {
+ new->start_endtype = ACC;
+ }
+ new->chimera_prob = ambig_prob_5;
+ }
+
+ } else if (trim_right_action == COMPUTE_TRIM) {
+ substring_trim_novel_spliceends(/*substring1*/NULL,/*substringN*/new,&ambig_end_length_5,&ambig_end_length_3,
+ &ambig_splicetype_5,&ambig_splicetype_3,&ambig_prob_5,&ambig_prob_3,
+ &sensedir,chroffset);
+ if (ambig_end_length_3 > 0) {
new->trim_right_splicep = true;
- } else {
- new->trim_right_splicep = false;
+ new->queryend -= (ambig_end_length_3 - new->trim_right);
+ new->alignend_trim += (ambig_end_length_3 - new->trim_right);
+ new->trim_right = ambig_end_length_3;
+ if (ambig_splicetype_3 == DONOR || ambig_splicetype_3 == ANTIDONOR) {
+ new->end_endtype = DON;
+ } else {
+ new->end_endtype = ACC;
+ }
+ new->chimera_prob_2 = ambig_prob_3;
}
- }
+ }
}
}
@@ -1993,11 +2940,11 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
} else if (plusp == true) {
new->nmismatches_bothdiff =
Genome_count_mismatches_substring(query_compress,new->left,/*pos5*/new->alignstart_trim-new->left,
- /*pos3*/new->alignend_trim - new->left,plusp,genestrand,first_read_p);
+ /*pos3*/new->alignend_trim - new->left,plusp,genestrand);
} else {
new->nmismatches_bothdiff =
Genome_count_mismatches_substring(query_compress,new->left,/*pos5*/new->alignend_trim - new->left,
- /*pos3*/new->alignstart_trim - new->left,plusp,genestrand,first_read_p);
+ /*pos3*/new->alignstart_trim - new->left,plusp,genestrand);
}
/* General test for goodness over trimmed region */
@@ -2029,7 +2976,7 @@ T
Substring_new_ambig (int querystart, int queryend, int splice_pos, int querylength,
Chrnum_T chrnum, Univcoord_T chroffset,
Univcoord_T chrhigh, Chrpos_T chrlength,
- int genomiclength, bool plusp, int genestrand, bool first_read_p,
+ bool plusp, int genestrand,
#ifdef LARGE_GENOMES
Uint8list_T ambcoords,
#else
@@ -2079,10 +3026,8 @@ Substring_new_ambig (int querystart, int queryend, int splice_pos, int queryleng
new->alignstart = new->alignstart_trim = 0;
new->alignend = new->alignend_trim = 0;
- new->genomiclength = genomiclength;
new->plusp = plusp;
new->genestrand = genestrand;
- new->first_read_p = first_read_p;
new->chimera_prob = 0.0;
new->chimera_knownp = false;
@@ -2113,6 +3058,8 @@ Substring_new_ambig (int querystart, int queryend, int splice_pos, int queryleng
new->trim_left = 0;
new->trim_right = querylength - queryend;
}
+ new->mandatory_trim_left = 0;
+ new->mandatory_trim_right = 0;
new->trim_left_splicep = new->trim_right_splicep = false;
@@ -2176,8 +3123,8 @@ Substring_set_unambiguous (double *donor_prob, double *acceptor_prob, Univcoord_
this->alignend = this->alignend_trim = this->genomicstart + this->queryend;
this->nmatches = (this->alignend - this->alignstart) - this->nmismatches_whole;
- debug2(printf("querypos %d..%d, genomiclength is %d, alignstart is %u (%u), alignend is %u (%u), genomicstart is %u, genomicend is %u\n",
- this->querystart,this->queryend,this->genomiclength,this->alignstart,this->alignstart - this->chroffset,
+ debug2(printf("querypos %d..%d, alignstart is %u (%u), alignend is %u (%u), genomicstart is %u, genomicend is %u\n",
+ this->querystart,this->queryend,this->alignstart,this->alignstart - this->chroffset,
this->alignend,this->alignend - this->chroffset,this->genomicstart,this->genomicend));
} else {
@@ -2189,8 +3136,8 @@ Substring_set_unambiguous (double *donor_prob, double *acceptor_prob, Univcoord_
this->alignstart = this->alignstart_trim = this->genomicstart - this->querystart;
this->nmatches = (this->alignstart - this->alignend) - this->nmismatches_whole;
- debug2(printf("querypos %d..%d, genomiclength is %d, alignstart is %u (%u), alignend is %u (%u), genomicstart is %u, genomicend is %u\n",
- this->querystart,this->queryend,this->genomiclength,this->alignstart,this->alignstart - this->chroffset,
+ debug2(printf("querypos %d..%d, alignstart is %u (%u), alignend is %u (%u), genomicstart is %u, genomicend is %u\n",
+ this->querystart,this->queryend,this->alignstart,this->alignstart - this->chroffset,
this->alignend,this->alignend - this->chroffset,this->genomicstart,this->genomicend));
}
@@ -2243,12 +3190,12 @@ Substring_compute_mapq (T this, Compress_T query_compress, char *quality_string,
splicecoord = this->ambcoords[0];
left = splicecoord - this->amb_splice_pos;
best_loglik = MAPQ_loglik(query_compress,left,mapq_start,mapq_end,
- this->querylength,quality_string,/*plusp*/true,this->genestrand,this->first_read_p);
+ this->querylength,quality_string,/*plusp*/true,this->genestrand);
for (i = 1; i < this->nambcoords; i++) {
splicecoord = this->ambcoords[i];
left = splicecoord - this->amb_splice_pos;
if ((loglik = MAPQ_loglik(query_compress,left,mapq_start,mapq_end,
- this->querylength,quality_string,/*plusp*/true,this->genestrand,this->first_read_p)) > best_loglik) {
+ this->querylength,quality_string,/*plusp*/true,this->genestrand)) > best_loglik) {
best_loglik = loglik;
}
}
@@ -2256,12 +3203,12 @@ Substring_compute_mapq (T this, Compress_T query_compress, char *quality_string,
splicecoord = this->ambcoords[0];
left = splicecoord - (this->querylength - this->amb_splice_pos);
best_loglik = MAPQ_loglik(query_compress,left,mapq_start,mapq_end,
- this->querylength,quality_string,/*plusp*/false,this->genestrand,this->first_read_p);
+ this->querylength,quality_string,/*plusp*/false,this->genestrand);
for (i = 1; i < this->nambcoords; i++) {
splicecoord = this->ambcoords[i];
left = splicecoord - (this->querylength - this->amb_splice_pos);
if ((loglik = MAPQ_loglik(query_compress,left,mapq_start,mapq_end,
- this->querylength,quality_string,/*plusp*/false,this->genestrand,this->first_read_p)) > best_loglik) {
+ this->querylength,quality_string,/*plusp*/false,this->genestrand)) > best_loglik) {
best_loglik = loglik;
}
}
@@ -2273,7 +3220,7 @@ Substring_compute_mapq (T this, Compress_T query_compress, char *quality_string,
debug2(printf("trim_left %d, trim_right %d, mapq_start = %d, mapq_end = %d\n",
this->trim_left,this->trim_right,mapq_start,mapq_end));
this->mapq_loglik = MAPQ_loglik(query_compress,this->left,mapq_start,mapq_end,
- this->querylength,quality_string,this->plusp,this->genestrand,this->first_read_p);
+ this->querylength,quality_string,this->plusp,this->genestrand);
debug2(printf("Substring %u..%u gets loglik %f\n",this->genomicstart - this->chroffset,
this->genomicend - this->chroffset,this->mapq_loglik));
}
@@ -2309,7 +3256,7 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
this->nmismatches_refdiff = 0;
} else {
- /* Was this->genomiclength, but fails for large insertions */
+ /* Used to be this->genomiclength, but doesn't work for large insertions */
#ifdef HAVE_ALLOCA
gbuffer = (char *) ALLOCA((querylength+1) * sizeof(char));
#else
@@ -2329,7 +3276,7 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
Genome_mark_mismatches(genomic_diff,querylength,query_compress_fwd,
this->left,/*pos5*/this->querystart,/*pos3*/this->queryend,
- /*plusp*/true,this->genestrand,this->first_read_p);
+ /*plusp*/true,this->genestrand);
}
/* Need to perform embellish to put dashes in */
@@ -2345,11 +3292,11 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
Genome_count_mismatches_substring_ref(query_compress_fwd,this->left,
/*pos5*/this->alignstart_trim - this->left,
/*pos3*/this->alignend_trim - this->left,
- /*plusp*/true,this->genestrand,this->first_read_p);
+ /*plusp*/true,this->genestrand);
Genome_mark_mismatches_ref(genomic_diff,querylength,query_compress_fwd,this->left,
/*pos5*/this->querystart,/*pos3*/this->queryend,
- /*plusp*/true,this->genestrand,this->first_read_p);
+ /*plusp*/true,this->genestrand);
if (output_sam_p == false) {
this->genomic_refdiff = embellish_genomic(genomic_diff,queryuc_ptr,this->querystart,this->queryend,
querylength,extraleft,extraright,this->genestrand);
@@ -2358,8 +3305,7 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
if (output_sam_p == true) {
this->genomic_refdiff = embellish_genomic_sam(genomic_diff,queryuc_ptr,this->querystart,this->queryend,
- querylength,this->genomiclength,
- this->genestrand,this->exactp);
+ querylength,this->genestrand,this->exactp);
}
if (0 && this->exactp == true && extraleft == 0 && extraright == 0) {
@@ -2381,7 +3327,7 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
this->nmismatches_refdiff = 0;
} else {
- /* Was this->genomiclength, but fails for large insertions */
+ /* Used to be this->genomiclength, but doesn't work for large insertions */
#ifdef HAVE_ALLOCA
gbuffer = (char *) ALLOCA((querylength+1) * sizeof(char));
#else
@@ -2402,7 +3348,7 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
Genome_mark_mismatches(genomic_diff,querylength,query_compress_rev,
this->left,/*pos5*/querylength - this->queryend,
/*pos3*/querylength - this->querystart,
- /*plusp*/false,this->genestrand,this->first_read_p);
+ /*plusp*/false,this->genestrand);
}
/* Need to perform embellish to put dashes in */
@@ -2418,12 +3364,12 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
Genome_count_mismatches_substring_ref(query_compress_rev,this->left,
/*pos5*/this->alignend_trim - this->left,
/*pos3*/this->alignstart_trim - this->left,/*plusp*/false,
- this->genestrand,this->first_read_p);
+ this->genestrand);
Genome_mark_mismatches_ref(genomic_diff,querylength,query_compress_rev,this->left,
/*pos5*/querylength - this->queryend,
/*pos3*/querylength - this->querystart,
- /*plusp*/false,this->genestrand,this->first_read_p);
+ /*plusp*/false,this->genestrand);
if (output_sam_p == false) {
this->genomic_refdiff = embellish_genomic(genomic_diff,/*not queryrc*/queryuc_ptr,this->querystart,this->queryend,
@@ -2433,8 +3379,7 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
if (output_sam_p == true) {
this->genomic_refdiff = embellish_genomic_sam(genomic_diff,/*not queryrc*/queryuc_ptr,this->querystart,this->queryend,
- querylength,this->genomiclength,
- this->genestrand,this->exactp);
+ querylength,this->genestrand,this->exactp);
}
if (0 && this->exactp == true && extraleft == 0 && extraright == 0) {
@@ -2488,11 +3433,6 @@ Substring_genestrand (T this) {
return this->genestrand;
}
-bool
-Substring_first_read_p (T this) {
- return this->first_read_p;
-}
-
char *
Substring_genomic_bothdiff (T this) {
return this->genomic_bothdiff;
@@ -2554,13 +3494,21 @@ Substring_end_endtype (T this) {
return this->end_endtype;
}
+#if 0
void
-Substring_set_endtypes (T this, Endtype_T start_endtype, Endtype_T end_endtype) {
+Substring_set_start_endtype (T this, Endtype_T start_endtype, int start_amb_length) {
this->start_endtype = start_endtype;
- this->end_endtype = end_endtype;
+ this->start_amb_length = start_amb_length;
return;
}
+void
+Substring_set_end_endtype (T this, Endtype_T end_endtype, int end_amb_length) {
+ this->end_endtype = end_endtype;
+ this->end_amb_length = end_amb_length;
+ return;
+}
+#endif
float
@@ -2588,6 +3536,16 @@ Substring_trim_right_splicep (T this) {
return this->trim_right_splicep;
}
+int
+Substring_mandatory_trim_left (T this) {
+ return this->mandatory_trim_left;
+}
+
+int
+Substring_mandatory_trim_right (T this) {
+ return this->mandatory_trim_right;
+}
+
int
Substring_querystart (T this) {
@@ -2753,11 +3711,6 @@ Substring_genomicend_chr (T this) {
return this->genomicend - this->chroffset;
}
-Chrpos_T
-Substring_genomiclength (T this) {
- return this->genomiclength;
-}
-
double
Substring_amb_donor_prob (T this) {
double max;
@@ -2947,6 +3900,9 @@ Substring_copy (T old) {
new->trim_left = old->trim_left;
new->trim_right = old->trim_right;
+ new->mandatory_trim_left = old->mandatory_trim_left;
+ new->mandatory_trim_right = old->mandatory_trim_right;
+
new->trim_left_splicep = old->trim_left_splicep;
new->trim_right_splicep = old->trim_right_splicep;
@@ -2975,10 +3931,8 @@ Substring_copy (T old) {
new->alignstart_trim = old->alignstart_trim;
new->alignend_trim = old->alignend_trim;
- new->genomiclength = old->genomiclength;
new->plusp = old->plusp;
new->genestrand = old->genestrand;
- new->first_read_p = old->first_read_p;
if (old->genomic_bothdiff == NULL) {
new->genomic_bothdiff = (char *) NULL;
@@ -3047,13 +4001,13 @@ Substring_copy (T old) {
T
Substring_new_startfrag (Univcoord_T startfrag_coord, int splice_pos, int nmismatches,
Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) {
T new;
int querystart, queryend;
Univcoord_T genomicstart, alignstart, alignend;
Endtype_T start_endtype, end_endtype;
- bool trim_left_p, trim_right_p;
+ Trimaction_T trim_left_action, trim_right_action;
/* Previously checked if left >= chroffset + chrlength to exclude
the duplicate length, but now excluding all translocations to
@@ -3074,8 +4028,8 @@ Substring_new_startfrag (Univcoord_T startfrag_coord, int splice_pos, int nmisma
queryend = splice_pos;
alignstart = genomicstart;
alignend = genomicstart + splice_pos;
- trim_left_p = true; /* querystart == 0 */
- trim_right_p = false;
+ trim_left_action = COMPUTE_TRIM; /* querystart == 0 */
+ trim_right_action = NO_TRIM;
} else {
genomicstart = left + querylength;
@@ -3088,16 +4042,15 @@ Substring_new_startfrag (Univcoord_T startfrag_coord, int splice_pos, int nmisma
queryend = querylength - splice_pos;
alignstart = genomicstart;
alignend = genomicstart - (querylength - splice_pos);
- trim_left_p = true; /* querystart == 0 */
- trim_right_p = false;
+ trim_left_action = COMPUTE_TRIM; /* querystart == 0 */
+ trim_right_action = NO_TRIM;
}
if ((new = Substring_new(nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,/*outofbounds_start*/0,/*outofbounds_end*/0,
- /*minlength*/0)) == NULL) {
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ trim_left_action,trim_right_action,/*outofbounds_start*/0,/*outofbounds_end*/0,
+ /*minlength*/0,/*sensedir*/SENSE_NULL)) == NULL) {
return (T) NULL;
}
@@ -3130,13 +4083,13 @@ Substring_new_startfrag (Univcoord_T startfrag_coord, int splice_pos, int nmisma
T
Substring_new_endfrag (Univcoord_T endfrag_coord, int splice_pos, int nmismatches,
Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) {
T new;
int querystart, queryend;
Univcoord_T genomicstart, alignstart, alignend;
Endtype_T start_endtype, end_endtype;
- bool trim_left_p, trim_right_p;
+ Trimaction_T trim_left_action, trim_right_action;
/* Previously checked if left >= chroffset + chrlength to exclude
the duplicate length, but now excluding all translocations to
@@ -3157,8 +4110,8 @@ Substring_new_endfrag (Univcoord_T endfrag_coord, int splice_pos, int nmismatche
queryend = querylength;
alignstart = genomicstart + splice_pos;
alignend = genomicstart + querylength;
- trim_left_p = false;
- trim_right_p = true; /* queryend == querylength */
+ trim_left_action = NO_TRIM;
+ trim_right_action = COMPUTE_TRIM; /* queryend == querylength */
} else {
genomicstart = left + querylength;
@@ -3171,16 +4124,15 @@ Substring_new_endfrag (Univcoord_T endfrag_coord, int splice_pos, int nmismatche
queryend = querylength;
alignstart = left + splice_pos;
alignend = left;
- trim_left_p = false;
- trim_right_p = true; /* queryend == querylength */
+ trim_left_action = NO_TRIM;
+ trim_right_action = COMPUTE_TRIM; /* queryend == querylength */
}
if ((new = Substring_new(nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,/*outofbounds_start*/0,/*outofbounds_end*/0,
- /*minlength*/0)) == NULL) {
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ trim_left_action,trim_right_action,/*outofbounds_start*/0,/*outofbounds_end*/0,
+ /*minlength*/0,/*sensedir*/SENSE_NULL)) == NULL) {
return (T) NULL;
}
@@ -3213,13 +4165,13 @@ Substring_new_endfrag (Univcoord_T endfrag_coord, int splice_pos, int nmismatche
T
Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, int donor_nmismatches,
double donor_prob, Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p, int sensedir,
+ int querylength, bool plusp, int genestrand, int sensedir,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) {
T new;
int querystart, queryend;
Univcoord_T genomicstart, genomicend, alignstart, alignend;
Endtype_T start_endtype, end_endtype;
- bool trim_left_p, trim_right_p;
+ Trimaction_T trim_left_action, trim_right_action;
/* Previously checked if left >= chroffset + chrlength to exclude
the duplicate length, but now excluding all translocations to
@@ -3240,8 +4192,8 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
queryend = donor_pos;
alignstart = genomicstart;
alignend = genomicstart + donor_pos;
- trim_left_p = true; /* querystart == 0 */
- trim_right_p = false;
+ trim_left_action = COMPUTE_TRIM; /* querystart == 0 */
+ trim_right_action = NO_TRIM;
} else if (sensedir == SENSE_ANTI) {
start_endtype = DON;
@@ -3251,8 +4203,8 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
queryend = querylength;
alignstart = genomicstart + donor_pos;
alignend = genomicend;
- trim_left_p = false;
- trim_right_p = true; /* queryend == querylength */
+ trim_left_action = NO_TRIM;
+ trim_right_action = COMPUTE_TRIM; /* queryend == querylength */
} else {
abort();
@@ -3269,8 +4221,8 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
queryend = querylength - donor_pos;
alignstart = genomicstart;
alignend = genomicstart - (querylength - donor_pos);
- trim_left_p = true; /* querystart == 0 */
- trim_right_p = false;
+ trim_left_action = COMPUTE_TRIM; /* querystart == 0 */
+ trim_right_action = NO_TRIM;
} else if (sensedir == SENSE_ANTI) {
start_endtype = DON;
@@ -3280,8 +4232,8 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
queryend = querylength;
alignstart = genomicstart - (querylength - donor_pos);
alignend = genomicend;
- trim_left_p = false;
- trim_right_p = true; /* queryend == querylength */
+ trim_left_action = NO_TRIM;
+ trim_right_action = COMPUTE_TRIM; /* queryend == querylength */
} else {
abort();
@@ -3290,10 +4242,9 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
if ((new = Substring_new(donor_nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,/*outofbounds_start*/0,/*outofbounds_end*/0,
- /*minlength*/0)) == NULL) {
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ trim_left_action,trim_right_action,/*outofbounds_start*/0,/*outofbounds_end*/0,
+ /*minlength*/0,sensedir)) == NULL) {
return (T) NULL;
}
@@ -3330,13 +4281,13 @@ Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, i
T
Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acceptor_pos, int acceptor_nmismatches,
double acceptor_prob, Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p, int sensedir,
+ int querylength, bool plusp, int genestrand, int sensedir,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) {
T new;
int querystart, queryend;
Univcoord_T genomicstart, genomicend, alignstart, alignend;
Endtype_T start_endtype, end_endtype;
- bool trim_left_p, trim_right_p;
+ Trimaction_T trim_left_action, trim_right_action;
/* Previously checked if left >= chroffset + chrlength to exclude
the duplicate length, but now excluding all translocations to
@@ -3357,8 +4308,8 @@ Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acc
queryend = querylength;
alignstart = genomicstart + acceptor_pos;
alignend = genomicend;
- trim_left_p = false;
- trim_right_p = true; /* queryend == querylength */
+ trim_left_action = NO_TRIM;
+ trim_right_action = COMPUTE_TRIM; /* queryend == querylength */
} else if (sensedir == SENSE_ANTI) {
start_endtype = END;
@@ -3368,8 +4319,8 @@ Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acc
queryend = acceptor_pos;
alignstart = genomicstart;
alignend = genomicstart + acceptor_pos;
- trim_left_p = true; /* querystart == 0 */
- trim_right_p = false;
+ trim_left_action = COMPUTE_TRIM; /* querystart == 0 */
+ trim_right_action = NO_TRIM;
} else {
abort();
@@ -3386,8 +4337,8 @@ Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acc
queryend = querylength;
alignstart = genomicstart - (querylength - acceptor_pos);
alignend = genomicend;
- trim_left_p = false;
- trim_right_p = true; /* queryend == querylength */
+ trim_left_action = NO_TRIM;
+ trim_right_action = COMPUTE_TRIM; /* queryend == querylength */
} else if (sensedir == SENSE_ANTI) {
start_endtype = END;
@@ -3397,8 +4348,8 @@ Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acc
queryend = querylength - acceptor_pos;
alignstart = genomicstart;
alignend = genomicstart - (querylength - acceptor_pos);
- trim_left_p = true; /* querystart == 0 */
- trim_right_p = false;
+ trim_left_action = COMPUTE_TRIM; /* querystart == 0 */
+ trim_right_action = NO_TRIM;
} else {
abort();
@@ -3407,10 +4358,9 @@ Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acc
if ((new = Substring_new(acceptor_nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- trim_left_p,trim_right_p,/*outofbounds_start*/0,/*outofbounds_end*/0,
- /*minlength*/0)) == NULL) {
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ trim_left_action,trim_right_action,/*outofbounds_start*/0,/*outofbounds_end*/0,
+ /*minlength*/0,sensedir)) == NULL) {
return (T) NULL;
}
@@ -3450,7 +4400,7 @@ Substring_new_shortexon (Univcoord_T acceptor_coord, int acceptor_knowni, Univco
int acceptor_pos, int donor_pos, int nmismatches,
double acceptor_prob, double donor_prob, Univcoord_T left,
Compress_T query_compress, int querylength,
- bool plusp, int genestrand, bool first_read_p, int sensedir,
+ bool plusp, int genestrand, int sensedir,
bool acceptor_ambp, bool donor_ambp,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength) {
T new;
@@ -3507,10 +4457,9 @@ Substring_new_shortexon (Univcoord_T acceptor_coord, int acceptor_knowni, Univco
if ((new = Substring_new(nmismatches,chrnum,chroffset,chrhigh,chrlength,
query_compress,start_endtype,end_endtype,querystart,queryend,querylength,
- alignstart,alignend,/*genomiclength*/querylength,
- /*exactp*/false,plusp,genestrand,first_read_p,
- /*trim_left_p*/false,/*trim_right_p*/false,
- /*outofbounds_start*/0,/*outofbounds_end*/0,/*minlength*/0)) == NULL) {
+ alignstart,alignend,/*exactp*/false,plusp,genestrand,
+ /*trim_left_action*/NO_TRIM,/*trim_right_action*/NO_TRIM,
+ /*outofbounds_start*/0,/*outofbounds_end*/0,/*minlength*/0,sensedir)) == NULL) {
return (T) NULL;
}
@@ -3814,7 +4763,7 @@ print_snp_labels (Filestring_T fp, T this, Shortread_T queryseq) {
interval = IIT_interval(snps_iit,snps[i]);
position = Interval_low(interval);
querypos = position - (this->genomicstart-this->chroffset) - 1;
- assert(querypos >= 0 && querypos < this->genomiclength);
+ /* assert(querypos >= 0 && querypos < this->genomiclength); */
#if 0
alleles = IIT_typestring(snps_iit,Interval_type(interval));
@@ -3839,7 +4788,7 @@ print_snp_labels (Filestring_T fp, T this, Shortread_T queryseq) {
interval = IIT_interval(snps_iit,snps[i]);
position = Interval_low(interval);
querypos = (this->genomicstart-this->chroffset) - position;
- assert(querypos >= 0 && querypos < this->genomiclength);
+ /* assert(querypos >= 0 && querypos < this->genomiclength); */
#if 0
/* printf("\n%d%c\n",querypos,c); */
@@ -4318,10 +5267,23 @@ Substring_print_alignment (Filestring_T fp, Junction_T pre_junction, T substring
FPRINTF(fp,"\t");
if (pre_junction == NULL) {
type1 = NO_JUNCTION;
+ /* Handle result of substring_trim_novel_spliceends */
if (invertp == false) {
- FPRINTF(fp,"start:%d",substring->trim_left); /* Previously distinguished between start and term */
+ if (substring->start_endtype == DON) {
+ FPRINTF(fp,"donor:%.2f",substring->trim_left,substring->chimera_prob);
+ } else if (substring->start_endtype == ACC) {
+ FPRINTF(fp,"acceptor:%.2f",substring->trim_left,substring->chimera_prob);
+ } else {
+ FPRINTF(fp,"start:%d",substring->trim_left);
+ }
} else {
- FPRINTF(fp,"start:%d",substring->trim_right); /* Previously distinguished between start and term */
+ if (substring->end_endtype == DON) {
+ FPRINTF(fp,"donor:%.2f",substring->trim_right,substring->chimera_prob_2);
+ } else if (substring->end_endtype == ACC) {
+ FPRINTF(fp,"acceptor:%.2f",substring->trim_right,substring->chimera_prob_2);
+ } else {
+ FPRINTF(fp,"start:%d",substring->trim_right);
+ }
}
} else if ((type1 = Junction_type(pre_junction)) == INS_JUNCTION) {
FPRINTF(fp,"ins:%d",Junction_nindels(pre_junction));
@@ -4351,10 +5313,23 @@ Substring_print_alignment (Filestring_T fp, Junction_T pre_junction, T substring
if (post_junction == NULL) {
type2 = NO_JUNCTION;
+ /* Handle result of substring_trim_novel_spliceends */
if (invertp == false) {
- FPRINTF(fp,"end:%d",substring->trim_right);
+ if (substring->end_endtype == DON) {
+ FPRINTF(fp,"donor:%.2f",substring->trim_right,substring->chimera_prob_2);
+ } else if (substring->end_endtype == ACC) {
+ FPRINTF(fp,"acceptor:%.2f",substring->trim_right,substring->chimera_prob_2);
+ } else {
+ FPRINTF(fp,"end:%d",substring->trim_right);
+ }
} else {
- FPRINTF(fp,"end:%d",substring->trim_left);
+ if (substring->start_endtype == DON) {
+ FPRINTF(fp,"donor:%.2f",substring->trim_left,substring->chimera_prob);
+ } else if (substring->start_endtype == ACC) {
+ FPRINTF(fp,"acceptor:%.2f",substring->trim_left,substring->chimera_prob);
+ } else {
+ FPRINTF(fp,"end:%d",substring->trim_left);
+ }
}
} else if ((type2 = Junction_type(post_junction)) == INS_JUNCTION) {
FPRINTF(fp,"ins:%d",Junction_nindels(post_junction));
@@ -4380,7 +5355,7 @@ Substring_print_alignment (Filestring_T fp, Junction_T pre_junction, T substring
abort();
}
- FPRINTF(fp,",matches:%d,sub:%d",substring->nmatches,substring->nmismatches_bothdiff);
+ FPRINTF(fp,",matches:%d,sub:%d",Substring_nmatches_posttrim(substring),substring->nmismatches_bothdiff);
if (print_nsnpdiffs_p) {
FPRINTF(fp,"+%d=%d",substring->nmismatches_refdiff - substring->nmismatches_bothdiff,substring->nmismatches_refdiff);
if (print_snplabels_p && substring->nmismatches_refdiff > substring->nmismatches_bothdiff) {
@@ -4473,6 +5448,7 @@ Substring_print_alignment (Filestring_T fp, Junction_T pre_junction, T substring
}
+#if 0
void
Substring_print_single (Filestring_T fp, T substring, Shortread_T queryseq,
char *chr, bool invertp) {
@@ -4522,8 +5498,10 @@ Substring_print_single (Filestring_T fp, T substring, Shortread_T queryseq,
return;
}
+#endif
+#if 0
void
Substring_print_insertion_1 (Filestring_T fp, T substring1, T substring2, int nindels,
Shortread_T queryseq, char *chr, bool invertp) {
@@ -4563,7 +5541,9 @@ Substring_print_insertion_1 (Filestring_T fp, T substring1, T substring2, int ni
return;
}
+#endif
+#if 0
void
Substring_print_insertion_2 (Filestring_T fp, T substring1, T substring2, int nindels,
Shortread_T queryseq, char *chr, bool invertp) {
@@ -4602,8 +5582,10 @@ Substring_print_insertion_2 (Filestring_T fp, T substring1, T substring2, int ni
return;
}
+#endif
+#if 0
void
Substring_print_deletion_1 (Filestring_T fp, T substring1, T substring2, int nindels,
char *deletion, Shortread_T queryseq, char *chr,
@@ -4640,8 +5622,10 @@ Substring_print_deletion_1 (Filestring_T fp, T substring1, T substring2, int nin
return;
}
+#endif
+#if 0
void
Substring_print_deletion_2 (Filestring_T fp, T substring1, T substring2, int nindels,
Shortread_T queryseq, char *chr, bool invertp) {
@@ -4679,6 +5663,7 @@ Substring_print_deletion_2 (Filestring_T fp, T substring1, T substring2, int nin
return;
}
+#endif
/* This logic used in splice part of SAM_print */
@@ -5298,12 +6283,12 @@ Substring_count_mismatches_region (T this, int trim_left, int trim_right,
if (this->plusp) {
return Genome_count_mismatches_substring(query_compress_fwd,this->left,/*pos5*/left_bound,
- /*pos3*/right_bound,/*plusp*/true,this->genestrand,this->first_read_p);
+ /*pos3*/right_bound,/*plusp*/true,this->genestrand);
} else {
return Genome_count_mismatches_substring(query_compress_rev,this->left,
/*pos5*/this->querylength - right_bound,
/*pos3*/this->querylength - left_bound,
- /*plusp*/false,this->genestrand,this->first_read_p);
+ /*plusp*/false,this->genestrand);
}
}
}
@@ -5715,3 +6700,5 @@ Substring_add_intron (List_T pairs, T substringA, T substringB, int querylength,
return pairs;
}
+
+
diff --git a/src/substring.h b/src/substring.h
index 32ee8b3..36810d0 100644
--- a/src/substring.h
+++ b/src/substring.h
@@ -1,4 +1,4 @@
-/* $Id: substring.h 173896 2015-09-12 00:11:40Z twu $ */
+/* $Id: substring.h 184484 2016-02-18 03:11:53Z twu $ */
#ifndef SUBSTRING_INCLUDED
#define SUBSTRING_INCLUDED
@@ -23,10 +23,12 @@
#else
#include "uintlist.h"
#endif
+#include "splicetrie_build.h" /* For Splicetype_T */
typedef enum {GMAP_NOT_APPLICABLE, GMAP_VIA_SUBSTRINGS, GMAP_VIA_SEGMENTS, GMAP_VIA_REGION} GMAP_source_T;
typedef enum {END, INS, DEL, FRAG, DON, ACC, AMB_DON, AMB_ACC, TERM} Endtype_T;
+typedef enum {NO_TRIM, PRE_TRIMMED, COMPUTE_TRIM} Trimaction_T;
extern char *
Endtype_string (Endtype_T endtype);
@@ -53,16 +55,16 @@ Substring_new (int nmismatches_whole, Chrnum_T chrnum, Univcoord_T chroffset,
Univcoord_T chrhigh, Chrpos_T chrlength,
Compress_T query_compress, Endtype_T start_endtype, Endtype_T end_endtype,
int querystart, int queryend, int querylength,
- Univcoord_T alignstart, Univcoord_T alignend, int genomiclength,
- bool exactp, bool plusp, int genestrand, bool first_read_p,
- bool trim_left_p, bool trim_right_p, int outofbounds_start, int outofbounds_end,
- int minlength);
+ Univcoord_T alignstart, Univcoord_T alignend,
+ bool exactp, bool plusp, int genestrand,
+ Trimaction_T trim_left_action, Trimaction_T trim_right_action, int outofbounds_start, int outofbounds_end,
+ int minlength, int sensedir);
extern T
Substring_new_ambig (int querystart, int queryend, int splice_pos, int querylength,
Chrnum_T chrnum, Univcoord_T chroffset,
Univcoord_T chrhigh, Chrpos_T chrlength,
- int genomiclength, bool plusp, int genestrand, bool first_read_p,
+ bool plusp, int genestrand,
#ifdef LARGE_GENOMES
Uint8list_T ambcoords,
#else
@@ -84,9 +86,6 @@ Substring_display_prep (T this, char *queryuc_ptr, int querylength,
Compress_T query_compress_fwd, Compress_T query_compress_rev,
Genome_T genome);
-extern bool
-Substring_bad_stretch_p (T this, Compress_T query_compress_fwd, Compress_T query_compress_rev);
-
extern void
Substring_free (T *old);
@@ -120,8 +119,6 @@ extern bool
Substring_plusp (T this);
extern int
Substring_genestrand (T this);
-extern bool
-Substring_first_read_p (T this);
extern char *
Substring_genomic_bothdiff (T this);
extern char *
@@ -145,7 +142,9 @@ Substring_start_endtype (T this);
extern Endtype_T
Substring_end_endtype (T this);
extern void
-Substring_set_endtypes (T this, Endtype_T start_endtype, Endtype_T end_endtype);
+Substring_set_start_endtype (T this, Endtype_T start_endtype, int start_amb_length);
+extern void
+Substring_set_end_endtype (T this, Endtype_T end_endtype, int end_amb_length);
extern float
Substring_mapq_loglik (T this);
extern int
@@ -157,6 +156,11 @@ Substring_trim_left_splicep (T this);
extern bool
Substring_trim_right_splicep (T this);
extern int
+Substring_mandatory_trim_left (T this);
+extern int
+Substring_mandatory_trim_right (T this);
+
+extern int
Substring_querystart (T this);
extern int
Substring_querystart_orig (T this);
@@ -211,8 +215,6 @@ extern Univcoord_T
Substring_genomicend (T this);
extern Chrpos_T
Substring_genomicend_chr (T this);
-extern Chrpos_T
-Substring_genomiclength (T this);
extern double
Substring_amb_donor_prob (T this);
@@ -260,30 +262,30 @@ Substring_copy (T old);
extern T
Substring_new_startfrag (Univcoord_T startfrag_coord, int splice_pos, int nmismatches,
Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
extern T
Substring_new_endfrag (Univcoord_T endfrag_coord, int splice_pos, int nmismatches,
Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p,
+ int querylength, bool plusp, int genestrand,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
extern T
Substring_new_donor (Univcoord_T donor_coord, int donor_knowni, int donor_pos, int donor_nmismatches,
double donor_prob, Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p, int sensedir,
+ int querylength, bool plusp, int genestrand, int sensedir,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
extern T
Substring_new_acceptor (Univcoord_T acceptor_coord, int acceptor_knowni, int acceptor_pos, int acceptor_nmismatches,
double acceptor_prob, Univcoord_T left, Compress_T query_compress,
- int querylength, bool plusp, int genestrand, bool first_read_p, int sensedir,
+ int querylength, bool plusp, int genestrand, int sensedir,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
extern T
Substring_new_shortexon (Univcoord_T acceptor_coord, int acceptor_knowni, Univcoord_T donor_coord, int donor_knowni,
int acceptor_pos, int donor_pos, int nmismatches,
double acceptor_prob, double donor_prob, Univcoord_T left,
Compress_T query_compress, int querylength,
- bool plusp, int genestrand, bool first_read_p, int sensedir,
+ bool plusp, int genestrand, int sensedir,
bool acceptor_ambp, bool donor_ambp,
Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Chrpos_T chrlength);
@@ -341,6 +343,11 @@ extern List_T
Substring_add_intron (List_T pairs, T substringA, T substringB, int querylength,
int hardclip_low, int hardclip_high, int queryseq_offset);
+extern void
+Substring_trim_novel_spliceends (T substring1, T substringN, int *ambig_end_length_5, int *ambig_end_length_3,
+ Splicetype_T *ambig_splicetype_5, Splicetype_T *ambig_splicetype_3,
+ double *ambig_prob_5, double *ambig_prob_3, int *sensedir);
+
#undef T
#endif
diff --git a/src/table.c b/src/table.c
index 0ac6e44..45ac503 100644
--- a/src/table.c
+++ b/src/table.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: table.c 153955 2014-11-24 17:54:45Z twu $";
+static char rcsid[] = "$Id: table.c 182426 2016-01-15 22:06:05Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -248,8 +248,8 @@ Table_keys_by_timeindex (T table, void *end) {
keyarray[j] = (void *) p->key;
}
keyarray[j] = end;
- FREE(buckets);
+ FREE(buckets);
return keyarray;
}
diff --git a/src/tableint.c b/src/tableint.c
index 6852b51..d8d4b08 100644
--- a/src/tableint.c
+++ b/src/tableint.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: tableint.c 99737 2013-06-27 19:33:03Z twu $";
+static char rcsid[] = "$Id: tableint.c 182426 2016-01-15 22:06:05Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -214,6 +214,7 @@ Tableint_keys_by_timeindex (T table, void *end) {
}
keyarray[j] = end;
+ FREE(buckets);
return keyarray;
}
diff --git a/src/tableuint.c b/src/tableuint.c
index 0449329..490167f 100644
--- a/src/tableuint.c
+++ b/src/tableuint.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: tableuint.c 99737 2013-06-27 19:33:03Z twu $";
+static char rcsid[] = "$Id: tableuint.c 182426 2016-01-15 22:06:05Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -214,6 +214,7 @@ Tableuint_keys_by_timeindex (T table, void *end) {
}
keyarray[j] = end;
+ FREE(buckets);
return keyarray;
}
diff --git a/src/tableuint8.c b/src/tableuint8.c
index 3dbbfbc..55e462b 100644
--- a/src/tableuint8.c
+++ b/src/tableuint8.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: tableuint8.c 153955 2014-11-24 17:54:45Z twu $";
+static char rcsid[] = "$Id: tableuint8.c 182426 2016-01-15 22:06:05Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -228,6 +228,7 @@ Tableuint8_keys_by_timeindex (T table, void *end) {
}
keyarray[j] = end;
+ FREE(buckets);
return keyarray;
}
diff --git a/src/translation.c b/src/translation.c
index b7586a8..328d487 100644
--- a/src/translation.c
+++ b/src/translation.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: translation.c 155282 2014-12-12 19:42:54Z twu $";
+static char rcsid[] = "$Id: translation.c 184469 2016-02-18 00:11:12Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -77,6 +77,7 @@ Translation_array_new (struct Pair_T *pairs, int translationlen) {
return new;
}
+#if 0
static void
Translation_dump (struct Pair_T *pairs, struct T *translation, int translationlen) {
int i;
@@ -98,6 +99,7 @@ Translation_dump (struct Pair_T *pairs, struct T *translation, int translationle
}
return;
}
+#endif
/************************************************************************/
@@ -575,7 +577,7 @@ static void
find_bounds_backward_fromstart (Frame_T *translation_frame, int *translation_starti,
int *translation_endi, int *translation_length,
bool *endstopp, struct T *translation, int translationlen,
- int cds_startpos, int querylength) {
+ int cds_startpos) {
Frame_T frame_fromstart;
int phase_fromstart;
int beststart0, bestend0;
@@ -776,7 +778,7 @@ translate_pairs_backward (struct Pair_T *pairs, int npairs, bool revcompp) {
#ifndef PMAP
static int
-count_cdna_forward_strict (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_cdna_forward_strict (int *nexti, struct Pair_T *pairs, int npairs, int starti) {
int ncdna = 0, j;
j = starti;
@@ -797,7 +799,7 @@ count_cdna_forward_strict (int *nexti, struct Pair_T *pairs, int npairs, int sta
static int
-count_cdna_forward (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_cdna_forward (int *nexti, struct Pair_T *pairs, int starti, int endi) {
int ncdna = 0, j;
j = starti;
@@ -817,7 +819,7 @@ count_cdna_forward (int *nexti, struct Pair_T *pairs, int npairs, int starti, in
static int
-count_cdna_forward_mod3 (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_cdna_forward_mod3 (int *nexti, struct Pair_T *pairs, int starti, int endi) {
int ncdna = 0, j;
j = starti;
@@ -838,7 +840,7 @@ count_cdna_forward_mod3 (int *nexti, struct Pair_T *pairs, int npairs, int start
#ifndef PMAP
static int
-count_cdna_backward_strict (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_cdna_backward_strict (int *nexti, struct Pair_T *pairs, int starti) {
int ncdna = 0, j;
j = starti;
@@ -858,7 +860,7 @@ count_cdna_backward_strict (int *nexti, struct Pair_T *pairs, int npairs, int st
#endif
static int
-count_cdna_backward (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_cdna_backward (int *nexti, struct Pair_T *pairs, int starti, int endi) {
int ncdna = 0, j;
j = starti;
@@ -878,7 +880,7 @@ count_cdna_backward (int *nexti, struct Pair_T *pairs, int npairs, int starti, i
static int
-count_cdna_backward_mod3 (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_cdna_backward_mod3 (int *nexti, struct Pair_T *pairs, int starti, int endi) {
int ncdna = 0, j;
j = starti;
@@ -898,8 +900,9 @@ count_cdna_backward_mod3 (int *nexti, struct Pair_T *pairs, int npairs, int star
}
+#if 0
static int
-count_genomic_strict (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_genomic_strict (int *nexti, struct Pair_T *pairs, int npairs, int starti) {
int ngenomic = 0, j;
j = starti;
@@ -918,10 +921,11 @@ count_genomic_strict (int *nexti, struct Pair_T *pairs, int npairs, int starti,
*nexti = j;
return ngenomic;
}
+#endif
-
+#if 0
static int
-count_genomic (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_genomic (int *nexti, struct Pair_T *pairs, int starti, int endi) {
int ngenomic = 0, j;
j = starti;
@@ -938,10 +942,11 @@ count_genomic (int *nexti, struct Pair_T *pairs, int npairs, int starti, int end
*nexti = j;
return ngenomic;
}
+#endif
-
+#if 0
static int
-count_genomic_mod3 (int *nexti, struct Pair_T *pairs, int npairs, int starti, int endi) {
+count_genomic_mod3 (int *nexti, struct Pair_T *pairs, int starti, int endi) {
int ngenomic = 0, j;
j = starti;
@@ -959,6 +964,7 @@ count_genomic_mod3 (int *nexti, struct Pair_T *pairs, int npairs, int starti, in
*nexti = j;
return 1; /* any answer that is not mod 0 */
}
+#endif
/************************************************************************/
@@ -999,7 +1005,7 @@ get_codon_forward (int *nexti, struct Pair_T *pairs, int npairs, int starti, boo
}
static int
-get_codon_backward (int *nexti, struct Pair_T *pairs, int npairs, int starti, bool revcompp) {
+get_codon_backward (int *nexti, struct Pair_T *pairs, int starti, bool revcompp) {
char nt2 = 'X', nt1 = 'X', nt0 = 'X';
int j2 = -1, j1 = -1, j0 = -1;
int ncdna = 0, j;
@@ -1126,7 +1132,7 @@ assign_cdna_backward (int ncdna, struct Pair_T *pairs, int npairs, bool revcompp
}
while (j < ncdna) {
pair = &(pairs[i]);
- codon = pair->aa_e = get_codon_backward(&nexti,pairs,npairs,i,revcompp);
+ codon = pair->aa_e = get_codon_backward(&nexti,pairs,i,revcompp);
debug2(Pair_dump_one(pair,true));
debug2(printf(" marked with amino acid %c\n",pair->aa_e));
i = nexti;
@@ -1149,7 +1155,7 @@ terminate_cdna_backward (struct Pair_T *pairs, int npairs, bool revcompp, int st
/* i > 1 is equivalent to i >= 2 */
while (i > 1 && lastcodon != '*') {
pair = &(pairs[i]);
- lastcodon = pair->aa_e = get_codon_backward(&nexti,pairs,npairs,i,revcompp);
+ lastcodon = pair->aa_e = get_codon_backward(&nexti,pairs,i,revcompp);
debug2(Pair_dump_one(pair,true));
debug2(printf(" marked with amino acid %c\n",pair->aa_e));
i = nexti;
@@ -1210,7 +1216,7 @@ mark_cdna_forward_strict (struct Pair_T *pairs, int npairs, bool revcompp, int s
while (i < npairs && codon != '*') {
pair = &(pairs[i]);
- ncdna = count_cdna_forward_strict(&nexti,pairs,npairs,i,endi);
+ ncdna = count_cdna_forward_strict(&nexti,pairs,npairs,i);
if (ncdna == 3) {
codon = assign_cdna_forward(ncdna,pairs,npairs,revcompp,i);
}
@@ -1238,7 +1244,7 @@ mark_cdna_forward (struct Pair_T *pairs, int npairs, bool revcompp, int starti,
if (pair->aaphase_g != 0) {
i++;
} else {
- ncdna = count_cdna_forward(&nexti,pairs,npairs,i,endi);
+ ncdna = count_cdna_forward(&nexti,pairs,i,endi);
if (ncdna == 3) {
assign_cdna_forward(ncdna,pairs,npairs,revcompp,i);
} else if ((ncdna % 3) == 0) {
@@ -1249,7 +1255,7 @@ mark_cdna_forward (struct Pair_T *pairs, int npairs, bool revcompp, int starti,
assign_cdna_forward(ncdna,pairs,npairs,revcompp,i);
} else {
debug2(printf("At %d, saw %d with mod != 0\n",pair->aapos,ncdna));
- ncdna_alt = count_cdna_forward_mod3(&nexti_alt,pairs,npairs,i,endi);
+ ncdna_alt = count_cdna_forward_mod3(&nexti_alt,pairs,i,endi);
debug2(printf(" Alternate search yields %d\n",ncdna_alt));
if ((ncdna_alt % 3) == 0) {
@@ -1294,7 +1300,7 @@ mark_cdna_backward_strict (struct Pair_T *pairs, int npairs, bool revcompp, int
while (i >= 0 && codon != '*') {
pair = &(pairs[i]);
- ncdna = count_cdna_backward_strict(&nexti,pairs,npairs,i,endi);
+ ncdna = count_cdna_backward_strict(&nexti,pairs,i);
if (ncdna == 3) {
codon = assign_cdna_backward(ncdna,pairs,npairs,revcompp,i);
}
@@ -1322,7 +1328,7 @@ mark_cdna_backward (struct Pair_T *pairs, int npairs, bool revcompp, int starti,
if (pair->aaphase_g != 0) {
i--;
} else {
- ncdna = count_cdna_backward(&nexti,pairs,npairs,i,endi);
+ ncdna = count_cdna_backward(&nexti,pairs,i,endi);
if (ncdna == 3) {
assign_cdna_backward(ncdna,pairs,npairs,revcompp,i);
} else if ((ncdna % 3) == 0) {
@@ -1333,7 +1339,7 @@ mark_cdna_backward (struct Pair_T *pairs, int npairs, bool revcompp, int starti,
assign_cdna_backward(ncdna,pairs,npairs,revcompp,i);
} else {
debug2(printf("At %d, saw %d with mod != 0\n",pair->aapos,ncdna));
- ncdna_alt = count_cdna_backward_mod3(&nexti_alt,pairs,npairs,i,endi);
+ ncdna_alt = count_cdna_backward_mod3(&nexti_alt,pairs,i,endi);
debug2(printf(" Alternate search yields %d\n",ncdna_alt));
if ((ncdna_alt % 3) == 0) {
@@ -1379,7 +1385,7 @@ mark_genomic_strict (struct Pair_T *pairs, int npairs, int starti, int endi) {
while (i < npairs && codon != '*') {
pair = &(pairs[i]);
- ngenomic = count_genomic_strict(&nexti,pairs,npairs,i,endi);
+ ngenomic = count_genomic_strict(&nexti,pairs,npairs,i);
if (ngenomic == 3) {
codon = assign_genomic(ngenomic,pairs,npairs,i);
}
@@ -1406,7 +1412,7 @@ mark_genomic (struct Pair_T *pairs, int npairs, int starti, int endi) {
if (pair->aaphase_e != 0) {
i++;
} else {
- ngenomic = count_genomic(&nexti,pairs,npairs,i,endi);
+ ngenomic = count_genomic(&nexti,pairs,i,endi);
if (ngenomic == 3) {
assign_genomic(ngenomic,pairs,npairs,i);
} else if ((ngenomic % 3) == 0) {
@@ -1417,7 +1423,7 @@ mark_genomic (struct Pair_T *pairs, int npairs, int starti, int endi) {
assign_genomic(ngenomic,pairs,npairs,i);
} else {
debug2(printf("At %d, saw %d with mod != 0\n",pair->aapos,ngenomic));
- ngenomic_alt = count_genomic_mod3(&nexti_alt,pairs,npairs,i,endi);
+ ngenomic_alt = count_genomic_mod3(&nexti_alt,pairs,i,endi);
debug2(printf(" Alternate search yields %d\n",ngenomic_alt));
if ((ngenomic_alt % 3) == 0) {
@@ -1527,7 +1533,7 @@ Translation_via_genomic (int *translation_leftpos, int *translation_rightpos, in
if (cds_startpos > 0) {
find_bounds_backward_fromstart(&translation_frame,&translation_starti,
&translation_endi,&(*translation_length),&endstopp,
- translation,npairs,cds_startpos,querylength);
+ translation,npairs,cds_startpos);
} else {
find_bounds_backward(&translation_frame,&translation_starti,
&translation_endi,&(*translation_length),&endstopp,
@@ -1884,8 +1890,7 @@ bound_via_reference (int *start, int *end, struct Pair_T *pairs, int npairs, boo
void
Translation_via_reference (int *relaastart, int *relaaend,
struct Pair_T *pairs, int npairs, bool watsonp, bool backwardp, bool revcompp,
- struct Pair_T *refpairs, int nrefpairs, bool refwatsonp,
- bool fixshiftp) {
+ struct Pair_T *refpairs, int nrefpairs, bool refwatsonp) {
struct T *translation;
int start, end, i;
@@ -1941,7 +1946,7 @@ Translation_via_reference (int *relaastart, int *relaaend,
return;
}
-#ifndef PMAP
+#if 0
static char
lookup_aa (int aapos, struct Pair_T *refpairs, int nrefpairs) {
int i;
@@ -1976,7 +1981,7 @@ next_aapos_fwd (struct Pair_T *pairs, int i, int npairs, int aapos) {
}
static int
-next_aapos_rev (struct Pair_T *pairs, int i, int npairs, int aapos) {
+next_aapos_rev (struct Pair_T *pairs, int i, int aapos) {
struct Pair_T *this;
this = &(pairs[i]);
@@ -2158,8 +2163,8 @@ print_large_deletion (Filestring_T fp, bool *printp, int lastaapos, int nextaapo
void
-Translation_print_comparison (Filestring_T fp, struct Pair_T *pairs, int npairs, struct Pair_T *refpairs, int nrefpairs,
- int cdna_direction, int relaastart, int relaaend, int maxmutations) {
+Translation_print_comparison (Filestring_T fp, struct Pair_T *pairs, int npairs,
+ int relaastart, int relaaend) {
int i, j;
int aapos, strlen_g, strlen_c, netchars;
bool printp = false;
@@ -2192,11 +2197,11 @@ Translation_print_comparison (Filestring_T fp, struct Pair_T *pairs, int npairs,
} else {
if ((aapos = pairs[i=npairs-1].aapos) == 0) {
- i = next_aapos_rev(pairs,0,npairs,0);
+ i = next_aapos_rev(pairs,/*i*/0,/*aapos*/0);
}
while (i >= 0) {
aapos = pairs[i].aapos;
- j = next_aapos_rev(pairs,i,npairs,aapos);
+ j = next_aapos_rev(pairs,i,aapos);
if (pairs[i].aa_g != ' ' && pairs[i].aa_e != ' ') {
/* not a frameshift */
fill_aa_rev(&strlen_g,&strlen_c,&netchars,aa_genomicseg,aa_queryseq,nt_genomicseg,nt_queryseq,
diff --git a/src/translation.h b/src/translation.h
index 215190f..03d0585 100644
--- a/src/translation.h
+++ b/src/translation.h
@@ -1,4 +1,4 @@
-/* $Id: translation.h 157221 2015-01-22 18:38:57Z twu $ */
+/* $Id: translation.h 184469 2016-02-18 00:11:12Z twu $ */
#ifndef TRANSLATION_INCLUDED
#define TRANSLATION_INCLUDED
@@ -30,11 +30,11 @@ Translation_via_genomic (int *translation_leftpos, int *translation_rightpos, in
extern void
Translation_via_reference (int *relaastart, int *relaaend,
struct Pair_T *pairs, int npairs, bool watsonp, bool backwardp, bool revcompp,
- struct Pair_T *refpairs, int nrefpairs, bool refwatsonp, bool fixshiftp);
+ struct Pair_T *refpairs, int nrefpairs, bool refwatsonp);
extern void
-Translation_print_comparison (Filestring_T fp, struct Pair_T *pairs, int npairs, struct Pair_T *refpairs, int nrefpairs,
- int cdna_direction, int relaastart, int relaaend, int maxmutations);
+Translation_print_comparison (Filestring_T fp, struct Pair_T *pairs, int npairs,
+ int relaastart, int relaaend);
#undef T
#endif
diff --git a/src/types.h b/src/types.h
index c7df5f2..63be96d 100644
--- a/src/types.h
+++ b/src/types.h
@@ -1,8 +1,8 @@
-/* $Id: types.h 168395 2015-06-26 17:13:13Z twu $ */
+/* $Id: types.h 181330 2015-12-19 13:10:42Z twu $ */
#ifndef TYPES_INCLUDED
#define TYPES_INCLUDED
#ifdef HAVE_CONFIG_H
-#include <config.h> /* For SIZEOF_UNSIGNED_LONG_LONG, SIZEOF_UNSIGNED_LONG, HAVE_64_BIT */
+#include <config.h> /* For SIZEOF_UNSIGNED_LONG_LONG, SIZEOF_UNSIGNED_LONG needed for HAVE_64_BIT */
#endif
/* Number of bits, such as index1part or basesize. Need to allow for negative values. */
@@ -31,21 +31,59 @@ typedef UINT4 Genomecomp_T;
/* Prefer to use unsigned long long, whic should be 8 bytes on all systems */
#if (SIZEOF_UNSIGNED_LONG_LONG == 8)
#define HAVE_64_BIT 1
-#define MAXIMUM_KMER 16
+#define MAXIMUM_KMER 18
typedef unsigned long long UINT8;
typedef unsigned long long Oligospace_T;
+/* 8765432187654321 */
+#define LEFT_A 0x0000000000000000
+#define LEFT_C 0x4000000000000000
+#define LEFT_G 0x8000000000000000
+#define LEFT_T 0xC000000000000000
+
+/* 8765432187654321 */
+#define RIGHT_A 0x0000000000000000
+#define RIGHT_C 0x0000000000000001
+#define RIGHT_G 0x0000000000000002
+#define RIGHT_T 0x0000000000000003
+
+
#elif (SIZEOF_UNSIGNED_LONG == 8)
#define HAVE_64_BIT 1
-#define MAXIMUM_KMER 16
+#define MAXIMUM_KMER 18
typedef unsigned long UINT8;
typedef unsigned long Oligospace_T;
+/* 8765432187654321 */
+#define LEFT_A 0x0000000000000000
+#define LEFT_C 0x4000000000000000
+#define LEFT_G 0x8000000000000000
+#define LEFT_T 0xC000000000000000
+
+/* 8765432187654321 */
+#define RIGHT_A 0x0000000000000000
+#define RIGHT_C 0x0000000000000001
+#define RIGHT_G 0x0000000000000002
+#define RIGHT_T 0x0000000000000003
+
+
#else
#define MAXIMUM_KMER 15
#define OLIGOSPACE_NOT_LONG
typedef unsigned int Oligospace_T;
+/* 87654321 */
+#define LEFT_A 0x00000000
+#define LEFT_C 0x40000000
+#define LEFT_G 0x80000000
+#define LEFT_T 0xC0000000
+
+/* 87654321 */
+#define RIGHT_A 0x00000000
+#define RIGHT_C 0x00000001
+#define RIGHT_G 0x00000002
+#define RIGHT_T 0x00000003
+
#endif
/* Contents of compressed offsets file. Storing as UINT4, even for
@@ -54,9 +92,14 @@ typedef unsigned int Oligospace_T;
words. */
typedef UINT4 Offsetscomp_T;
+#if 0
+/* Obsolete with handling of k-mers > 16. Use Oligospace_T instead */
/* Holds a k-mer. Can be UINT4 as long as k <= 16. */
/* Some procedures use Shortoligomer_T, which should be the same */
typedef UINT4 Storedoligomer_T;
+#else
+typedef UINT4 Shortoligomer_T;
+#endif
/* Definitions */
diff --git a/src/uint8list.c b/src/uint8list.c
index 6559466..7c8d9e5 100644
--- a/src/uint8list.c
+++ b/src/uint8list.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: uint8list.c 166641 2015-05-29 21:13:04Z twu $";
+static char rcsid[] = "$Id: uint8list.c 183888 2016-02-05 20:33:29Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -265,19 +265,19 @@ Uint8list_to_string (T this) {
} else {
strlength = 0;
for (i = 0, p = this; i < n-1; i++, p = Uint8list_next(p)) {
- sprintf(Buffer,"%u,",Uint8list_head(p));
+ sprintf(Buffer,"%llu,",Uint8list_head(p));
strlength += strlen(Buffer);
}
- sprintf(Buffer,"%u",Uint8list_head(p));
+ sprintf(Buffer,"%llu",Uint8list_head(p));
strlength += strlen(Buffer);
string = (char *) CALLOC(strlength + 1,sizeof(char));
string[0] = '\0';
for (i = 0, p = this; i < n-1; i++, p = Uint8list_next(p)) {
- sprintf(Buffer,"%u,",Uint8list_head(p));
+ sprintf(Buffer,"%llu,",Uint8list_head(p));
strcat(string,Buffer);
}
- sprintf(Buffer,"%u",Uint8list_head(p));
+ sprintf(Buffer,"%llu",Uint8list_head(p));
strcat(string,Buffer);
}
diff --git a/src/uniqscan.c b/src/uniqscan.c
index 77699cc..5025626 100644
--- a/src/uniqscan.c
+++ b/src/uniqscan.c
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: uniqscan.c 186090 2016-03-17 22:21:17Z twu $";
+static char rcsid[] = "$Id: uniqscan.c 186737 2016-03-30 23:36:12Z twu $";
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
@@ -115,10 +115,15 @@ static int ngap = 3;
************************************************************************/
static Univ_IIT_T chromosome_iit = NULL;
+static Univ_IIT_T altscaffold_iit = NULL;
static int circular_typeint = -1;
static int nchromosomes = 0;
static bool *circularp = NULL;
static bool any_circular_p;
+
+static bool *altlocp = NULL;
+static Univcoord_T *alias_starts = NULL;
+static Univcoord_T *alias_ends = NULL;
static Indexdb_T indexdb = NULL;
static Indexdb_T indexdb2 = NULL; /* For cmet or atoi */
static Genome_T genome = NULL;
@@ -156,7 +161,8 @@ static Access_mode_T positions_access = USE_ALLOCATE;
static Access_mode_T genome_access = USE_ALLOCATE;
#endif
-static int pairmax;
+static int pairmax_linear;
+static int pairmax_circular;
static int pairmax_dna = 1000;
static int pairmax_rna = 200000;
static int expected_pairlength = 200;
@@ -414,7 +420,8 @@ uniqueness_scan (bool from_right_p) {
char *result, *subsequence, sequence[1024];
int fulllength, sublength;
Stage3end_T *stage3array;
- int npaths, first_absmq, second_absmq;
+ int npaths, npaths_primary, npaths_altloc;
+ int first_absmq, second_absmq;
Floors_T *floors_array;
Shortread_T queryseq1;
@@ -457,14 +464,15 @@ uniqueness_scan (bool from_right_p) {
queryseq1 = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,/*filterp*/false,sequence,/*long_sequence*/NULL,
/*sequence_length*/fulllength,/*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,
/*barcode_length*/0,/*invertp*/0,/*copy_acc_p*/false,/*skipp*/false);
- stage3array = Stage1_single_read(&npaths,&first_absmq,&second_absmq,
+ stage3array = Stage1_single_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,
queryseq1,indexdb,indexdb2,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,/*distantsplicing_penalty*/100,min_shortend,
- oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ oligoindices_minor,pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*keep_floors_p*/true);
+ npaths = npaths_primary + npaths_altloc;
/* printf("%d: %d\n",sublength,npaths); */
if (from_right_p == true) {
@@ -501,14 +509,15 @@ uniqueness_scan (bool from_right_p) {
queryseq1 = Shortread_new(/*acc*/NULL,/*restofheader*/NULL,/*filterp*/false,subsequence,/*long_sequence*/NULL,
/*sequence_length*/sublength,/*quality*/NULL,/*long_quality*/NULL,/*quality_length*/0,
/*barcode_length*/0,/*invertp*/0,/*copy_acc_p*/false,/*skipp*/false);
- stage3array = Stage1_single_read(&npaths,&first_absmq,&second_absmq,
+ stage3array = Stage1_single_read(&npaths_primary,&npaths_altloc,&first_absmq,&second_absmq,
queryseq1,indexdb,indexdb2,indexdb_size_threshold,
floors_array,user_maxlevel_float,user_mincoverage_float,
indel_penalty_middle,indel_penalty_end,
allow_end_indels_p,max_end_insertions,max_end_deletions,min_indel_end_matches,
localsplicing_penalty,/*distantsplicing_penalty*/100,min_shortend,
- oligoindices_major,oligoindices_minor,pairpool,diagpool,cellpool,
+ oligoindices_minor,pairpool,diagpool,cellpool,
dynprogL,dynprogM,dynprogR,/*keep_floors_p*/true);
+ npaths = npaths_primary + npaths_altloc;
/* printf("%d: %d\n",sublength,npaths); */
if (from_right_p == true) {
@@ -966,20 +975,24 @@ main (int argc, char *argv[]) {
}
if (novelsplicingp == true && knownsplicingp == true) {
- pairmax = pairmax_rna;
+ pairmax_linear = pairmax_rna;
+ pairmax_circular = pairmax_dna;
shortsplicedist_known = shortsplicedist;
} else if (knownsplicingp == true) {
- pairmax = pairmax_rna;
+ pairmax_linear = pairmax_rna;
+ pairmax_circular = pairmax_dna;
shortsplicedist_known = shortsplicedist;
} else if (novelsplicingp == true) {
- pairmax = pairmax_rna;
+ pairmax_linear = pairmax_rna;
+ pairmax_circular = pairmax_dna;
shortsplicedist_known = 0;
} else {
/* Appears to be DNA-Seq */
- pairmax = pairmax_dna;
+ pairmax_linear = pairmax_dna;
+ pairmax_circular = pairmax_dna;
shortsplicedist = shortsplicedist_known = 0U;
}
@@ -1008,11 +1021,28 @@ main (int argc, char *argv[]) {
fprintf(stderr,"IIT file %s is not valid\n",iitfile);
exit(9);
} else {
+ FREE(iitfile);
nchromosomes = Univ_IIT_total_nintervals(chromosome_iit);
circular_typeint = Univ_IIT_typeint(chromosome_iit,"circular");
circularp = Univ_IIT_circularp(&any_circular_p,chromosome_iit);
+
+ iitfile = (char *) CALLOC(strlen(genomesubdir)+strlen("/")+
+ strlen(fileroot)+strlen(".altscaffold.iit")+1,sizeof(char));
+ sprintf(iitfile,"%s/%s.altscaffold.iit",genomesubdir,fileroot);
+ if ((altscaffold_iit = Univ_IIT_read(iitfile,/*readonlyp*/true,/*add_iit_p*/false)) == NULL) {
+ /* fprintf(stderr,"No altscaffold file found\n"); */
+ altlocp = (bool *) CALLOC(nchromosomes+1,sizeof(bool));
+ alias_starts = (Univcoord_T *) CALLOC(nchromosomes+1,sizeof(Univcoord_T));
+ alias_ends = (Univcoord_T *) CALLOC(nchromosomes+1,sizeof(Univcoord_T));
+
+ } else {
+ fprintf(stderr,"Found altscaffold file found\n");
+ altlocp = Univ_IIT_altlocp(&alias_starts,&alias_ends,chromosome_iit,altscaffold_iit);
+ Univ_IIT_free(&altscaffold_iit);
+ }
+
+ FREE(iitfile);
}
- FREE(iitfile);
if (snps_root == NULL) {
@@ -1029,7 +1059,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metct",/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find metct index file. Need to run cmetindex first\n");
exit(9);
}
@@ -1038,7 +1068,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metga",/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find metga index file. Need to run cmetindex first\n");
exit(9);
}
@@ -1054,7 +1084,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1063,7 +1093,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1079,7 +1109,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1088,7 +1118,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1099,7 +1129,7 @@ main (int argc, char *argv[]) {
genomesubdir,fileroot,IDX_FILESUFFIX,/*snps_root*/NULL,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find offsets file %s.%s*offsets, needed for GSNAP\n",fileroot,IDX_FILESUFFIX);
exit(9);
}
@@ -1132,7 +1162,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metct",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find metct index file. Need to run cmetindex first\n");
exit(9);
}
@@ -1140,7 +1170,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"metga",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find metga index file. Need to run cmetindex first\n");
exit(9);
}
@@ -1156,7 +1186,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1164,7 +1194,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1180,7 +1210,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2itc",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2itc index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1188,7 +1218,7 @@ main (int argc, char *argv[]) {
modedir,fileroot,/*idx_filesuffix*/"a2iag",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false)) == NULL) {
+ /*sharedp*/false,/*multiple_sequences_p*/false)) == NULL) {
fprintf(stderr,"Cannot find a2iag index file. Need to run atoiindex first\n");
exit(9);
}
@@ -1198,7 +1228,7 @@ main (int argc, char *argv[]) {
snpsdir,fileroot,/*idx_filesuffix*/"ref",snps_root,
required_index1part,required_interval,
expand_offsets_p,offsetsstrm_access,positions_access,
- /*sharedp*/false);
+ /*sharedp*/false,/*multiple_sequences_p*/false);
if (indexdb == NULL) {
fprintf(stderr,"Cannot find snps index file for %s in directory %s\n",snps_root,snpsdir);
exit(9);
@@ -1211,7 +1241,7 @@ main (int argc, char *argv[]) {
sprintf(iitfile,"%s/%s",mapdir,snps_root);
fprintf(stderr,"Reading SNPs file %s/%s...",mapdir,snps_root);
if ((snps_iit = IIT_read(iitfile,/*name*/NULL,/*readonlyp*/true,/*divread*/READ_ALL,
- /*divstring*/NULL,/*add_iit_p*/true,/*labels_read_p*/true)) == NULL) {
+ /*divstring*/NULL,/*add_iit_p*/true)) == NULL) {
fprintf(stderr,"SNPs file %s.iit not found in %s.\n",snps_root,mapdir);
if (user_snpsdir == NULL) {
fprintf(stderr,"Available files:\n");
@@ -1264,7 +1294,7 @@ main (int argc, char *argv[]) {
genome,genomealt,mode,/*maxpaths_search*/10,
splicesites,splicetypes,splicedists,nsplicesites,
novelsplicingp,knownsplicingp,/*find_dna_chimeras_p*/false,distances_observed_p,
- subopt_levels,max_middle_insertions,max_middle_deletions,
+ subopt_levels,min_indel_end_matches,max_middle_insertions,max_middle_deletions,
shortsplicedist,shortsplicedist_known,shortsplicedist_novelend,min_intronlength,
min_distantsplicing_end_matches,min_distantsplicing_identity,
nullgap,maxpeelback,maxpeelback_distalmedial,
@@ -1293,8 +1323,8 @@ main (int argc, char *argv[]) {
Univ_IIT_genomelength(chromosome_iit,/*with_circular_alias*/false));
Stage3_setup(/*splicingp*/novelsplicingp == true || knownsplicingp == true,novelsplicingp,
/*require_splicedir_p*/false,splicing_iit,splicing_divint_crosstable,
- donor_typeint,acceptor_typeint,
- splicesites,min_intronlength,max_deletionlength,/*min_indel_end_matches*/6,
+ donor_typeint,acceptor_typeint,splicesites,altlocp,alias_starts,alias_ends,
+ min_intronlength,max_deletionlength,/*min_indel_end_matches*/6,
maxpeelback_distalmedial,nullgap,extramaterial_end,extramaterial_paired,
extraband_single,extraband_end,extraband_paired,
ngap,maxintronlen,/*output_sam_p*/false,/*homopolymerp*/false,
@@ -1303,11 +1333,11 @@ main (int argc, char *argv[]) {
chromosome_iit,nchromosomes,circular_typeint,genes_iit,genes_divint_crosstable,
/*tally_iit*/NULL,/*tally_divint_crosstable*/NULL,
/*runlength_iit*/NULL,/*runlength_divint_crosstable*/NULL,
- distances_observed_p,pairmax,expected_pairlength,pairlength_deviation,
+ distances_observed_p,pairmax_linear,pairmax_circular,expected_pairlength,pairlength_deviation,
localsplicing_penalty,indel_penalty_middle,antistranded_penalty,
- favor_multiexon_p,gmap_min_nconsecutive,index1part,index1interval,
- novelsplicingp,/*merge_samechr_p*/false,circularp,/*failedinput_root*/NULL,
- /*print_m8_p*/false,/*want_random_p*/true);
+ favor_multiexon_p,gmap_min_nconsecutive,/*end_detail*/1,subopt_levels,
+ novelsplicingp,shortsplicedist,/*merge_samechr_p*/false,circularp,altlocp,alias_starts,alias_ends,
+ /*failedinput_root*/NULL,/*print_m8_p*/false,/*want_random_p*/true);
uniqueness_scan(from_right_p);
@@ -1365,6 +1395,12 @@ main (int argc, char *argv[]) {
IIT_free(&snps_iit);
}
+ if (altlocp != NULL) {
+ FREE(alias_ends);
+ FREE(alias_starts);
+ FREE(altlocp);
+ }
+
if (circularp != NULL) {
FREE(circularp);
}
@@ -1582,6 +1618,8 @@ Usage: gsnap [OPTIONS...] <FASTA file>, or\n\
fprintf(stdout,"\
--pairmax-dna=INT Max total genomic length for DNA-Seq paired reads, or other reads\n\
without splicing (default 1000). Used if -N or -s is not specified.\n\
+ This value is also used for circular chromosomes when splicing in\n\
+ linear chromosomes is allowed\n\
--pairmax-rna=INT Max total genomic length for RNA-Seq paired reads, or other reads\n\
that could have a splice (default 200000). Used if -N or -s is specified.\n\
Should probably match the value for -w, --localsplicedist.\n\
diff --git a/tests/Makefile.in b/tests/Makefile.in
index 5cb4615..ee36e37 100644
--- a/tests/Makefile.in
+++ b/tests/Makefile.in
@@ -44,6 +44,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/ltsugar.m4 \
$(top_srcdir)/config/ltversion.m4 \
$(top_srcdir)/config/lt~obsolete.m4 $(top_srcdir)/acinclude.m4 \
+ $(top_srcdir)/config/ax_compiler_vendor.m4 \
$(top_srcdir)/config/pagesize.m4 \
$(top_srcdir)/config/madvise-flags.m4 \
$(top_srcdir)/config/mmap-flags.m4 \
@@ -52,7 +53,6 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/shm-flags.m4 \
$(top_srcdir)/config/ax_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
- $(top_srcdir)/config/builtin-popcount.m4 \
$(top_srcdir)/config/struct-stat64.m4 \
$(top_srcdir)/config/expand.m4 $(top_srcdir)/config/perl.m4 \
$(top_srcdir)/config/fopen.m4 $(top_srcdir)/config/asm-bsr.m4 \
@@ -133,7 +133,6 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
-POPCNT_CFLAGS = @POPCNT_CFLAGS@
PTHREAD_CC = @PTHREAD_CC@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
PTHREAD_LIBS = @PTHREAD_LIBS@
@@ -141,7 +140,11 @@ RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
-SIMD_CFLAGS = @SIMD_CFLAGS@
+SIMD_AVX2_CFLAGS = @SIMD_AVX2_CFLAGS@
+SIMD_SSE2_CFLAGS = @SIMD_SSE2_CFLAGS@
+SIMD_SSE4_1_CFLAGS = @SIMD_SSE4_1_CFLAGS@
+SIMD_SSE4_2_CFLAGS = @SIMD_SSE4_2_CFLAGS@
+SIMD_SSSE3_CFLAGS = @SIMD_SSSE3_CFLAGS@
STRIP = @STRIP@
VERSION = @VERSION@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/tests/coords1.test.ok b/tests/coords1.test.ok
index d83526d..d41506e 100644
--- a/tests/coords1.test.ok
+++ b/tests/coords1.test.ok
@@ -1,5 +1,6 @@
# To rename a chromosome, edit each occurrence of that chromosome in the gmap_coordinates
# The strain column has information copied from NCBI md files, but is not otherwise used by gmap_setup
# To exclude a contig, place a '#' sign at the beginning of the line
-#contig gmap_coordinates linear/circular strain
+# The <primary> field means the primary segment for the given (altloc) contig
+#contig gmap_coordinates linear/circular/<primary> strain
chr17test chr17test:1..200000 linear
diff --git a/util/Makefile.in b/util/Makefile.in
index 0f440f3..8524aa8 100644
--- a/util/Makefile.in
+++ b/util/Makefile.in
@@ -53,6 +53,7 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/ltsugar.m4 \
$(top_srcdir)/config/ltversion.m4 \
$(top_srcdir)/config/lt~obsolete.m4 $(top_srcdir)/acinclude.m4 \
+ $(top_srcdir)/config/ax_compiler_vendor.m4 \
$(top_srcdir)/config/pagesize.m4 \
$(top_srcdir)/config/madvise-flags.m4 \
$(top_srcdir)/config/mmap-flags.m4 \
@@ -61,7 +62,6 @@ am__aclocal_m4_deps = $(top_srcdir)/config/libtool.m4 \
$(top_srcdir)/config/shm-flags.m4 \
$(top_srcdir)/config/ax_mpi.m4 \
$(top_srcdir)/config/acx_pthread.m4 \
- $(top_srcdir)/config/builtin-popcount.m4 \
$(top_srcdir)/config/struct-stat64.m4 \
$(top_srcdir)/config/expand.m4 $(top_srcdir)/config/perl.m4 \
$(top_srcdir)/config/fopen.m4 $(top_srcdir)/config/asm-bsr.m4 \
@@ -168,7 +168,6 @@ PACKAGE_TARNAME = @PACKAGE_TARNAME@
PACKAGE_VERSION = @PACKAGE_VERSION@
PATH_SEPARATOR = @PATH_SEPARATOR@
PERL = @PERL@
-POPCNT_CFLAGS = @POPCNT_CFLAGS@
PTHREAD_CC = @PTHREAD_CC@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
PTHREAD_LIBS = @PTHREAD_LIBS@
@@ -176,7 +175,11 @@ RANLIB = @RANLIB@
SED = @SED@
SET_MAKE = @SET_MAKE@
SHELL = @SHELL@
-SIMD_CFLAGS = @SIMD_CFLAGS@
+SIMD_AVX2_CFLAGS = @SIMD_AVX2_CFLAGS@
+SIMD_SSE2_CFLAGS = @SIMD_SSE2_CFLAGS@
+SIMD_SSE4_1_CFLAGS = @SIMD_SSE4_1_CFLAGS@
+SIMD_SSE4_2_CFLAGS = @SIMD_SSE4_2_CFLAGS@
+SIMD_SSSE3_CFLAGS = @SIMD_SSSE3_CFLAGS@
STRIP = @STRIP@
VERSION = @VERSION@
ZLIB_LIBS = @ZLIB_LIBS@
diff --git a/util/fa_coords.pl.in b/util/fa_coords.pl.in
index b4bc642..7460d77 100644
--- a/util/fa_coords.pl.in
+++ b/util/fa_coords.pl.in
@@ -13,10 +13,11 @@ undef($opt_E); # Interpret argument as a command
undef($opt_g); # gunzip each file first
#undef($opt_S); # Do not order chromosomes
undef($opt_c); # Circular chromosomes
+undef($opt_2); # File with altscaffold info
undef($opt_n); # File with substitute chromosome names
undef($opt_f); # File with input FASTA source filenames
use Getopt::Std;
-getopts("o:CEgc:n:f:");
+getopts("o:CEgc:2:n:f:");
# Usage: fa_coords [-o <output>] [-C] [-E] [-g] [-n <namefile>] [-f <sourcefiles>]
@@ -31,7 +32,7 @@ if (defined($circular = $opt_c)) {
$ncircular++;
}
close($FP);
- print STDERR "read $circular chromosomes\n";
+ print STDERR "read $ncircular circular chromosomes\n";
} else {
foreach $chr (split ",",$circular) {
$circularp{$chr} = 1;
@@ -39,6 +40,28 @@ if (defined($circular = $opt_c)) {
}
}
+if (defined($altscaffold = $opt_2)) {
+ if (-e $altscaffold) {
+ print STDERR "Reading altscaffold info from the file $altscaffold...";
+ $naltloc = 0;
+ $FP = new IO::File($altscaffold);
+ while (defined($line = <$FP>)) {
+ chop $line;
+ ($alt_scaf_acc,$primary_chr,$orientation,$alt_scaf_start,$alt_scaf_stop,$primary_start,$primary_end) = split /\t/,$line;
+ if (!defined($alt_scaf_acc)) {
+ die $line;
+ }
+ # Cannot include a space inside of the string
+ $altscaffold_info{$alt_scaf_acc} = "$alt_scaf_start..$alt_scaf_stop,$primary_chr:$primary_start..$primary_end";
+ $naltloc++;
+ }
+ close($FP);
+ print STDERR "read $naltloc alternate scaffolds\n";
+ } else {
+ die "Could not find file $altscaffold";
+ }
+}
+
if (!defined($outfile = $opt_o)) {
$outfile = "coords.txt";
}
@@ -96,7 +119,8 @@ if ($#{$output} < 0) {
print $OUT "# To rename a chromosome, edit each occurrence of that chromosome in the gmap_coordinates\n";
print $OUT "# The strain column has information copied from NCBI md files, but is not otherwise used by gmap_setup\n";
print $OUT "# To exclude a contig, place a '#' sign at the beginning of the line\n";
- print $OUT "#contig" . "\t" . "gmap_coordinates" . "\t" . "linear/circular" . "\t" . "strain\n";
+ print $OUT "# The <primary> field means the primary segment for the given (altloc) contig\n";
+ print $OUT "#contig" . "\t" . "gmap_coordinates" . "\t" . "linear/circular/<primary>" . "\t" . "strain\n";
#if (defined($opt_S)) {
#@sorted = @ {$output};
@@ -281,6 +305,8 @@ sub parse_fa_files {
}
if (defined($circularp{$chr})) {
$string .= "\tcircular";
+ } elsif (defined($altscaffold_info{$chr})) {
+ $string .= "\t" . $altscaffold_info{$chr};
} else {
$string .= "\tlinear";
}
@@ -453,6 +479,8 @@ sub parse_fa_files {
}
if (defined($circularp{$chr})) {
$string .= "\tcircular";
+ } elsif (defined($altscaffold_info{$chr})) {
+ $string .= "\t" . $altscaffold_info{$chr};
} else {
$string .= "\tlinear";
}
diff --git a/util/gmap_build.pl.in b/util/gmap_build.pl.in
index 3bc13c0..8867fb5 100644
--- a/util/gmap_build.pl.in
+++ b/util/gmap_build.pl.in
@@ -1,5 +1,5 @@
#! @PERL@
-# $Id: gmap_build.pl.in 184522 2016-02-18 17:51:14Z twu $
+# $Id: gmap_build.pl.in 184524 2016-02-18 17:51:39Z twu $
use warnings;
@@ -42,7 +42,8 @@ GetOptions(
'w=s' => \$sleeptime, # waits (sleeps) this many seconds between steps. Useful if there is a delay in the filesystem.
- 'c|circular=s' => \$circular, # Circular chromosomes
+ 'c|circular=s' => \$circular, # Circular chromosomes
+ '2|altscaffold=s' => \$altscaffold, # File with altscaffold info
'e|nmessages=s' => \$nmessages # Max number of warnings or messages to print
);
@@ -113,6 +114,12 @@ if (defined($circular)) {
$circular_flag = "";
}
+if (defined($altscaffold)) {
+ $altscaffold_flag = "-2 $altscaffold";
+} else {
+ $altscaffold_flag = "";
+}
+
if (defined($nmessages)) {
$nmessages_flag = "-e $nmessages";
} else {
@@ -160,7 +167,7 @@ $dbdir = create_db($destdir,$dbname);
create_genome_version($dbdir,$dbname);
-create_coords($mdfile,$fasta_pipe,$gunzip_flag,$circular_flag,$contigs_mapped_flag,$chrnamefile,
+create_coords($mdfile,$fasta_pipe,$gunzip_flag,$circular_flag,$altscaffold_flag,$contigs_mapped_flag,$chrnamefile,
$bindir,$coordsfile,$fasta_sources);
if (!(-s "$coordsfile")) {
die "ERROR: $coordsfile not found";
@@ -228,18 +235,18 @@ sub create_genome_version {
}
sub create_coords {
- my ($mdfile, $fasta_pipe, $gunzip_flag, $circular_flag, $contigs_mapped_flag, $chrnamefile,
+ my ($mdfile, $fasta_pipe, $gunzip_flag, $circular_flag, $altscaffold_flag, $contigs_mapped_flag, $chrnamefile,
$bindir, $coordsfile, $fasta_sources) = @_;
my ($cmd, $rc);
if (defined($mdfile)) {
- # MD file cannot specify that a chromosome is circular
+ # MD file cannot specify that a chromosome is circular or altscaffold
$cmd = "\"$bindir/md_coords\" -o \"$coordsfile\" $mdfile";
} else {
if (defined($fasta_pipe)) {
- $cmd = "$fasta_pipe | \"$bindir/fa_coords\" $circular_flag $contigs_mapped_flag -o \"$coordsfile\"";
+ $cmd = "$fasta_pipe | \"$bindir/fa_coords\" $circular_flag $altscaffold_flag $contigs_mapped_flag -o \"$coordsfile\"";
} else {
- $cmd = "\"$bindir/fa_coords\" $gunzip_flag $circular_flag $contigs_mapped_flag -o \"$coordsfile\"";
+ $cmd = "\"$bindir/fa_coords\" $gunzip_flag $circular_flag $altscaffold_flag $contigs_mapped_flag -o \"$coordsfile\"";
}
if (defined($chrnamefile)) {
$cmd .= " -n $chrnamefile";
@@ -432,11 +439,11 @@ Options:
-q INT sampling interval for genomoe (allowed: 1-3, default 3)
-s, --sort=STRING Sort chromosomes using given method:
- none - use chromosomes as found in FASTA file(s)
- alpha - sort chromosomes alphabetically (chr10 before chr 1)
- numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY
- chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU
- names - sort chromosomes based on file provided to --names flag
+ none - use chromosomes as found in FASTA file(s)
+ alpha - sort chromosomes alphabetically (chr10 before chr 1)
+ numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY
+ chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU
+ names - sort chromosomes based on file provided to --names flag
-g, --gunzip Files are gzipped, so need to gunzip each file first
-E, --fasta-pipe=STRING Interpret argument as a command, instead of a list of FASTA files
@@ -445,7 +452,11 @@ Options:
-c, --circular=STRING Circular chromosomes (either a list of chromosomes separated by a comma, or
a filename containing circular chromosomes, one per line). If you use the
--names feature, then you should use the original name of the chromosome,
- not the substitute name, for this option.
+ not the substitute name, for this option.
+
+ -2, --altscaffold=STRING File with alt scaffold info, listing alternate scaffolds, one per line, tab-delimited,
+ with the following fields: (1) alt_scaf_acc, (2) parent_name, (3) orientation,
+ (4) alt_scaf_start, (5) alt_scaf_stop, (6) parent_start, (7) parent_end.
-e, --nmessages=INT Maximum number of messages (warnings, contig reports) to report (default 50)
diff --git a/util/gmap_process.pl.in b/util/gmap_process.pl.in
index 10bace0..7303105 100644
--- a/util/gmap_process.pl.in
+++ b/util/gmap_process.pl.in
@@ -76,11 +76,18 @@ sub read_coords {
$universal_coord{$contig} = $universal_coord;
($chrstart,$chrend) = $coords{$contig} =~ /\S+:(\d+)\.\.(\d+)/;
- if (defined($fields[2]) && $fields[2] eq "circular") {
+ if (!defined($fields[2])) {
+ $universal_coord += $chrend - $chrstart + 1;
+ } elsif ($fields[2] eq "circular") {
$circularp{$contig} = 1;
$universal_coord += $chrend - $chrstart + 1;
$universal_coord += $chrend - $chrstart + 1;
+ } elsif ($fields[2] eq "primary") {
+ # Linear and primary
+ $universal_coord += $chrend - $chrstart + 1;
} else {
+ # Altloc
+ $primary{$contig} = $fields[2];
$universal_coord += $chrend - $chrstart + 1;
}
}
@@ -153,6 +160,8 @@ sub process_fasta {
printf (">%s\t%s\t%u",$contig,$coords{$contig},$universal_coord{$contig});
if (defined($circularp{$contig})) {
print "\tcircular";
+ } elsif (defined($primary{$contig})) {
+ print "\t" . $primary{$contig};
}
print "\n";
$printp = 1;
--
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